From 031a228c662236535bcb5062cf5dd5922306aafb Mon Sep 17 00:00:00 2001 From: cbioportal import user Date: Thu, 28 Nov 2024 23:54:10 -0500 Subject: [PATCH 1/6] Initial TARGET Data Release --- crdc/gdc/alal_target_gdc/README.md | 149 ++++++++++++++++++ .../alal_target_gdc/case_lists/cases_all.txt | 6 + .../case_lists/cases_sequenced.txt | 6 + .../alal_target_gdc/data_clinical_patient.txt | 3 + .../alal_target_gdc/data_clinical_sample.txt | 3 + .../alal_target_gdc/data_mrna_seq_fpkm.txt | 3 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 3 + .../data_mrna_seq_read_counts.txt | 3 + ...eq_read_counts_zscores_ref_all_samples.txt | 3 + .../gdc/alal_target_gdc/data_mrna_seq_tpm.txt | 3 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 3 + crdc/gdc/alal_target_gdc/data_mutations.txt | 3 + .../alal_target_gdc/data_timeline_status.txt | 3 + .../alal_target_gdc/meta_clinical_patient.txt | 4 + .../alal_target_gdc/meta_clinical_sample.txt | 4 + .../alal_target_gdc/meta_mrna_seq_fpkm.txt | 8 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 8 + .../meta_mrna_seq_read_counts.txt | 8 + ...eq_read_counts_zscores_ref_all_samples.txt | 8 + .../gdc/alal_target_gdc/meta_mrna_seq_tpm.txt | 8 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 8 + crdc/gdc/alal_target_gdc/meta_mutations.txt | 8 + crdc/gdc/alal_target_gdc/meta_study.txt | 7 + .../alal_target_gdc/meta_timeline_status.txt | 4 + .../alal_target_gdc-validation.html | 3 + crdc/gdc/aml_target_gdc/README.md | 149 ++++++++++++++++++ .../aml_target_gdc/case_lists/cases_all.txt | 6 + .../aml_target_gdc/case_lists/cases_cna.txt | 6 + .../case_lists/cases_cnaseq.txt | 6 + .../case_lists/cases_sequenced.txt | 6 + .../aml_target_gdc/data_clinical_patient.txt | 3 + .../aml_target_gdc/data_clinical_sample.txt | 3 + crdc/gdc/aml_target_gdc/data_cna.txt | 3 + .../gdc/aml_target_gdc/data_mrna_seq_fpkm.txt | 3 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 3 + .../data_mrna_seq_read_counts.txt | 3 + ...eq_read_counts_zscores_ref_all_samples.txt | 3 + crdc/gdc/aml_target_gdc/data_mrna_seq_tpm.txt | 3 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 3 + crdc/gdc/aml_target_gdc/data_mutations.txt | 3 + .../aml_target_gdc/data_timeline_status.txt | 3 + .../aml_target_gdc/meta_clinical_patient.txt | 4 + .../aml_target_gdc/meta_clinical_sample.txt | 4 + crdc/gdc/aml_target_gdc/meta_cna.txt | 8 + .../gdc/aml_target_gdc/meta_mrna_seq_fpkm.txt | 8 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 8 + .../meta_mrna_seq_read_counts.txt | 8 + ...eq_read_counts_zscores_ref_all_samples.txt | 8 + crdc/gdc/aml_target_gdc/meta_mrna_seq_tpm.txt | 8 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 8 + crdc/gdc/aml_target_gdc/meta_mutations.txt | 8 + crdc/gdc/aml_target_gdc/meta_study.txt | 7 + .../aml_target_gdc/meta_timeline_status.txt | 4 + .../aml_target_gdc-validation.html | 3 + crdc/gdc/bll_target_gdc/README.md | 149 ++++++++++++++++++ .../bll_target_gdc/case_lists/cases_all.txt | 6 + .../bll_target_gdc/case_lists/cases_cna.txt | 6 + .../case_lists/cases_cnaseq.txt | 6 + .../case_lists/cases_sequenced.txt | 6 + .../bll_target_gdc/data_clinical_patient.txt | 3 + .../bll_target_gdc/data_clinical_sample.txt | 3 + crdc/gdc/bll_target_gdc/data_cna.txt | 3 + .../gdc/bll_target_gdc/data_mrna_seq_fpkm.txt | 3 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 3 + .../data_mrna_seq_read_counts.txt | 3 + ...eq_read_counts_zscores_ref_all_samples.txt | 3 + crdc/gdc/bll_target_gdc/data_mrna_seq_tpm.txt | 3 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 3 + crdc/gdc/bll_target_gdc/data_mutations.txt | 3 + .../bll_target_gdc/data_timeline_status.txt | 3 + .../bll_target_gdc/meta_clinical_patient.txt | 4 + .../bll_target_gdc/meta_clinical_sample.txt | 4 + crdc/gdc/bll_target_gdc/meta_cna.txt | 8 + .../gdc/bll_target_gdc/meta_mrna_seq_fpkm.txt | 8 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 8 + .../meta_mrna_seq_read_counts.txt | 8 + ...eq_read_counts_zscores_ref_all_samples.txt | 8 + crdc/gdc/bll_target_gdc/meta_mrna_seq_tpm.txt | 8 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 8 + crdc/gdc/bll_target_gdc/meta_mutations.txt | 8 + crdc/gdc/bll_target_gdc/meta_study.txt | 7 + .../bll_target_gdc/meta_timeline_status.txt | 4 + .../bll_target_gdc-validation.html | 3 + crdc/gdc/nbl_target_gdc/README.md | 149 ++++++++++++++++++ .../nbl_target_gdc/case_lists/cases_all.txt | 6 + .../case_lists/cases_sequenced.txt | 6 + .../nbl_target_gdc/data_clinical_patient.txt | 3 + .../nbl_target_gdc/data_clinical_sample.txt | 3 + .../gdc/nbl_target_gdc/data_mrna_seq_fpkm.txt | 3 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 3 + .../data_mrna_seq_read_counts.txt | 3 + ...eq_read_counts_zscores_ref_all_samples.txt | 3 + crdc/gdc/nbl_target_gdc/data_mrna_seq_tpm.txt | 3 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 3 + crdc/gdc/nbl_target_gdc/data_mutations.txt | 3 + .../nbl_target_gdc/data_timeline_status.txt | 3 + .../nbl_target_gdc/meta_clinical_patient.txt | 4 + .../nbl_target_gdc/meta_clinical_sample.txt | 4 + .../gdc/nbl_target_gdc/meta_mrna_seq_fpkm.txt | 8 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 8 + .../meta_mrna_seq_read_counts.txt | 8 + ...eq_read_counts_zscores_ref_all_samples.txt | 8 + crdc/gdc/nbl_target_gdc/meta_mrna_seq_tpm.txt | 8 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 8 + crdc/gdc/nbl_target_gdc/meta_mutations.txt | 8 + crdc/gdc/nbl_target_gdc/meta_study.txt | 7 + .../nbl_target_gdc/meta_timeline_status.txt | 4 + .../nbl_target_gdc-validation.html | 3 + crdc/gdc/os_target_gdc/README.md | 149 ++++++++++++++++++ .../os_target_gdc/case_lists/cases_all.txt | 6 + .../os_target_gdc/case_lists/cases_cna.txt | 6 + .../os_target_gdc/case_lists/cases_cnaseq.txt | 6 + .../case_lists/cases_sequenced.txt | 6 + .../os_target_gdc/data_clinical_patient.txt | 3 + .../os_target_gdc/data_clinical_sample.txt | 3 + crdc/gdc/os_target_gdc/data_cna.txt | 3 + crdc/gdc/os_target_gdc/data_mrna_seq_fpkm.txt | 3 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 3 + .../data_mrna_seq_read_counts.txt | 3 + ...eq_read_counts_zscores_ref_all_samples.txt | 3 + crdc/gdc/os_target_gdc/data_mrna_seq_tpm.txt | 3 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 3 + crdc/gdc/os_target_gdc/data_mutations.txt | 3 + .../os_target_gdc/data_timeline_status.txt | 3 + .../os_target_gdc/meta_clinical_patient.txt | 4 + .../os_target_gdc/meta_clinical_sample.txt | 4 + crdc/gdc/os_target_gdc/meta_cna.txt | 8 + crdc/gdc/os_target_gdc/meta_mrna_seq_fpkm.txt | 8 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 8 + .../meta_mrna_seq_read_counts.txt | 8 + ...eq_read_counts_zscores_ref_all_samples.txt | 8 + crdc/gdc/os_target_gdc/meta_mrna_seq_tpm.txt | 8 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 8 + crdc/gdc/os_target_gdc/meta_mutations.txt | 8 + crdc/gdc/os_target_gdc/meta_study.txt | 7 + .../os_target_gdc/meta_timeline_status.txt | 4 + .../os_target_gdc-validation.html | 3 + crdc/gdc/wt_target_gdc/README.md | 149 ++++++++++++++++++ .../wt_target_gdc/case_lists/cases_all.txt | 6 + .../case_lists/cases_sequenced.txt | 6 + .../wt_target_gdc/data_clinical_patient.txt | 3 + .../wt_target_gdc/data_clinical_sample.txt | 3 + crdc/gdc/wt_target_gdc/data_mrna_seq_fpkm.txt | 3 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 3 + .../data_mrna_seq_read_counts.txt | 3 + ...eq_read_counts_zscores_ref_all_samples.txt | 3 + crdc/gdc/wt_target_gdc/data_mrna_seq_tpm.txt | 3 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 3 + crdc/gdc/wt_target_gdc/data_mutations.txt | 3 + .../wt_target_gdc/data_timeline_status.txt | 3 + .../wt_target_gdc/meta_clinical_patient.txt | 4 + .../wt_target_gdc/meta_clinical_sample.txt | 4 + crdc/gdc/wt_target_gdc/meta_mrna_seq_fpkm.txt | 8 + ..._mrna_seq_fpkm_zscores_ref_all_samples.txt | 8 + .../meta_mrna_seq_read_counts.txt | 8 + ...eq_read_counts_zscores_ref_all_samples.txt | 8 + crdc/gdc/wt_target_gdc/meta_mrna_seq_tpm.txt | 8 + ...a_mrna_seq_tpm_zscores_ref_all_samples.txt | 8 + crdc/gdc/wt_target_gdc/meta_mutations.txt | 8 + crdc/gdc/wt_target_gdc/meta_study.txt | 7 + .../wt_target_gdc/meta_timeline_status.txt | 4 + .../wt_target_gdc-validation.html | 3 + 162 files changed, 1683 insertions(+) create mode 100644 crdc/gdc/alal_target_gdc/README.md create mode 100644 crdc/gdc/alal_target_gdc/case_lists/cases_all.txt create mode 100644 crdc/gdc/alal_target_gdc/case_lists/cases_sequenced.txt create mode 100644 crdc/gdc/alal_target_gdc/data_clinical_patient.txt create mode 100644 crdc/gdc/alal_target_gdc/data_clinical_sample.txt create mode 100644 crdc/gdc/alal_target_gdc/data_mrna_seq_fpkm.txt create mode 100644 crdc/gdc/alal_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/alal_target_gdc/data_mrna_seq_read_counts.txt create mode 100644 crdc/gdc/alal_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/alal_target_gdc/data_mrna_seq_tpm.txt create mode 100644 crdc/gdc/alal_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/alal_target_gdc/data_mutations.txt create mode 100644 crdc/gdc/alal_target_gdc/data_timeline_status.txt create mode 100644 crdc/gdc/alal_target_gdc/meta_clinical_patient.txt create mode 100644 crdc/gdc/alal_target_gdc/meta_clinical_sample.txt create mode 100644 crdc/gdc/alal_target_gdc/meta_mrna_seq_fpkm.txt create mode 100644 crdc/gdc/alal_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/alal_target_gdc/meta_mrna_seq_read_counts.txt create mode 100644 crdc/gdc/alal_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/alal_target_gdc/meta_mrna_seq_tpm.txt create mode 100644 crdc/gdc/alal_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/alal_target_gdc/meta_mutations.txt create mode 100644 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crdc/gdc/os_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/os_target_gdc/meta_mrna_seq_tpm.txt create mode 100644 crdc/gdc/os_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/os_target_gdc/meta_mutations.txt create mode 100644 crdc/gdc/os_target_gdc/meta_study.txt create mode 100644 crdc/gdc/os_target_gdc/meta_timeline_status.txt create mode 100644 crdc/gdc/os_target_gdc/validation_reports/os_target_gdc-validation.html create mode 100644 crdc/gdc/wt_target_gdc/README.md create mode 100644 crdc/gdc/wt_target_gdc/case_lists/cases_all.txt create mode 100644 crdc/gdc/wt_target_gdc/case_lists/cases_sequenced.txt create mode 100644 crdc/gdc/wt_target_gdc/data_clinical_patient.txt create mode 100644 crdc/gdc/wt_target_gdc/data_clinical_sample.txt create mode 100644 crdc/gdc/wt_target_gdc/data_mrna_seq_fpkm.txt create mode 100644 crdc/gdc/wt_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/wt_target_gdc/data_mrna_seq_read_counts.txt create mode 100644 crdc/gdc/wt_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/wt_target_gdc/data_mrna_seq_tpm.txt create mode 100644 crdc/gdc/wt_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/wt_target_gdc/data_mutations.txt create mode 100644 crdc/gdc/wt_target_gdc/data_timeline_status.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_clinical_patient.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_clinical_sample.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_mrna_seq_fpkm.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_mrna_seq_read_counts.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_mrna_seq_tpm.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_mutations.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_study.txt create mode 100644 crdc/gdc/wt_target_gdc/meta_timeline_status.txt create mode 100644 crdc/gdc/wt_target_gdc/validation_reports/wt_target_gdc-validation.html diff --git a/crdc/gdc/alal_target_gdc/README.md b/crdc/gdc/alal_target_gdc/README.md new file mode 100644 index 0000000000..4815d45474 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/README.md @@ -0,0 +1,149 @@ +# Comments & assumptions made during curation + +## General + +- Study is updated once every 3 months with latest data from [ISB-CGC BigQuery tables](https://isb-cgc.appspot.com/bq_meta_search/) + - The ISB-CGC tables allow easy access to data collected from multiple NCI-CRDC repositories including the GDC, PDC, and others. The TARGET data in this study comes from the GDC and is accessed through these tables. +- Reference genome used: hg38 +- TARGET started using the hg38 genome as of GDC release 32. For more information, refer to the [GDC release notes](https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-320). + +- Only tumor sample data is included (no normal samples) +- [GDC project webpage](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P3) + +## Clinical data + +- **Patient data:** Retrieved from `isb-cgc-bq.TARGET_versioned.clinical_gdc_r40`. ISB-CGC data was created in April 2024. +- **Sample data:** Retrieved from `isb-cgc-bq.TARGET_versioned.per_sample_file_metadata_hg38_gdc_r40`. ISB-CGC data was created in April 2024. + +### Survival data + +Survival fields are calculated from the clinical data and added as new columns in the clinical file. + +- `OS_STATUS` is converted from `demo__vital_status` +- `OS_MONTHS` is converted from `demo__days_to_death`, falls back to `diag__days_to_last_follow_up` + + + + +### Timeline data + +- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +- For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. + +- Birth timeline events are removed, as they (1) push other events to the far right of the graph and (2) can potentially be used to identify the patient. + +The following status values are supported in `data_timeline_status.txt`: + +- `__time0__` +- `demo__days_to_death` +- `diag__days_to_last_follow_up` +### Other transformations + +- `"not reported"` values are replaced with blanks. +- If a clinical field is missing for the entire study, the column is removed from the data file. +- `RACE`, `ETHNICITY`, and `SEX` are capitalized. +- `AGE` is converted from days to years. + +## CNA data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.copy_number_gene_level_hg38_gdc_r36`. ISB-CGC data was created in March 2023. +- Transformations + - Copy number values from the BigQuery tables are converted from [ASCAT](https://www.pnas.org/doi/10.1073/pnas.1009843107https://www.pnas.org/doi/10.1073/pnas.1009843107) to GISTIC 2.0 using the following thresholds: + +| ASCAT Value | GISTIC Value | Meaning | +|---|---|---| +| X = 0 | -2 | Deep loss | +| X = 1 | -1 | Single-copy loss | +| X = 2 | 0 | Diploid | +| 2 < X < 7 | 1 | Low-level gain | +| 7 ≤ X | 2 | Amplification | + +Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on the cBioPortal website. As a result these conversion thresholds affect how many samples show up in the CNA chart, which can be inconsistent with legacy versions of this study. We chose ASCAT ≥ 7 as the amplification threshold because it resulted in the least deviation from our legacy studies. + + + +## mRNA Expression data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.RNAseq_hg38_gdc_r35`. ISB-CGC data was created in December 2022. +- The `unstranded`, `tpm_unstranded`, and `fpkm_uq_unstranded` columns are pulled and each mapped to their own data file. + - The regular FPKM values are excluded because [FPKM-UQ provides a more stable metric](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#upper-quartile-fpkm). +- Transformations: see [Genomic data transformations](#genomic-data-transformations) + + + +## Mutation data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.masked_somatic_mutation_hg38_gdc_r40`. ISB-CGC data was created in July 2024. +- The MAF is annotated with Genome Nexus in order to avoid issues with the isoform mapping. Parameters used: + - Endpoint: https://grch38.genomenexus.org/ + - Isoform override: mskcc + - Replace gene symbols and Entrez IDs + - Post interval size: 500 +- Mutation data may be missing for some samples-- this reflects a lack of data availability in ISB-CGC. + +## Expression data transformations (CNA / mRNA) + +- Ensembl gene IDs are mapped to Entrez IDs using the [Genome Nexus hg38 canonical transcript file](https://github.com/genome-nexus/genome-nexus-importer/blob/master/data/grch38_ensembl95/export/ensembl_biomart_canonical_transcripts_per_hgnc.txt). Any genes that cannot be converted using this file are dropped. + - Prior to conversion, we also filter out a small number of duplicate Ensembl genes. These genes have copies containing data for both the X and the Y chromosomes. +- If a sample has multiple aliquots, it has to be condensed to 1 before it can imported into cBioPortal. This is done by choosing the aliquot ID with the highest sort value (eg. highest plate number), following [the same policy](https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844334036/FAQ#FAQ-replicateFilteringQ%3AWhatdoyoudowhenmultiplealiquotbarcodesexistforagivensample%2Fportion%2Fanalytecombination%3F) used by GDAC used to condense aliquot data in their studies. + +## Post-processing steps + + - Samples that lack any genomic data are removed from the clinical sample file. + - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - Case lists are generated under `case_lists/` using a curation-provided script. + - The validator script is run and the HTML report is saved under `validation_reports/`. + +## List of remapped columns + +### Clinical patient + +| Original | cBioPortal | +|---|---| +| submitter_id | PATIENT_ID | +| case_id | OTHER_PATIENT_ID | +| demo__ethnicity | ETHNICITY | +| demo__gender | SEX | +| demo__race | RACE | +| demo__vital_status | VITAL_STATUS | +| diag__age_at_diagnosis | AGE | +| diag__classification_of_tumor | TUMOR_CLASSIFICATION | +| diag__cog_neuroblastoma_risk_group | COG_NEUROBLASTOMA_RISK_GROUP | +| diag__icd_10_code | ICD_10 | +| diag__inss_stage | INSS_STAGE | +| diag__last_known_disease_status | DISEASE_STATUS | +| diag__metastasis_at_diagnosis | METASTASIS_AT_DIAGNOSIS | +| diag__morphology | MORPHOLOGY | +| diag__path__necrosis_percent | PATHOLOGY_NECROSIS_PERCENT | +| diag__primary_diagnosis | PRIMARY_DIAGNOSIS | +| diag__site_of_resection_or_biopsy | BIOPSY_SITE | +| diag__year_of_diagnosis | YEAR_OF_DIAGNOSIS | +| disease_type | DISEASE_TYPE | +| index_date | INDEX_DATE | +| primary_site | PRIMARY_SITE_PATIENT | +| proj__name | PROJECT_NAME | +| proj__project_id | PROJECT_ID | + + +### Clinical sample + +| Original | cBioPortal | +|---|---| +| case_barcode | PATIENT_ID | +| sample_barcode | SAMPLE_ID | +| sample_gdc_id | OTHER_SAMPLE_ID | +| sample_type_name | SAMPLE_TYPE | +| primary_site | PRIMARY_SITE | +| days_to_collection | DAYS_TO_COLLECTION | +| days_to_sample_procurement | DAYS_TO_SPECIMEN_COLLECTION | +| is_ffpe | IS_FFPE | + + + +### Mutation + +| Original | cBioPortal | +|---|---| +| sample_barcode_tumor | Tumor_Sample_Barcode | +| sample_barcode_normal | Matched_Norm_Sample_Barcode | \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/case_lists/cases_all.txt b/crdc/gdc/alal_target_gdc/case_lists/cases_all.txt new file mode 100644 index 0000000000..fd12817a40 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: alal_target_gdc +stable_id: alal_target_gdc_all +case_list_name: All samples +case_list_description: All samples (233 samples) +case_list_category: all_cases_in_study +case_list_ids: TARGET-15-SJMPAL042796-09A TARGET-15-SJMPAL016342-09B TARGET-15-SJMPAL011914-09B TARGET-15-SJMPAL042943-09A TARGET-15-SJMPAL044948-09A TARGET-15-SJMPAL046471-09A.1 TARGET-15-PASZVW-09B TARGET-15-SJMPAL012419-09A TARGET-15-SJMPAL046471-09A TARGET-15-SJMPAL012426-09A.3 TARGET-15-SJMPAL041120-09A TARGET-15-SJMPAL043770-09B TARGET-15-SJMPAL040030-09A.1 TARGET-15-SJMPAL042789-09A.3 TARGET-15-SJMPAL043769-03B TARGET-20-SJAML040268-09A TARGET-20-SJAML045742-09A TARGET-15-SJMPAL040030-09A.3 TARGET-15-SJMPAL012418-09A.2 TARGET-15-SJMPAL042795-09A.2 TARGET-15-SJMPAL044950-09A TARGET-20-SJAML003320-09A TARGET-15-SJMPAL041122-09A.1 TARGET-15-SJMPAL016343-09A.1 TARGET-15-SJMPAL040030-09A.4 TARGET-15-SJMPAL041119-09A.1 TARGET-20-SJAML016570-09A TARGET-15-SJMPAL041119-09B TARGET-15-SJMPAL012419-09B TARGET-20-SJAML007113-09A TARGET-15-SJMPAL044953-09A TARGET-15-SJMPAL016343-09A TARGET-15-SJMPAL012422-09A TARGET-20-SJAML003322-09A TARGET-15-SJMPAL016340-09A TARGET-15-SJMPAL017981-03A TARGET-15-SJMPAL011912-09A.1 TARGET-15-SJMPAL040036-03A.2 TARGET-15-SJMPAL017978-09A TARGET-15-PARWPU-09A.1 TARGET-15-SJMPAL042799-09A TARGET-15-SJMPAL040031-09A.2 TARGET-20-SJAML045741-09A TARGET-15-SJMPAL046470-09A.1 TARGET-15-SJMPAL046467-09A TARGET-15-SJMPAL040030-09A.2 TARGET-15-SJMPAL040037-09A.2 TARGET-15-SJMPAL043512-09B TARGET-15-SJMPAL016342-09A.3 TARGET-15-SJMPAL012421-09B TARGET-20-SJAML007112-09A TARGET-15-SJMPAL040033-09A TARGET-15-SJMPAL046468-09A TARGET-15-SJMPAL040039-09A TARGET-15-SJMPAL012422-09A.1 TARGET-15-SJMPAL040038-09A TARGET-15-SJMPAL041117-09A TARGET-15-SJMPAL046466-09A TARGET-15-SJMPAL016342-09A.2 TARGET-15-SJMPAL041119-09A TARGET-15-SJMPAL011912-09A TARGET-15-SJMPAL040037-09A.1 TARGET-15-SJMPAL041122-09A.2 TARGET-15-SJMPAL046470-09A.2 TARGET-15-SJMPAL016344-09A TARGET-15-SJMPAL042801-09A TARGET-15-SJMPAL016447-09A.1 TARGET-15-SJMPAL041122-09A TARGET-15-SJMPAL043505-09B TARGET-15-SJMPAL042795-09A.3 TARGET-15-SJMPAL016343-09A.3 TARGET-20-SJAML045740-09A TARGET-15-PAVFTF-09B TARGET-15-SJMPAL041117-09A.1 TARGET-15-SJMPAL040459-09B TARGET-15-SJMPAL043508-09B TARGET-15-SJMPAL041120-09B TARGET-15-SJMPAL041118-09A.2 TARGET-15-SJMPAL042793-09A TARGET-15-SJMPAL042792-09A.2 TARGET-15-SJMPAL043775-09B TARGET-15-SJMPAL016447-09A TARGET-15-SJMPAL017973-09A.2 TARGET-15-SJMPAL043514-09A TARGET-15-SJMPAL044956-09A TARGET-15-SJMPAL040027-09A.1 TARGET-15-SJMPAL046469-09A TARGET-15-SJMPAL042789-09A.1 TARGET-15-SJMPAL041117-09B TARGET-15-SJMPAL011913-09A TARGET-20-SJAML045737-09A TARGET-15-SJMPAL043511-09B TARGET-15-SJMPAL017981-03A.2 TARGET-15-SJMPAL040034-09A TARGET-15-SJMPAL011911-03A.1 TARGET-15-SJMPAL041117-09A.2 TARGET-15-SJMPAL040036-03A TARGET-15-SJMPAL040031-09A.1 TARGET-15-SJMPAL043773-03B TARGET-15-SJMPAL012425-09A.2 TARGET-15-SJMPAL017978-09A.2 TARGET-15-SJMPAL012420-09A TARGET-15-SJMPAL040031-09A.4 TARGET-20-SJAML045736-09A TARGET-15-SJMPAL042794-09A.3 TARGET-15-SJMLL003311-09A.2 TARGET-15-SJMPAL046466-09A.1 TARGET-15-SJMPAL042946-09A TARGET-15-SJMPAL042794-09A TARGET-15-SJMPAL043512-09A TARGET-15-SJMPAL040027-09A.3 TARGET-15-SJMPAL040033-09A.2 TARGET-15-SJMPAL040036-03B TARGET-15-SJMPAL040038-09B TARGET-15-SJMPAL043771-09B TARGET-15-SJMPAL041120-09A.1 TARGET-15-SJMPAL017973-09A.1 TARGET-15-SJMPAL042791-09B TARGET-15-SJMPAL017976-09A.2 TARGET-15-SJMPAL040037-09A.4 TARGET-15-SJMPAL040033-09A.3 TARGET-15-PARWPU-09B TARGET-15-SJMPAL044949-09A TARGET-15-SJMPAL012422-09A.2 TARGET-15-SJMPAL012422-09A.3 TARGET-15-SJMPAL040025-09B TARGET-15-SJMPAL041122-09A.3 TARGET-15-SJMLL003311-09A.1 TARGET-15-SJMPAL042789-09A.2 TARGET-15-SJMPAL041118-09A.1 TARGET-20-SJAML045735-09A TARGET-15-SJMPAL042798-09A TARGET-15-SJMPAL016447-09A.3 TARGET-15-SJMPAL017976-09A.3 TARGET-15-SJMPAL012418-09A.3 TARGET-15-SJMPAL012417-09A TARGET-15-SJMPAL042787-09A.2 TARGET-15-SJMPAL040036-03A.3 TARGET-15-SJMPAL046471-09A.2 TARGET-15-SJMPAL042794-09A.2 TARGET-15-SJMPAL040037-09B TARGET-15-SJMPAL043774-09B TARGET-15-SJMPAL040025-09A.1 TARGET-15-SJMPAL017981-03A.3 TARGET-20-SJAML045734-09A TARGET-15-SJMPAL042794-09B TARGET-15-SJMPAL042941-09A.2 TARGET-15-SJMPAL040031-09A TARGET-15-SJMPAL012426-09A.2 TARGET-15-SJMPAL042793-09B TARGET-15-SJMPAL040031-09A.3 TARGET-15-SJMPAL043510-09A TARGET-15-SJMPAL017981-03A.1 TARGET-15-PAREAT-09B TARGET-15-SJMPAL016342-09A.1 TARGET-15-SJMPAL040025-09A.2 TARGET-15-SJMPAL042792-09A TARGET-15-SJMPAL040039-09B TARGET-15-SJMPAL040024-09A TARGET-15-SJMPAL012426-09A.1 TARGET-15-SJMPAL040024-09A.1 TARGET-15-SJMPAL042792-09A.1 TARGET-15-PARWPU-09A TARGET-15-SJMPAL042797-09A TARGET-15-SJMPAL012424-03A.2 TARGET-15-SJMPAL017975-03A.1 TARGET-15-SJMPAL040035-03A TARGET-15-SJMPAL011914-09A TARGET-15-SJMPAL040459-09A TARGET-15-SJMPAL017977-09A TARGET-15-SJMPAL017978-09A.1 TARGET-15-SJMPAL044957-09A TARGET-15-SJMPAL017975-03B TARGET-15-SJMPAL040026-09A TARGET-15-SJMPAL046470-09A TARGET-15-SJMPAL042801-09B TARGET-15-SJMPAL042792-09A.3 TARGET-15-SJMPAL042794-09A.1 TARGET-15-SJMPAL011915-09A TARGET-15-SJMPAL040038-09A.1 TARGET-15-SJMPAL040032-09A.1 TARGET-15-SJMPAL017975-03A.2 TARGET-20-SJAML045738-09A TARGET-15-SJMPAL017973-09A TARGET-15-SJMPAL022667-09A TARGET-15-SJMPAL042791-09A TARGET-15-SJMPAL042787-09B TARGET-15-SJMPAL040033-09A.1 TARGET-15-SJMPAL041118-09A.3 TARGET-15-SJMPAL046466-09A.2 TARGET-15-SJMPAL042787-09A.1 TARGET-15-SJMPAL012425-09A.1 TARGET-15-SJMPAL012425-09A TARGET-15-SJMPAL012420-09A.1 TARGET-15-SJMPAL016342-09A TARGET-15-SJMPAL016343-09A.2 TARGET-15-SJMPAL040027-09A TARGET-15-SJMPAL040036-03A.1 TARGET-15-SJMPAL042798-09B TARGET-15-SJMPAL016448-09A TARGET-15-SJMPAL043768-09B TARGET-15-SJMPAL011911-03A TARGET-15-SJMPAL017976-09A.1 TARGET-15-SJMPAL040039-09A.2 TARGET-15-SJMPAL040039-09A.1 TARGET-15-SJMPAL042795-09A.1 TARGET-15-PAUFIB-09B TARGET-15-SJMPAL012424-03A.1 TARGET-15-SJMPAL041118-09A TARGET-15-SJMPAL042799-09B TARGET-15-SJMPAL041119-09A.2 TARGET-15-SJMPAL040025-09A TARGET-15-PARWPU-09A.2 TARGET-15-SJMPAL040030-09A TARGET-15-SJMPAL012418-09A TARGET-15-SJMPAL043773-40A TARGET-15-SJMPAL012419-09A.1 TARGET-15-SJMPAL040024-09A.2 TARGET-15-SJMPAL040036-03A.4 TARGET-15-SJMPAL012420-09A.2 TARGET-15-SJMPAL043767-09B TARGET-15-SJMPAL042787-09A TARGET-15-PARWPU-09A.3 TARGET-15-SJMPAL012418-09A.1 TARGET-15-SJMPAL040037-09A TARGET-15-SJMPAL042946-09B TARGET-15-SJMPAL017978-09A.3 TARGET-15-SJMPAL017975-03A TARGET-15-SJMPAL046468-09A.1 TARGET-15-SJMPAL016447-09A.2 TARGET-15-SJMPAL046472-09A TARGET-15-SJMPAL040027-09A.2 TARGET-20-SJAML045739-09A diff --git a/crdc/gdc/alal_target_gdc/case_lists/cases_sequenced.txt b/crdc/gdc/alal_target_gdc/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..8a1539dbab --- /dev/null +++ b/crdc/gdc/alal_target_gdc/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: alal_target_gdc +stable_id: alal_target_gdc_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (117 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: TARGET-15-SJMPAL042943-09A TARGET-15-SJMPAL012422-09A.2 TARGET-15-SJMPAL012422-09A.3 TARGET-15-SJMPAL046471-09A.1 TARGET-15-SJMPAL041122-09A.3 TARGET-15-SJMPAL012426-09A.3 TARGET-15-SJMPAL040027-09A.2 TARGET-15-SJMLL003311-09A.1 TARGET-15-SJMPAL042789-09A.2 TARGET-15-SJMPAL041118-09A.1 TARGET-15-SJMPAL016447-09A.3 TARGET-15-SJMPAL017976-09A.3 TARGET-15-SJMPAL012418-09A.3 TARGET-15-SJMPAL040030-09A.1 TARGET-15-SJMPAL042789-09A.3 TARGET-15-SJMPAL042787-09A.2 TARGET-15-SJMPAL040036-03A.3 TARGET-15-SJMPAL046471-09A.2 TARGET-15-SJMPAL042794-09A.2 TARGET-15-SJMPAL040030-09A.3 TARGET-15-SJMPAL040025-09A.1 TARGET-15-SJMPAL012418-09A.2 TARGET-15-SJMPAL017981-03A.3 TARGET-15-SJMPAL042795-09A.2 TARGET-15-SJMPAL044950-09A TARGET-15-SJMPAL042941-09A.2 TARGET-15-SJMPAL041122-09A.1 TARGET-15-SJMPAL016343-09A.1 TARGET-15-SJMPAL040030-09A.4 TARGET-15-SJMPAL012426-09A.2 TARGET-15-SJMPAL041119-09A.1 TARGET-15-SJMPAL040031-09A.3 TARGET-15-SJMPAL017981-03A.1 TARGET-15-SJMPAL016342-09A.1 TARGET-15-SJMPAL040025-09A.2 TARGET-15-SJMPAL011912-09A.1 TARGET-15-SJMPAL012426-09A.1 TARGET-15-SJMPAL040024-09A.1 TARGET-15-SJMPAL042792-09A.1 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TARGET-15-SJMPAL017978-09A.3 TARGET-15-SJMPAL041120-09A.1 TARGET-15-SJMPAL017973-09A.1 TARGET-15-SJMPAL046468-09A.1 TARGET-15-SJMPAL017976-09A.2 TARGET-15-SJMPAL016447-09A.2 TARGET-15-SJMPAL040037-09A.4 TARGET-15-SJMPAL040033-09A.3 TARGET-15-SJMPAL016342-09A.2 diff --git a/crdc/gdc/alal_target_gdc/data_clinical_patient.txt b/crdc/gdc/alal_target_gdc/data_clinical_patient.txt new file mode 100644 index 0000000000..b417733496 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:062b6dc52a8238850a300d2ce05de13158bcc595d797208821c20cb4be057d1e +size 48451 diff --git a/crdc/gdc/alal_target_gdc/data_clinical_sample.txt b/crdc/gdc/alal_target_gdc/data_clinical_sample.txt new file mode 100644 index 0000000000..4fd80b1ff3 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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b/crdc/gdc/alal_target_gdc/data_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..b007e873e2 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/data_mrna_seq_read_counts.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b91216d82e77d2f598dd95f78c4b8d0f013fb6bc4ea7799f7dd1f6f013a8c3d4 +size 14643050 diff --git a/crdc/gdc/alal_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt b/crdc/gdc/alal_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..bfb7b30ace --- /dev/null +++ b/crdc/gdc/alal_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4cce73f123f1a5baf7768648f74370e2b5a7aa3b3b5bcec098e8908081be4906 +size 36968309 diff --git a/crdc/gdc/alal_target_gdc/data_mrna_seq_tpm.txt b/crdc/gdc/alal_target_gdc/data_mrna_seq_tpm.txt new file mode 100644 index 0000000000..a468b55333 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/data_mrna_seq_tpm.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8f45612efee8d5244ca2c1cbc76c654935e4eb2f1e21c5776597d7bafb5e05a6 +size 31693257 diff --git a/crdc/gdc/alal_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/alal_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..8d62b4bea2 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f9ebd6c94391530c66669601d5307c3d7e065b5a5cded0808bcbb7f2ce9f43c1 +size 37469243 diff --git a/crdc/gdc/alal_target_gdc/data_mutations.txt b/crdc/gdc/alal_target_gdc/data_mutations.txt new file mode 100644 index 0000000000..c2935f28b4 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a2a9d2f4aa695aa96f2bdd0f58833158006e9b8b1d114d1326c28841bc7190bf +size 561347 diff --git a/crdc/gdc/alal_target_gdc/data_timeline_status.txt b/crdc/gdc/alal_target_gdc/data_timeline_status.txt new file mode 100644 index 0000000000..b4128ea3a0 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/data_timeline_status.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f3f40ca7d74977611c4e9385fbd91d13f380b26a0df03ac727709f9258705b21 +size 6812 diff --git a/crdc/gdc/alal_target_gdc/meta_clinical_patient.txt b/crdc/gdc/alal_target_gdc/meta_clinical_patient.txt new file mode 100644 index 0000000000..d6b5de2ba3 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_clinical_sample.txt b/crdc/gdc/alal_target_gdc/meta_clinical_sample.txt new file mode 100644 index 0000000000..2ed3308c35 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_mrna_seq_fpkm.txt b/crdc/gdc/alal_target_gdc/meta_mrna_seq_fpkm.txt new file mode 100644 index 0000000000..007c38c4e4 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_mrna_seq_fpkm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_fpkm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (FPKM) +profile_description: mRNA expression from capture (RNA Seq FPKM) +data_filename: data_mrna_seq_fpkm.txt \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt b/crdc/gdc/alal_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..87ec9b44b1 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_fpkm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression fpkm Zscores +profile_description: mRNA expression from capture (RNA Seq FPKM) zscores +data_filename: data_mrna_seq_fpkm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_mrna_seq_read_counts.txt b/crdc/gdc/alal_target_gdc/meta_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..0b04e27f24 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_mrna_seq_read_counts.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: rna_seq_mrna +show_profile_in_analysis_tab: false +profile_name: mRNA expression +profile_description: Expression levels +data_filename: data_mrna_seq_read_counts.txt \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt b/crdc/gdc/alal_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..9c6049db1c --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_read_counts_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression Zscores +profile_description: mRNA expression from capture read count zscores +data_filename: data_mrna_seq_read_counts_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_mrna_seq_tpm.txt b/crdc/gdc/alal_target_gdc/meta_mrna_seq_tpm.txt new file mode 100644 index 0000000000..05b5a5031b --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_mrna_seq_tpm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_tpm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (TPM) +profile_description: mRNA expression from capture (RNA Seq TPM) +data_filename: data_mrna_seq_tpm.txt \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/alal_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..f2515ad970 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_tpm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression tpm Zscores +profile_description: mRNA expression from capture (RNA Seq TPM) zscores +data_filename: data_mrna_seq_tpm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_mutations.txt b/crdc/gdc/alal_target_gdc/meta_mutations.txt new file mode 100644 index 0000000000..82f5ffb024 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +data_filename: data_mutations.txt +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutation data. +profile_name: Mutations \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_study.txt b/crdc/gdc/alal_target_gdc/meta_study.txt new file mode 100644 index 0000000000..ce75b406e0 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: alal +cancer_study_identifier: alal_target_gdc +name: Acute Leukemias of Ambiguous Lineage - Phase III (TARGET, GDC) +short_name: ALAL +description: TARGET Acute Leukemias of Ambiguous Lineage - Phase III. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +reference_genome: hg38 +groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/meta_timeline_status.txt b/crdc/gdc/alal_target_gdc/meta_timeline_status.txt new file mode 100644 index 0000000000..513d5657f8 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/meta_timeline_status.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: alal_target_gdc +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_timeline_status.txt \ No newline at end of file diff --git a/crdc/gdc/alal_target_gdc/validation_reports/alal_target_gdc-validation.html b/crdc/gdc/alal_target_gdc/validation_reports/alal_target_gdc-validation.html new file mode 100644 index 0000000000..1c619ea367 --- /dev/null +++ b/crdc/gdc/alal_target_gdc/validation_reports/alal_target_gdc-validation.html @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7ba5c5e42028af829449745ecde24acca2382f11ab0d78d2667e8ee3f5753922 +size 3136116 diff --git a/crdc/gdc/aml_target_gdc/README.md b/crdc/gdc/aml_target_gdc/README.md new file mode 100644 index 0000000000..ac86cf6396 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/README.md @@ -0,0 +1,149 @@ +# Comments & assumptions made during curation + +## General + +- Study is updated once every 3 months with latest data from [ISB-CGC BigQuery tables](https://isb-cgc.appspot.com/bq_meta_search/) + - The ISB-CGC tables allow easy access to data collected from multiple NCI-CRDC repositories including the GDC, PDC, and others. The TARGET data in this study comes from the GDC and is accessed through these tables. +- Reference genome used: hg38 +- TARGET started using the hg38 genome as of GDC release 32. For more information, refer to the [GDC release notes](https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-320). + +- Only tumor sample data is included (no normal samples) +- [GDC project webpage](https://portal.gdc.cancer.gov/projects/TARGET-AML) + +## Clinical data + +- **Patient data:** Retrieved from `isb-cgc-bq.TARGET_versioned.clinical_gdc_r40`. ISB-CGC data was created in April 2024. +- **Sample data:** Retrieved from `isb-cgc-bq.TARGET_versioned.per_sample_file_metadata_hg38_gdc_r40`. ISB-CGC data was created in April 2024. + +### Survival data + +Survival fields are calculated from the clinical data and added as new columns in the clinical file. + +- `OS_STATUS` is converted from `demo__vital_status` +- `OS_MONTHS` is converted from `demo__days_to_death`, falls back to `diag__days_to_last_follow_up` + + + + +### Timeline data + +- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +- For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. + +- Birth timeline events are removed, as they (1) push other events to the far right of the graph and (2) can potentially be used to identify the patient. + +The following status values are supported in `data_timeline_status.txt`: + +- `__time0__` +- `demo__days_to_death` +- `diag__days_to_last_follow_up` +### Other transformations + +- `"not reported"` values are replaced with blanks. +- If a clinical field is missing for the entire study, the column is removed from the data file. +- `RACE`, `ETHNICITY`, and `SEX` are capitalized. +- `AGE` is converted from days to years. + +## CNA data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.copy_number_gene_level_hg38_gdc_r36`. ISB-CGC data was created in March 2023. +- Transformations + - Copy number values from the BigQuery tables are converted from [ASCAT](https://www.pnas.org/doi/10.1073/pnas.1009843107https://www.pnas.org/doi/10.1073/pnas.1009843107) to GISTIC 2.0 using the following thresholds: + +| ASCAT Value | GISTIC Value | Meaning | +|---|---|---| +| X = 0 | -2 | Deep loss | +| X = 1 | -1 | Single-copy loss | +| X = 2 | 0 | Diploid | +| 2 < X < 7 | 1 | Low-level gain | +| 7 ≤ X | 2 | Amplification | + +Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on the cBioPortal website. As a result these conversion thresholds affect how many samples show up in the CNA chart, which can be inconsistent with legacy versions of this study. We chose ASCAT ≥ 7 as the amplification threshold because it resulted in the least deviation from our legacy studies. + + + +## mRNA Expression data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.RNAseq_hg38_gdc_r35`. ISB-CGC data was created in December 2022. +- The `unstranded`, `tpm_unstranded`, and `fpkm_uq_unstranded` columns are pulled and each mapped to their own data file. + - The regular FPKM values are excluded because [FPKM-UQ provides a more stable metric](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#upper-quartile-fpkm). +- Transformations: see [Genomic data transformations](#genomic-data-transformations) + + + +## Mutation data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.masked_somatic_mutation_hg38_gdc_r40`. ISB-CGC data was created in July 2024. +- The MAF is annotated with Genome Nexus in order to avoid issues with the isoform mapping. Parameters used: + - Endpoint: https://grch38.genomenexus.org/ + - Isoform override: mskcc + - Replace gene symbols and Entrez IDs + - Post interval size: 500 +- Mutation data may be missing for some samples-- this reflects a lack of data availability in ISB-CGC. + +## Expression data transformations (CNA / mRNA) + +- Ensembl gene IDs are mapped to Entrez IDs using the [Genome Nexus hg38 canonical transcript file](https://github.com/genome-nexus/genome-nexus-importer/blob/master/data/grch38_ensembl95/export/ensembl_biomart_canonical_transcripts_per_hgnc.txt). Any genes that cannot be converted using this file are dropped. + - Prior to conversion, we also filter out a small number of duplicate Ensembl genes. These genes have copies containing data for both the X and the Y chromosomes. +- If a sample has multiple aliquots, it has to be condensed to 1 before it can imported into cBioPortal. This is done by choosing the aliquot ID with the highest sort value (eg. highest plate number), following [the same policy](https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844334036/FAQ#FAQ-replicateFilteringQ%3AWhatdoyoudowhenmultiplealiquotbarcodesexistforagivensample%2Fportion%2Fanalytecombination%3F) used by GDAC used to condense aliquot data in their studies. + +## Post-processing steps + + - Samples that lack any genomic data are removed from the clinical sample file. + - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - Case lists are generated under `case_lists/` using a curation-provided script. + - The validator script is run and the HTML report is saved under `validation_reports/`. + +## List of remapped columns + +### Clinical patient + +| Original | cBioPortal | +|---|---| +| submitter_id | PATIENT_ID | +| case_id | OTHER_PATIENT_ID | +| demo__ethnicity | ETHNICITY | +| demo__gender | SEX | +| demo__race | RACE | +| demo__vital_status | VITAL_STATUS | +| diag__age_at_diagnosis | AGE | +| diag__classification_of_tumor | TUMOR_CLASSIFICATION | +| diag__cog_neuroblastoma_risk_group | COG_NEUROBLASTOMA_RISK_GROUP | +| diag__icd_10_code | ICD_10 | +| diag__inss_stage | INSS_STAGE | +| diag__last_known_disease_status | DISEASE_STATUS | +| diag__metastasis_at_diagnosis | METASTASIS_AT_DIAGNOSIS | +| diag__morphology | MORPHOLOGY | +| diag__path__necrosis_percent | PATHOLOGY_NECROSIS_PERCENT | +| diag__primary_diagnosis | PRIMARY_DIAGNOSIS | +| diag__site_of_resection_or_biopsy | BIOPSY_SITE | +| diag__year_of_diagnosis | YEAR_OF_DIAGNOSIS | +| disease_type | DISEASE_TYPE | +| index_date | INDEX_DATE | +| primary_site | PRIMARY_SITE_PATIENT | +| proj__name | PROJECT_NAME | +| proj__project_id | PROJECT_ID | + + +### Clinical sample + +| Original | cBioPortal | +|---|---| +| case_barcode | PATIENT_ID | +| sample_barcode | SAMPLE_ID | +| sample_gdc_id | OTHER_SAMPLE_ID | +| sample_type_name | SAMPLE_TYPE | +| primary_site | PRIMARY_SITE | +| days_to_collection | DAYS_TO_COLLECTION | +| days_to_sample_procurement | DAYS_TO_SPECIMEN_COLLECTION | +| is_ffpe | IS_FFPE | + + + +### Mutation + +| Original | cBioPortal | +|---|---| +| sample_barcode_tumor | Tumor_Sample_Barcode | +| sample_barcode_normal | Matched_Norm_Sample_Barcode | \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/case_lists/cases_all.txt b/crdc/gdc/aml_target_gdc/case_lists/cases_all.txt new file mode 100644 index 0000000000..a308b262d4 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: aml_target_gdc +stable_id: aml_target_gdc_all +case_list_name: All samples +case_list_description: All samples (2330 samples) +case_list_category: all_cases_in_study +case_list_ids: TARGET-20-PASCFW-09A TARGET-20-PAWIEJ-09A TARGET-20-PAEMDG-09A TARGET-20-PACDZR-09A TARGET-20-PAXMGU-09A TARGET-20-PAVJPL-09A TARGET-20-PACEFU-09A TARGET-20-PASTPU-09A TARGET-20-PAVYVR-09A TARGET-20-PAYGWX-Unsorted-09A TARGET-20-PASBHI-09A TARGET-20-PASYCJ-09A TARGET-20-PARSGS-09A TARGET-20-PASKUA-40A TARGET-20-PARDMG-09A TARGET-20-PANKBX-09A TARGET-20-PANWYJ-03A TARGET-20-PAEARG-09A TARGET-20-PAUVWF-09A TARGET-20-PATILU-09A TARGET-20-PAXJZX-09A TARGET-20-PAXCWR-09A TARGET-20-PAVFHK-03A TARGET-20-PANTEL-03A TARGET-20-PAVDXR-09A TARGET-20-PAWNYX-09A TARGET-20-PAXEHH-09A TARGET-20-PALSSP-09A TARGET-20-PAWJDM-09A TARGET-20-PAWMFH-09A TARGET-20-PAVVAM-09A TARGET-20-PASJUC-09A TARGET-20-PASXSF-09A TARGET-20-PAVAKA-09A TARGET-20-PARUSN-09A TARGET-20-PASMPC-03A TARGET-20-PARDFM-03A TARGET-20-PAXCWZ-09A TARGET-20-PANPSV-03A TARGET-20-PANFMG-09A TARGET-20-PAVMED-09A TARGET-20-PAVMZL-09A TARGET-20-PASULX-09A TARGET-20-PASSYV-03A TARGET-20-PAVIGB-09A TARGET-20-PASVVM-09A TARGET-20-PASIXF-09A TARGET-20-PAUYWJ-09A TARGET-20-PAUNBR-09A TARGET-20-PAXJMY-09A TARGET-20-PARSXZ-03A TARGET-20-PAVGBH-09A TARGET-20-PARPEK-03A TARGET-20-PATFYN-09A TARGET-20-PANUTX-09A TARGET-20-PAVWZV-09A TARGET-20-PAULDS-09A TARGET-20-PAWFBA-09A TARGET-20-PASARK-09A TARGET-20-PAWLRX-09A TARGET-20-PASGCJ-03A TARGET-20-PASGMZ-03A TARGET-20-PAVAWS-09A TARGET-20-PAWKLE-09A TARGET-20-PAVPXS-03A TARGET-20-PARZYN-03A TARGET-20-PAULTY-09A TARGET-20-PASPKE-09A TARGET-20-PAYDNH-09A TARGET-20-PATKLS-09A TARGET-20-PASSNX-09A TARGET-20-PARJKM-09A TARGET-20-PAVKBW-09A TARGET-20-PATDLI-09A TARGET-20-PAVDMY-09A TARGET-20-PAMXZY-09A TARGET-20-PARBCV-09A TARGET-20-PAWKGX-09A TARGET-20-PAVHLI-40A TARGET-20-PAKRUP-09A TARGET-20-PAUPSX-09A TARGET-20-PAYDUC-09A TARGET-20-PAVRTN-09A TARGET-20-PAYIRH-Unsorted-09A TARGET-20-PAWMFY-03A TARGET-20-PAXHPH-09A TARGET-20-PAXHCC-09A TARGET-20-PAUMTZ-09A TARGET-20-PAUUXA-09A TARGET-20-PAUTKL-09A TARGET-20-PAMYGX-09A TARGET-20-PASTIE-03A TARGET-20-PARYEB-09A TARGET-20-PAWYEK-09A TARGET-20-PAXCVU-09A TARGET-20-PASGGK-03A TARGET-20-PASUCA-09A TARGET-20-PAYLEK-Sorted-CD34neg-Lymphoid-09A TARGET-20-PAREWJ-09A TARGET-20-PASPFE-09A TARGET-20-PAUNVN-09A TARGET-20-PAUUYJ-09A TARGET-20-PAUSXS-09A TARGET-20-PARAEF-09A TARGET-20-PARVAF-09A TARGET-20-PAVDBT-09A TARGET-20-PASRSS-09A TARGET-20-PAUVXT-03A TARGET-20-PAUSBA-09A TARGET-20-PANTNA-09A TARGET-20-PAWTLZ-09A TARGET-20-PAVGXF-09A TARGET-21-PASFHK-09A TARGET-20-PASAXB-09A TARGET-20-PAVGNC-09A TARGET-20-PAEPTD-09A TARGET-20-PATBVX-09A TARGET-20-PATAWB-09A TARGET-20-PAUNVK-09A TARGET-20-PAXLWH-09A TARGET-20-PATFDF-09A TARGET-20-PAVCFR-09A TARGET-20-PAWYNC-09A TARGET-20-PATVRA-09A TARGET-20-PATGXE-09A TARGET-20-PASRZX-09A TARGET-20-PAUUTI-09A TARGET-20-PAWKJC-09A TARGET-20-PANKFG-09A TARGET-20-PAYKGV-Sorted-CD34pos-09A TARGET-20-PAVCPM-09A TARGET-20-PAVWJV-09A TARGET-20-PAXJYU-09A TARGET-20-PAUMAR-03A TARGET-20-PARHUP-09A TARGET-20-PAWAMM-03A TARGET-20-PAXMLN-09A TARGET-20-PANLRE-09A TARGET-20-PARXMP-09A TARGET-20-PASFZN-09A TARGET-20-PAYKSD-Sorted-CD34pos-09A TARGET-20-PAXLDI-09A TARGET-20-PADZYW-09A TARGET-20-PASVUI-03A TARGET-20-PANZXI-09A TARGET-20-PASZEI-09A TARGET-20-PAUZJX-09A TARGET-20-PAVBVA-09A TARGET-20-PAYHGK-Sorted-leukemic-09A TARGET-20-PAUMMG-09A TARGET-20-PAUKDH-09A TARGET-20-PAPWIU-09A TARGET-20-PAXGPE-09A TARGET-20-PAVNUW-03A TARGET-20-PAXKTZ-09A TARGET-21-PATKWH-41A TARGET-20-PARCHW-09A TARGET-20-PAXBAV-09A TARGET-21-PATHIU-09A TARGET-20-PAPZCL-09A TARGET-20-PAVMWJ-09A TARGET-20-PATCVL-03A TARGET-20-PAWFTV-03A TARGET-20-PARWDZ-09A TARGET-20-PARVTI-09A TARGET-20-PASNDH-09A TARGET-20-PAYHMK-Sorted-non-leukemic-09A TARGET-20-PASMYS-09A TARGET-20-PASTHA-09A TARGET-20-PAWGYG-09A TARGET-20-PASCWG-09A TARGET-20-PAPZXN-09A TARGET-20-PASAFM-09A TARGET-20-PAWCLC-09A TARGET-20-PASDVA-09A TARGET-20-PANUTB-09A TARGET-20-PAUXCD-09A TARGET-20-PAWGEG-09A TARGET-20-PAUURD-09A TARGET-20-PAWMIP-09A TARGET-20-PAYKGV-Unsorted-09A TARGET-20-PAVLWY-09A TARGET-20-WSUAML-50A TARGET-20-PAWHRB-03A TARGET-20-PAWLAN-09A TARGET-20-PAXMAY-09A TARGET-20-PASIZB-09A TARGET-20-PASBII-09A TARGET-20-PAXMCG-09A TARGET-20-PAWGEM-09A TARGET-20-PANSGV-09A TARGET-20-PAXKEZ-09A TARGET-20-PAKKZL-09A TARGET-20-PAXHGG-09A TARGET-20-PAXETX-09A TARGET-20-PARKFB-03A TARGET-20-PARKFB-09A TARGET-20-PAUWCF-09A TARGET-20-PAXBEF-09A TARGET-20-PAVUPS-09A TARGET-20-PAWWEE-09A TARGET-20-PAKLPD-09A TARGET-20-PAWSWR-09A TARGET-20-PARAIC-09A TARGET-20-PAXCCW-09A TARGET-20-PAVKKI-03A TARGET-20-MV411AZAD11-50A TARGET-20-PAWWMJ-09A TARGET-20-PAXAXY-09A TARGET-20-PAYIET-09A TARGET-20-PAECCE-09A TARGET-20-PAXBPF-09A TARGET-20-PAVVAT-09A TARGET-20-PAWSED-03A TARGET-20-PAXLHS-09A TARGET-20-PAUWYG-09A TARGET-20-PAVVAB-09A TARGET-20-PARLHW-09A TARGET-20-PAPAWN-09A TARGET-20-PAWMHE-09A TARGET-20-PAWEKL-09A TARGET-20-PAXAFS-03A TARGET-20-PAWSCV-09A TARGET-20-PAXJGS-09A TARGET-20-PAWWWL-09A TARGET-20-PATAUU-09A TARGET-20-PASXDS-09A TARGET-20-PASZAF-03A TARGET-20-PAWWZL-09A TARGET-20-PARKLC-09A TARGET-20-PAVYNF-09A TARGET-20-PANWHP-09A TARGET-20-PASWLN-09A TARGET-20-TF1-50A TARGET-20-PATCBV-09A TARGET-20-PASLGD-09A TARGET-20-CMS-50A TARGET-20-PAXJAA-09A TARGET-20-PARILH-03A TARGET-21-PASDXR-41A TARGET-20-PAUZTH-09A TARGET-20-PABLDZ-09A TARGET-20-PAVPFR-09A TARGET-20-PALSFT-03A TARGET-20-PAXDXW-09A TARGET-20-PAWUTL-09A TARGET-20-PANEET-09A TARGET-20-PAWAWL-09A TARGET-20-PAWDBS-09A TARGET-20-PAUHTE-09A TARGET-20-PAWIUS-09A TARGET-21-PASNKZ-09A TARGET-20-PAVACZ-09A TARGET-20-PARJHP-03A TARGET-20-PASFNP-09A TARGET-20-PATDRL-09A TARGET-20-PASRIN-03A TARGET-20-PAVSEJ-09A TARGET-20-PANJFJ-09A TARGET-20-PAWEKU-09A TARGET-21-PATAIJ-09A TARGET-20-PAUTJD-03A TARGET-20-PAWXSX-09A TARGET-20-PASECW-09A TARGET-20-PAEENN-09A TARGET-20-PAVTRM-03A TARGET-20-PAXDNI-09A TARGET-20-PANGCM-03A TARGET-20-PANAEV-09A TARGET-20-PANXAF-03A TARGET-20-PALBHS-09A TARGET-20-PASRRG-03A TARGET-20-PAURVI-09A TARGET-20-PAWLTL-09A TARGET-20-PAVBIY-09A TARGET-20-PAXEBW-09A TARGET-20-KasumiD1-50A TARGET-20-PATWYU-09A TARGET-20-PATDMY-09A TARGET-20-PARPLC-03A TARGET-20-PAXVJC-09A TARGET-20-PAUZRT-09A TARGET-20-PASFFS-09A TARGET-20-PASZLJ-09A TARGET-20-PATGHV-09A TARGET-20-PASPYR-09A TARGET-20-PAUVCB-09A TARGET-21-PASLZE-09A TARGET-20-PAVMNA-09A TARGET-20-PAUYNI-09A TARGET-20-PAVCJB-09A TARGET-20-PAUUKK-09A TARGET-20-PASRIN-09A TARGET-20-PAYEKY-09A TARGET-20-PATCTM-09A TARGET-20-PAWMIX-09A TARGET-20-PAXKZA-09A TARGET-20-PAXXND-09A TARGET-20-PARMZC-09A TARGET-20-PASPWC-03A TARGET-20-PAVAUU-03A TARGET-20-PAVBYN-09A TARGET-20-PAXCLE-03A TARGET-20-PASDGX-09A TARGET-20-PAVGAM-09A TARGET-20-PAUHGM-09A TARGET-20-PAWNIX-09A TARGET-20-PARENB-09A TARGET-20-PATBWH-09A TARGET-20-PAVKAH-09A TARGET-20-PANTRL-09A TARGET-20-PAYASV-09A TARGET-20-PAXFHW-09A TARGET-20-PAELYU-09A TARGET-20-PAWWWE-09A TARGET-20-PASRTP-40A TARGET-20-PATAKC-09A TARGET-20-PAVTWM-09A TARGET-20-PAUYXM-09A TARGET-20-PASMSZ-40A TARGET-20-PARCUK-09A TARGET-20-PAVCVD-09A TARGET-20-PAVEDT-09A TARGET-20-PATIAB-09A TARGET-20-PAWZIX-09A TARGET-20-PAVUPX-09A TARGET-20-PARIMT-40A TARGET-20-PAWEFF-03A TARGET-20-PANKFZ-09A TARGET-20-PAXBIE-09A TARGET-20-PAXLNX-09A TARGET-20-PASEFD-09A TARGET-20-PAVBNV-09A TARGET-20-PAUGNU-03A TARGET-20-PAWRUF-09A TARGET-20-PAWMUZ-09A TARGET-20-PAVNIX-09A TARGET-20-PAWECG-09A TARGET-20-PAVLJH-09A TARGET-20-PAVZYI-09A TARGET-20-PARBLP-09A TARGET-20-PAVULK-09A TARGET-20-PANJIM-09A TARGET-20-PAXGRE-03A TARGET-20-PASXLJ-09A TARGET-20-PANTWV-09A TARGET-20-PAURYA-09A TARGET-20-PASSLT-09A TARGET-20-PATIAK-09A TARGET-20-PARMST-09A TARGET-20-PAWURP-09A TARGET-20-PASTTJ-03A TARGET-20-PAUSBP-09A TARGET-20-PAPZFV-09A TARGET-20-PATDLH-03A TARGET-20-PAXKAH-09A TARGET-20-PAWVLB-09A TARGET-20-PANLLX-09A TARGET-20-PAXKSZ-09A TARGET-20-PATBIP-09A TARGET-20-PATKKI-09A TARGET-20-PAVNAN-09A TARGET-20-PAWRGZ-09A TARGET-20-PAXLYF-40A TARGET-20-PALKYG-09A TARGET-20-PANBWF-09A TARGET-20-PAWMLN-03A TARGET-20-REH-50A TARGET-20-PASVVS-09A TARGET-20-PAVLKG-09A TARGET-20-PARVUC-03A TARGET-20-PATLBI-03A TARGET-20-PAYGWX-Sorted-non-leukemic-09A TARGET-20-PAUNHG-09A TARGET-20-PAVKVT-09A TARGET-20-PAWCKH-09A TARGET-20-PARCEV-09A TARGET-20-PAUZAM-09A TARGET-20-PAWNYK-09A TARGET-20-PAPZJT-40A TARGET-20-PAYHVK-Sorted-leukemic-09A TARGET-20-PASMYP-03A TARGET-20-PAVLDU-09A TARGET-20-PAWMGH-09A TARGET-20-IGROV1-50A TARGET-20-PASGMZ-09A TARGET-20-PAVPKA-40A TARGET-20-PARUUB-09A TARGET-20-PAUSTZ-09A TARGET-20-PANNHB-09A TARGET-20-PAWWCW-40A TARGET-20-PAXDVZ-09A TARGET-20-PAWIHN-09A TARGET-20-PAPXVK-03A TARGET-20-PAXMAD-09A TARGET-20-PAPUEM-03A TARGET-20-PAWHIZ-09A TARGET-20-PARERV-09A TARGET-20-PASCCS-09A TARGET-20-PASUMD-09A TARGET-20-PASVFG-03A TARGET-20-PATMNY-09A TARGET-20-PAWMJY-09A TARGET-20-PATGUB-09A TARGET-20-PAWRUX-03A TARGET-20-PAWCCR-09A TARGET-20-PAVPWB-09A TARGET-20-PAWSBW-09A TARGET-20-PAVAGA-09A TARGET-20-PAXBXI-09A TARGET-21-PASVJS-09A TARGET-20-PAXLVV-09A TARGET-20-PASIBG-09A TARGET-20-PAVAYH-09A TARGET-20-PASDXR-09A TARGET-20-PARNIH-09A TARGET-20-PANBYS-09A TARGET-20-PARCAU-09A TARGET-20-PARDYG-03A TARGET-20-PARIEG-09A TARGET-20-PAUXKD-09A TARGET-20-KasumiAZAD5-50A TARGET-20-PATKEA-09A TARGET-20-PARIHK-09A TARGET-20-PATESX-09A TARGET-20-PARXYR-03A TARGET-20-PAUHFI-09A TARGET-21-PATISD-41A TARGET-20-PAUJBK-09A TARGET-20-PAUSCS-09A TARGET-20-PAEJBT-09A TARGET-20-PARLXL-09A TARGET-20-PASFHK-09A TARGET-20-PAVPLM-09A TARGET-20-PASAYA-09A TARGET-20-PALFZW-09A TARGET-20-PAWUNI-09A TARGET-20-PAWGKS-09A TARGET-20-PASBGZ-09A TARGET-20-PAVRGN-09A TARGET-20-PARIHK-03A TARGET-20-PAXEEY-09A TARGET-20-PAUVMN-09A TARGET-20-PAVBIH-09A TARGET-20-PAPXUF-09A TARGET-21-PARBTV-09A TARGET-21-PASDKZ-41A TARGET-20-PARHSA-09A TARGET-20-PARPHH-03A TARGET-20-PASPIX-09A TARGET-20-PAWWXU-09A TARGET-20-PAWDWA-09A TARGET-20-PASXIS-09A TARGET-20-PASYRR-09A TARGET-20-PASTUH-03A TARGET-20-PAPWFN-09A TARGET-20-PALRKH-09A TARGET-20-PAWUUY-09A TARGET-20-PASDTY-03A TARGET-20-PAWHFW-09A TARGET-20-PAUTIK-09A TARGET-20-PAVTDW-09A TARGET-20-PARKJZ-03A TARGET-20-PARHXT-03A TARGET-20-PASHBI-09A TARGET-20-PATEFH-09A TARGET-20-PAXLEE-09A TARGET-20-PAVANX-09A TARGET-20-PAVAAS-09A TARGET-20-PAXMKU-09A TARGET-20-PAXMPG-09A TARGET-20-PAXJFT-09A TARGET-20-PAVPCA-09A TARGET-20-PAWRVC-09A TARGET-20-PAUPNN-03A TARGET-20-PAPAEG-09A TARGET-21-PATKKJ-41A TARGET-20-PAWGFC-09A TARGET-20-PAPSCM-09A TARGET-20-PAVPDN-09A TARGET-20-PAXGHE-09A TARGET-20-PAXFWY-09A TARGET-20-PARXBT-09A TARGET-20-PANTPW-09A TARGET-20-PAEFEJ-09A TARGET-20-PAXKZN-09A TARGET-20-PAXEES-09A TARGET-20-PASFFX-09A TARGET-20-PASZER-09A TARGET-20-PASSUW-09A TARGET-20-PAXLXM-09A TARGET-20-PANVGP-09A TARGET-20-PAVXPB-09A TARGET-20-PAWEKW-09A TARGET-20-PARRTH-09A TARGET-20-PASFFS-03A TARGET-20-PAUPDB-03A TARGET-20-PATKJB-09A TARGET-20-PARGMH-03A TARGET-20-PAWZZN-09A TARGET-20-PAWCKI-09A TARGET-20-PATENX-09A TARGET-20-PASAUN-09A TARGET-20-PAWFFJ-09A TARGET-20-PAVDRG-09A TARGET-20-PAVHWK-09A TARGET-20-PAVTKK-09A TARGET-20-PAWTHU-09A TARGET-20-PAYKYZ-Unsorted-09A TARGET-20-PALVKV-09A TARGET-20-PAVLBB-09A TARGET-20-PANYBI-09A TARGET-20-PAWEBG-40A TARGET-20-PAWWJN-09A TARGET-20-PAUUPR-09A TARGET-20-PARNTM-09A TARGET-20-PAVHUF-09A TARGET-20-PARHJV-09A 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TARGET-20-PAWXPN-09A TARGET-20-PAVFYL-09A TARGET-20-PASNLR-03A TARGET-20-PAVWPW-09A TARGET-20-PARSHM-03A TARGET-20-PAVPJM-09A TARGET-20-PAYJAX-Unsorted-09A TARGET-20-PAXLMN-09A TARGET-20-PAKLTN-09A TARGET-20-PATGTF-09A TARGET-20-PAXHDA-09A TARGET-20-PAVBZY-03A TARGET-20-PAWCGM-09A TARGET-20-PASKFW-09A TARGET-20-PAVXME-09A TARGET-20-PASYYW-09A TARGET-21-PASTZK-41A TARGET-20-PASAZL-09A TARGET-20-PAWENM-09A TARGET-21-PASFHK-41A TARGET-20-PARMGH-03A TARGET-20-PAVUEF-09A TARGET-20-PAPAPD-09A TARGET-20-PAWZNG-03A TARGET-20-PAXMCH-09A TARGET-20-PAUNLX-09A TARGET-20-PARGXP-03A TARGET-21-PARXYR-03A TARGET-20-PAVYKS-09A TARGET-20-PAPBEJ-09A TARGET-20-PAXGNI-09A TARGET-20-PASFJB-09A TARGET-20-PAYCIT-09A TARGET-20-PAWPKR-03A TARGET-20-PAERAH-09A TARGET-20-PASMGW-40A TARGET-20-PAVXZH-09A TARGET-20-PAXGES-09A TARGET-20-PAXVBY-09A TARGET-21-PARBTV-41A TARGET-20-PAWHKK-03A TARGET-20-PAXGVH-09A TARGET-20-PAREHK-03A TARGET-20-PAVALK-09A TARGET-20-PAXIFA-09A TARGET-20-PAVHLI-03A TARGET-20-PAWRPD-09A TARGET-20-PADYIR-09A TARGET-20-PAVSNL-09A TARGET-20-PARDPM-03A TARGET-20-PASYRE-03A TARGET-20-PAWGVW-09A TARGET-20-PAVCCX-03A TARGET-20-PAWEYY-40A TARGET-20-PAXMCV-09A TARGET-20-PANUNT-09A TARGET-20-PANRIK-09A TARGET-20-PASUVD-09A TARGET-20-PANIDZ-09A TARGET-20-PAUMJB-09A TARGET-20-PAWRKX-09A TARGET-20-PABHKY-03A TARGET-20-PAUSBK-09A TARGET-20-PASXEA-09A TARGET-20-PAYKXV-Sorted-CD34neg-Lymphoid-09A TARGET-20-PASDIR-09A TARGET-20-PARHJA-09A TARGET-20-PAULNJ-09A TARGET-20-PARMZF-09A TARGET-20-PAWEDY-09A TARGET-20-PAXICE-09A TARGET-20-PAVSCL-09A TARGET-20-PAWUUE-09A TARGET-20-PAXKWG-09A TARGET-20-PAUVER-09A TARGET-20-PAVAVV-09A TARGET-20-PAUNYJ-03A TARGET-20-PAVLPL-09A TARGET-20-PAUVCL-09A TARGET-20-PABHET-03A TARGET-20-PARYFA-09A TARGET-20-PARXFZ-03A TARGET-20-PARDDY-09A TARGET-20-PAVESI-03A TARGET-20-PATZIS-09A TARGET-20-PAWMPH-09A TARGET-20-PAVWRI-09A TARGET-20-PAYHRE-Sorted-non-leukemic-09A TARGET-20-PARZYF-09A TARGET-20-PAWNSL-09A TARGET-20-PAWUEX-09A TARGET-20-PATBFL-09A TARGET-20-PARDZW-09A TARGET-20-PAWRPX-09A TARGET-20-PATHVG-03A TARGET-20-PAVTWF-09A TARGET-20-PAXMBS-09A TARGET-20-PASFEW-09A TARGET-20-PASMHY-03A TARGET-20-PAWBSJ-09A TARGET-20-PAVIDD-03A TARGET-20-PAVTIP-09A TARGET-20-PAXGDG-09A TARGET-20-PAUIIB-09A TARGET-20-PAWXCK-09A TARGET-20-PAXLVU-09A TARGET-20-PASINN-09A TARGET-20-PAWWMZ-09A TARGET-20-PAWHAB-09A TARGET-20-PAMYJX-09A TARGET-20-PARUDL-03A TARGET-20-PAYHVK-Sorted-non-leukemic-09A TARGET-20-PAPZZE-09A TARGET-20-PAVKXE-03A TARGET-20-PAVDBD-09A TARGET-20-PAWTPD-09A TARGET-20-PAVAUA-09A TARGET-20-PARASV-03A TARGET-20-PASFLM-09A TARGET-20-PARPWL-09A TARGET-20-PAWWFF-09A TARGET-20-PAXGPF-09A TARGET-20-PAXCFI-03A TARGET-20-PAUVEF-09A TARGET-20-PAWWUN-09A TARGET-20-PAYKSD-Unsorted-09A TARGET-20-MV411AZAD5-50A TARGET-20-PASUGU-09A TARGET-20-PAYIRH-Sorted-non-leukemic-09A TARGET-20-PARTST-09A TARGET-20-PASJTM-09A TARGET-20-PAYGYM-Sorted-leukemic-09A TARGET-20-PAWDBB-09A TARGET-20-PAVWBW-09A TARGET-20-PASBPW-09A TARGET-20-PAUNSV-09A TARGET-20-PATELV-09A TARGET-20-PAYHRE-Sorted-leukemic-09A TARGET-20-PANRBV-03A TARGET-20-PAPXAZ-09A TARGET-20-PAEERJ-09A TARGET-20-PAWLKE-09A TARGET-20-PAWVNC-09A TARGET-20-PAUGHD-03A TARGET-20-PAWKXH-09A TARGET-20-PAUPTI-09A TARGET-20-PARBLV-03A TARGET-20-PAVXFA-09A TARGET-20-PAXLBH-09A TARGET-20-PARYTI-09A TARGET-20-PAXACP-09A diff --git a/crdc/gdc/aml_target_gdc/case_lists/cases_cna.txt b/crdc/gdc/aml_target_gdc/case_lists/cases_cna.txt new file mode 100644 index 0000000000..5f9596b15b --- /dev/null +++ b/crdc/gdc/aml_target_gdc/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: aml_target_gdc +stable_id: aml_target_gdc_cna +case_list_name: Samples with CNA data +case_list_description: Samples with CNA data (68 samples) +case_list_category: all_cases_with_cna_data +case_list_ids: TARGET-20-PARUCB-09A TARGET-20-PASEGC-09A TARGET-20-PASBHI-09A TARGET-20-PARINM-09A TARGET-20-PARZUU-09A TARGET-20-PARIZR-09A TARGET-20-PARDMG-09A TARGET-20-PARVAI-09A TARGET-20-PANSBH-09A TARGET-20-PARIHK-03A TARGET-20-PARMZC-09A TARGET-20-PATAST-09A TARGET-20-PATDNN-09A TARGET-20-PARGXP-03A TARGET-20-PASDUD-09A TARGET-20-PASAFM-09A TARGET-20-PAKIYW-09A TARGET-20-PANUTB-09A TARGET-20-PAERAH-09A TARGET-20-PARMME-09A TARGET-20-PASBBE-09A TARGET-20-PARBFZ-03A TARGET-20-PASPTM-09A TARGET-20-PASFVP-09A TARGET-20-PASARK-09A TARGET-20-PARUNX-09A TARGET-20-PAEEYP-09A TARGET-20-PASIZX-09A TARGET-20-PANVGP-09A TARGET-20-PANCSC-09A TARGET-20-PASBPK-09A TARGET-20-PANTWV-09A TARGET-20-PARWAS-09A TARGET-20-PARZYL-09A TARGET-20-PARYFN-09A TARGET-20-PANKNB-09A TARGET-20-PARBXE-09A TARGET-20-PAMYGX-09A TARGET-20-PARDZW-09A TARGET-20-PASDJY-09A TARGET-20-PASGZS-09A TARGET-20-PARCEV-09A TARGET-20-PAKKBK-09A TARGET-20-PASFEW-09A TARGET-20-PASSSI-09A TARGET-20-PAKRZG-09A TARGET-20-PARLSW-09A TARGET-20-PARXEC-09A TARGET-20-PANGTF-09A TARGET-20-PASIEP-09A TARGET-20-PASMGW-09A TARGET-20-PAPZIZ-09A TARGET-20-PASCCS-09A TARGET-20-PASFNP-09A TARGET-20-PARUWX-09A TARGET-20-PARVUA-03A TARGET-20-PASZZE-09A TARGET-20-PARGVC-03A TARGET-20-PALGKX-09A TARGET-20-PASRTP-09A TARGET-20-PARIEG-09A TARGET-20-PASBPW-09A TARGET-20-PARYCG-03A TARGET-20-PARHBA-03A TARGET-20-PANHYK-09A TARGET-20-PARYXV-09A TARGET-20-PASBSB-03A TARGET-20-PAPVZK-09A diff --git a/crdc/gdc/aml_target_gdc/case_lists/cases_cnaseq.txt b/crdc/gdc/aml_target_gdc/case_lists/cases_cnaseq.txt new file mode 100644 index 0000000000..40b8d24519 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: aml_target_gdc +stable_id: aml_target_gdc_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (55 samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: TARGET-20-PARUCB-09A TARGET-20-PANTWV-09A TARGET-20-PARWAS-09A TARGET-20-PARZYL-09A TARGET-20-PASEGC-09A TARGET-20-PASBHI-09A TARGET-20-PARZUU-09A TARGET-20-PARINM-09A TARGET-20-PASIZX-09A TARGET-20-PARDMG-09A TARGET-20-PARMZC-09A TARGET-20-PAMYGX-09A TARGET-20-PANSBH-09A TARGET-20-PARIHK-03A TARGET-20-PATAST-09A TARGET-20-PARDZW-09A TARGET-20-PARCEV-09A TARGET-20-PAKKBK-09A TARGET-20-PASFEW-09A TARGET-20-PATDNN-09A TARGET-20-PASDUD-09A TARGET-20-PASSSI-09A TARGET-20-PAKRZG-09A TARGET-20-PASMGW-09A TARGET-20-PARXEC-09A TARGET-20-PANGTF-09A TARGET-20-PASIEP-09A TARGET-20-PARLSW-09A TARGET-20-PAPZIZ-09A TARGET-20-PAERAH-09A TARGET-20-PASCCS-09A TARGET-20-PASFNP-09A TARGET-20-PARUWX-09A TARGET-20-PARMME-09A TARGET-20-PASBBE-09A TARGET-20-PASZZE-09A TARGET-20-PARBFZ-03A TARGET-20-PARVUA-03A TARGET-20-PASPTM-09A TARGET-20-PARGVC-03A TARGET-20-PALGKX-09A TARGET-20-PASFVP-09A TARGET-20-PASARK-09A TARGET-20-PASRTP-09A TARGET-20-PARIEG-09A TARGET-20-PASBPW-09A TARGET-20-PARYCG-03A TARGET-20-PARHBA-03A TARGET-20-PANHYK-09A TARGET-20-PARYXV-09A TARGET-20-PARUNX-09A TARGET-20-PASBSB-03A TARGET-20-PAEEYP-09A TARGET-20-PANVGP-09A TARGET-20-PANCSC-09A diff --git a/crdc/gdc/aml_target_gdc/case_lists/cases_sequenced.txt b/crdc/gdc/aml_target_gdc/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..c54d13ddbc --- /dev/null +++ b/crdc/gdc/aml_target_gdc/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: aml_target_gdc +stable_id: aml_target_gdc_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (497 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: TARGET-20-PASCFW-09A TARGET-20-PATGRP-09A TARGET-20-PASTPU-09A TARGET-20-PASBHI-09A TARGET-20-PASYCJ-09A TARGET-20-PASMTK-09A TARGET-20-PARDMG-09A TARGET-20-PATILU-09A TARGET-20-PARUSN-09A TARGET-20-PASMPC-03A TARGET-20-PASWGL-09A TARGET-20-PARDFM-03A TARGET-20-PARCVP-09A TARGET-20-PASULX-09A TARGET-20-PASSYV-03A TARGET-20-PATCXL-03A TARGET-20-PANPTM-09A TARGET-20-PARANT-09A TARGET-20-PASARK-09A TARGET-20-PASGCJ-03A TARGET-20-PARGDB-03A TARGET-20-PARSFK-09A TARGET-20-PARXJW-09A TARGET-20-PANJGR-09A TARGET-20-PATDYY-09A TARGET-20-PATLBC-03A TARGET-20-PARZYN-03A TARGET-20-PASPKE-09A TARGET-20-PATKLS-09A TARGET-20-PASSNX-09A TARGET-20-PASGEM-03A TARGET-20-PARJKM-09A TARGET-20-PATDLI-09A TARGET-20-PARBCV-09A TARGET-20-PARVZU-03A TARGET-20-PASPIN-09A TARGET-20-PARUTH-09A TARGET-20-PARNJC-09A TARGET-20-PAMYGX-09A TARGET-20-PASTIE-03A TARGET-20-PARYEB-09A TARGET-20-PASJRD-03A TARGET-20-PASUCA-09A TARGET-20-PATFNK-09A TARGET-20-PASPFE-09A TARGET-20-PARVAF-09A TARGET-20-PASSSI-09A TARGET-20-PARXEC-09A TARGET-20-PASMGW-09A TARGET-20-PASRSS-09A TARGET-20-PANTNA-09A TARGET-20-PASWWD-03A TARGET-20-PARZWH-09A TARGET-20-PATBVX-09A TARGET-20-PASZZE-09A TARGET-20-PATFDF-09A TARGET-20-PANKFG-09A TARGET-20-PATFGL-03A TARGET-20-PARHUP-09A TARGET-20-PANLRE-09A TARGET-20-PASFZN-09A TARGET-20-PASKGD-09A TARGET-20-PARAFA-09A TARGET-20-PASKPI-09A TARGET-20-PAPWIU-09A TARGET-20-PARZUU-09A TARGET-20-PARFXF-09A TARGET-20-PARKHV-09A TARGET-20-PATEWX-09A TARGET-20-PATBJK-09A TARGET-20-PARFWM-09A TARGET-20-PARVTI-09A TARGET-20-PASNDH-09A TARGET-20-PATEID-09A TARGET-20-PASMYS-09A TARGET-20-PASTHA-09A TARGET-20-PASDVA-09A TARGET-20-PARNPC-09A TARGET-20-PASBII-09A TARGET-20-PARKFB-03A TARGET-20-PARHKZ-09A TARGET-20-PARLHW-09A TARGET-20-PAPAWN-09A TARGET-20-PASXYG-09A TARGET-20-PASANW-09A TARGET-20-PATAUU-09A TARGET-20-PASXDS-09A TARGET-20-PASZAF-03A TARGET-20-PASGGK-09A TARGET-20-PANWHP-09A TARGET-20-PASKNV-09A TARGET-20-PASLGD-09A TARGET-20-PATCBV-09A TARGET-20-PARILH-03A TARGET-20-PATMFM-09A TARGET-20-PARUAD-09A TARGET-20-PAPZIZ-09A TARGET-20-PASPXN-09A TARGET-20-PATBUR-09A TARGET-20-PARWXU-40A TARGET-20-PARJHP-03A TARGET-20-PASFNP-09A TARGET-20-PATCPY-09A TARGET-20-PATDRL-09A TARGET-20-PASPLU-09A TARGET-20-PATDRB-09A TARGET-20-PASMTB-09A TARGET-20-PARLFE-03A TARGET-20-PANGCM-03A TARGET-20-PANAEV-09A TARGET-20-PARYCG-03A TARGET-20-PATBPW-09A TARGET-20-PASWAJ-09A TARGET-20-PARUEX-09A TARGET-20-PASKRM-09A TARGET-20-PATDMY-09A TARGET-20-PARPLC-03A TARGET-20-PASPTW-09A TARGET-20-PASFFS-09A TARGET-20-PASZLJ-09A TARGET-20-PASEGC-09A TARGET-20-PASELK-03A TARGET-20-PARIMT-03A TARGET-20-PASRIN-09A TARGET-20-PASYTW-03A TARGET-20-PATCTM-09A TARGET-20-PASREH-09A TARGET-20-PARTWN-09A TARGET-20-PARMZC-09A TARGET-20-PASPWC-03A TARGET-20-PARHYP-09A TARGET-20-PARRDD-09A TARGET-20-PANLIZ-09A TARGET-20-PATAKC-09A TARGET-20-PATDVM-03A TARGET-20-PAPUSR-09A TARGET-20-PATCYP-03A TARGET-20-PARCUK-09A TARGET-20-PARAUM-09A TARGET-20-PASTSH-09A TARGET-20-PANKFZ-09A TARGET-20-PASHMK-09A TARGET-20-PARBZJ-09A TARGET-20-PARLSL-09A TARGET-20-PARBLP-09A TARGET-20-PASVMU-03A TARGET-20-PASXLJ-09A TARGET-20-PASBNA-03A TARGET-20-PATHIW-09A TARGET-20-PANTWV-09A TARGET-20-PARZYL-09A TARGET-20-PARXYC-09A TARGET-20-PATIAK-09A TARGET-20-PASTTJ-03A TARGET-20-PAPZFV-09A TARGET-20-PARVSF-09A TARGET-20-PATBIP-09A TARGET-20-PATKKI-09A TARGET-20-PASVVS-09A TARGET-20-PATAKZ-09A TARGET-20-PARCEV-09A TARGET-20-PASXGT-03A TARGET-20-PAPZJT-40A TARGET-20-PAKKBK-09A TARGET-20-PASMYP-03A TARGET-20-PATKAH-09A TARGET-20-PARUUB-09A TARGET-20-PARERV-09A TARGET-20-PASCCS-09A TARGET-20-PASUMD-09A TARGET-20-PASVFG-03A TARGET-20-PATLVC-09A TARGET-20-PATMNY-09A TARGET-20-PATALD-09A TARGET-20-PATDRZ-09A TARGET-20-PASSGX-09A TARGET-20-PASCRZ-03A TARGET-20-PARFRN-03A TARGET-20-PARGYS-09A TARGET-20-PASDXR-09A TARGET-20-PALGKX-09A TARGET-20-PARNIH-09A TARGET-20-PARIEG-09A TARGET-20-PARHBA-03A TARGET-20-PASURR-09A TARGET-20-PARUCB-09A TARGET-20-PARLXL-09A TARGET-20-PATJNI-09A TARGET-20-PANLKB-09A TARGET-20-PARCIN-09A TARGET-20-PASBGZ-09A TARGET-20-PANSBH-09A TARGET-20-PARIHK-03A TARGET-20-PARYFN-03A TARGET-20-PASPIX-09A TARGET-20-PASDUD-09A TARGET-20-PASXIS-09A TARGET-20-PASYRR-09A TARGET-20-PASTUH-03A TARGET-20-PATJPY-09A TARGET-20-PARKJZ-03A TARGET-20-PARHXT-03A TARGET-20-PARVLH-09A TARGET-20-PASHBI-09A TARGET-20-PATEFH-09A TARGET-20-PASVPJ-09A TARGET-20-PAEIKD-09A TARGET-20-PARSAA-03A TARGET-20-PANTPW-09A TARGET-20-PANUUA-09A TARGET-20-PASFFX-09A TARGET-20-PASZER-09A TARGET-20-PASSUW-09A TARGET-20-PANVGP-09A TARGET-20-PATIDY-09A TARGET-20-PARRTH-09A TARGET-20-PARBVE-09A TARGET-20-PARGMH-03A TARGET-20-PADZCG-09A TARGET-20-PATENX-09A TARGET-20-PASAUN-09A TARGET-20-PARTAL-09A TARGET-20-PARXNG-09A TARGET-20-PARNTM-09A TARGET-20-PASRAT-09A TARGET-20-PARMMN-09A TARGET-20-PARHJV-09A TARGET-20-PAEFGT-09A TARGET-20-PATBIZ-03A TARGET-20-PAPWHS-09A TARGET-20-PASFTR-03A TARGET-20-PANGTF-09A TARGET-20-PASHYZ-09A TARGET-20-PASIEJ-09A TARGET-20-PAPVDV-09A TARGET-20-PARPZP-09A TARGET-20-PATKBT-03A TARGET-20-PAPWYK-09A TARGET-20-PARZMZ-03A TARGET-20-PATMFW-09A TARGET-20-PASZBM-09A TARGET-20-PARSAN-09A TARGET-20-PASNKC-09A TARGET-20-PARCVS-03A TARGET-20-PARYXV-09A TARGET-20-PATFCZ-09A TARGET-20-PASFYF-03A TARGET-20-PARDEV-03A TARGET-20-PASKAS-09A TARGET-20-PASYTG-09A TARGET-20-PAPUNR-09A TARGET-20-PASTEI-09A TARGET-20-PARNXW-03A TARGET-20-PANVGE-09A TARGET-20-PARYVW-09A TARGET-20-PARNIN-03A TARGET-20-PASCGC-03A TARGET-20-PANDIX-09A TARGET-20-PASLTS-09A TARGET-20-PASFRD-09A TARGET-20-PARRHB-03A TARGET-20-PASCGR-03A TARGET-20-PASTZD-09A TARGET-20-PATDNN-09A TARGET-20-PASIGA-09A TARGET-20-PARWCG-09A TARGET-20-PASFIE-09A TARGET-20-PAPVCN-09A TARGET-20-PASSHZ-09A TARGET-20-PARWXU-09A TARGET-20-PARCZL-09A TARGET-20-PASJNM-09A TARGET-20-PARJVU-03A TARGET-20-PARBFZ-03A TARGET-20-PASPGA-09A TARGET-20-PASPTM-09A TARGET-20-PARDRM-03A TARGET-20-PASLSI-09A TARGET-20-PASBST-09A TARGET-20-PAMVKZ-09A TARGET-20-PATGXW-09A TARGET-20-PATMIK-09A TARGET-20-PASYWV-09A TARGET-20-PATDIC-09A TARGET-20-PASGWH-09A TARGET-20-PAPXJT-09A TARGET-20-PARPBF-09A TARGET-20-PATJYT-03A TARGET-20-PASADG-03A TARGET-20-PASGKA-09A TARGET-20-PARHKX-09A TARGET-20-PASNDA-09A TARGET-20-PARCZP-09A TARGET-20-PARGTL-09A TARGET-20-PASFJB-03A TARGET-20-PARFAL-09A TARGET-20-PASDZT-09A TARGET-20-PARNNT-09A TARGET-20-PARTYK-03A TARGET-20-PASARM-03A TARGET-20-PATHAE-09A TARGET-20-PASYDA-09A TARGET-20-PARBRA-09A TARGET-20-PATANY-09A TARGET-20-PASZJR-09A TARGET-20-PANYNR-09A TARGET-20-PAEFGR-09A TARGET-20-PASWIM-09A TARGET-20-PASXVC-09A TARGET-20-PASZUT-09A TARGET-20-PASILA-09A TARGET-20-PASXNR-09A TARGET-20-PATJWN-09A TARGET-20-PARLMY-09A TARGET-20-PARUXJ-09A TARGET-20-PARJYP-03A TARGET-20-PATLHB-03A TARGET-20-PARTXH-09A TARGET-20-PANLJN-09A TARGET-20-PARVUA-03A TARGET-20-PATCWP-03A TARGET-20-PASGZV-03A TARGET-20-PARJRG-09A TARGET-20-PANHYK-09A TARGET-20-PATAIJ-09A TARGET-20-PASSDX-09A TARGET-20-PARXCG-09A TARGET-20-PARBEL-09A TARGET-20-PARPPY-03A TARGET-20-PARXNP-03A TARGET-20-PATJXZ-03A TARGET-20-PAREFM-09A TARGET-20-PATAIY-09A TARGET-20-PASVWE-09A TARGET-20-PAPVGE-09A TARGET-20-PASENE-09A TARGET-20-PASGCE-40A TARGET-20-PARVXT-09A TARGET-20-PARWWW-03A TARGET-20-PARZHT-09A TARGET-20-PARUBE-09A TARGET-20-PARBIU-09A TARGET-20-PARDYL-09A TARGET-20-PANGJY-09A TARGET-20-PARMLW-09A TARGET-20-PATAVF-09A TARGET-20-PARJLW-09A TARGET-20-PARYGA-03A TARGET-20-PASYVX-09A TARGET-20-PARWAS-09A TARGET-20-PANVGP-03A TARGET-20-PASBCT-09A TARGET-20-PASXAH-09A TARGET-20-PASBDC-09A TARGET-20-PASUUD-09A TARGET-20-PARPDS-09A TARGET-20-PATFDF-40A TARGET-20-PASVTP-09A TARGET-20-PAMYAS-09A TARGET-20-PANZWB-09A TARGET-20-PARJWH-09A TARGET-20-PARFMY-09A TARGET-20-PATJLP-09A TARGET-20-PASSWG-03A TARGET-20-PAPZYS-09A TARGET-20-PASEYM-09A TARGET-20-PASIEP-09A TARGET-20-PASXSS-03A TARGET-20-PASLTF-09A TARGET-20-PANPLS-03A TARGET-20-PASHWN-09A TARGET-20-PATEIA-03A TARGET-20-PARUWX-09A TARGET-20-PATFMR-09A TARGET-20-PASZEB-09A TARGET-20-PASJPW-09A TARGET-20-PARFUZ-09A TARGET-20-PAPVKG-09A TARGET-20-PASZYU-03A TARGET-20-PASFIT-09A TARGET-20-PASLPU-09A TARGET-20-PARPCT-09A TARGET-20-PARHVI-03A TARGET-20-PARXVI-09A TARGET-20-PASTBK-09A TARGET-20-PATHZC-09A TARGET-20-PANINI-09A TARGET-20-PASLSD-03A TARGET-20-PASGFI-03A TARGET-20-PASXJY-09A TARGET-20-PATAST-09A TARGET-20-PANDER-09A TARGET-20-PARPEK-09A TARGET-20-PASSVI-09A TARGET-20-PARCCH-03A TARGET-20-PANBZH-09A TARGET-20-PARZVE-03A TARGET-20-PASVAN-03A TARGET-20-PARMME-09A TARGET-20-PASXAP-09A TARGET-20-PASBBE-09A TARGET-20-PASWPD-09A TARGET-20-PARURX-09A TARGET-20-PASDET-09A TARGET-20-PASANH-09A TARGET-20-PASFVP-09A TARGET-20-PASUAF-09A TARGET-20-PAPXWI-09A TARGET-20-PARUNX-09A TARGET-20-PAEEYP-09A TARGET-20-PARMIZ-09A TARGET-20-PASCBW-09A TARGET-20-PARZVA-09A TARGET-20-PANCSC-09A TARGET-20-PASZJT-09A TARGET-20-PASVZC-09A TARGET-20-PATFRY-09A TARGET-20-PASYJI-09A TARGET-20-PATCLR-09A TARGET-20-PASZZL-09A TARGET-20-PANSJB-09A TARGET-20-PATBRA-03A TARGET-20-PATABB-09A TARGET-20-PASPSV-09A TARGET-20-PASRJL-09A TARGET-20-PAKRZG-09A TARGET-20-PARLSW-09A TARGET-20-PARLVL-09A TARGET-20-PANNJI-09A TARGET-20-PARAHF-09A TARGET-20-PASLYX-09A TARGET-20-PASHWV-09A TARGET-20-PARXDI-09A TARGET-20-PASGZK-09A TARGET-20-PATEMV-09A TARGET-20-PASBSB-03A TARGET-20-PARUCB-03A TARGET-20-PASLSE-03A TARGET-20-PASVYL-09A TARGET-20-PAPYUI-09A TARGET-20-PASJYX-09A TARGET-20-PATHWS-09A TARGET-20-PATJKC-09A TARGET-20-PARLUS-03A TARGET-20-PARINM-09A TARGET-20-PARSHM-03A TARGET-20-PARTYV-09A TARGET-20-PATGTF-09A TARGET-20-PASFZB-09A TARGET-20-PAPVWB-09A TARGET-20-PAKTCX-09A TARGET-20-PAERAH-09A TARGET-20-PARMHD-09A TARGET-20-PARPPY-40A TARGET-20-PATKYC-09A TARGET-20-PASMGW-40A TARGET-20-PARNFR-03A TARGET-20-PARMIX-03A TARGET-20-PARDPM-03A TARGET-20-PASYRE-03A TARGET-20-PASUVD-09A TARGET-20-PATELT-09A TARGET-20-PASIZX-09A TARGET-20-PASXEA-09A TARGET-20-PARHJA-09A TARGET-20-PARMZF-09A TARGET-20-PATEMK-09A TARGET-20-PANKKE-09A TARGET-20-PATEEA-09A TARGET-20-PARZYF-09A TARGET-20-PARPBA-09A TARGET-20-PARDZW-09A TARGET-20-PATHVG-03A TARGET-20-PASFEW-09A TARGET-20-PASMHY-03A TARGET-20-PAKSMZ-03A TARGET-20-PASINN-09A TARGET-20-PARUDL-03A TARGET-20-PARDDA-09A TARGET-20-PARHVK-09A TARGET-20-PASVSS-09A TARGET-20-PARASV-03A TARGET-20-PARPWL-09A TARGET-20-PARKCX-09A TARGET-20-PASUGU-09A TARGET-20-PASAFH-09A TARGET-20-PARGVC-03A TARGET-20-PASJTM-09A TARGET-20-PARLGT-09A TARGET-20-PASRTP-09A TARGET-20-PASLDL-09A TARGET-20-PASLHH-09A TARGET-20-PASBPW-09A TARGET-20-PAPXAZ-09A TARGET-20-PASJXN-09A TARGET-20-PARYTI-09A TARGET-20-PASBYL-09A diff --git a/crdc/gdc/aml_target_gdc/data_clinical_patient.txt b/crdc/gdc/aml_target_gdc/data_clinical_patient.txt new file mode 100644 index 0000000000..169e91b96c --- /dev/null +++ b/crdc/gdc/aml_target_gdc/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8f7319e71a8fc515bd961a960e0d89b756f5a355a91642aea26df3d5c02a64ef +size 832371 diff --git a/crdc/gdc/aml_target_gdc/data_clinical_sample.txt b/crdc/gdc/aml_target_gdc/data_clinical_sample.txt new file mode 100644 index 0000000000..7e058ac4bd --- /dev/null +++ b/crdc/gdc/aml_target_gdc/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:50f13d063041f2ed7a3b0705907c4eb97fcdb6b5d813092454a7d01c788761b6 +size 435909 diff --git a/crdc/gdc/aml_target_gdc/data_cna.txt b/crdc/gdc/aml_target_gdc/data_cna.txt new file mode 100644 index 0000000000..630acb1db0 --- 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sha256:91633d8a6e493da55459bfce8748a870a3f00e0bdf7504b109c2f017879ba4ed +size 673127630 diff --git a/crdc/gdc/aml_target_gdc/data_mrna_seq_read_counts.txt b/crdc/gdc/aml_target_gdc/data_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..e778ddb4ff --- /dev/null +++ b/crdc/gdc/aml_target_gdc/data_mrna_seq_read_counts.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:439fadb30efe17c165b3aef2c495be80bd0097a5504015b826a9864028ae3a56 +size 259001588 diff --git a/crdc/gdc/aml_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt b/crdc/gdc/aml_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..b037b2676c --- /dev/null +++ b/crdc/gdc/aml_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1d0c5fdd5ce98192f3a35922394f27e2795940eb60f1dd68759c1a9bef447616 +size 664941618 diff --git a/crdc/gdc/aml_target_gdc/data_mrna_seq_tpm.txt b/crdc/gdc/aml_target_gdc/data_mrna_seq_tpm.txt new file mode 100644 index 0000000000..ddeb7463fe --- /dev/null +++ b/crdc/gdc/aml_target_gdc/data_mrna_seq_tpm.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:90b90b2dcbee97e233f6de5ec2226c88fc2266aff15f73dd221e04e5aa125d11 +size 551469922 diff --git a/crdc/gdc/aml_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/aml_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..e0afff6399 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a00c324e72911ac32afc6ebe1ed7799d6bced08d8ae5a112b35950f6381ad9f2 +size 670690989 diff --git a/crdc/gdc/aml_target_gdc/data_mutations.txt b/crdc/gdc/aml_target_gdc/data_mutations.txt new file mode 100644 index 0000000000..37be4415d6 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3d3c438acccd0ef83be57c94351eee4bfe8d49582e8359b7ef094416a516a97d +size 484606 diff --git a/crdc/gdc/aml_target_gdc/data_timeline_status.txt b/crdc/gdc/aml_target_gdc/data_timeline_status.txt new file mode 100644 index 0000000000..64690945f7 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/data_timeline_status.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5f4b425d98e93cdca42bbc5bba04cd62e69187c6b4f304cb75fc76006ae4c36d +size 127083 diff --git a/crdc/gdc/aml_target_gdc/meta_clinical_patient.txt b/crdc/gdc/aml_target_gdc/meta_clinical_patient.txt new file mode 100644 index 0000000000..0a7b4ae168 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_clinical_sample.txt b/crdc/gdc/aml_target_gdc/meta_clinical_sample.txt new file mode 100644 index 0000000000..3084f5c23a --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_cna.txt b/crdc/gdc/aml_target_gdc/meta_cna.txt new file mode 100644 index 0000000000..37a97f856a --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +stable_id: cna +show_profile_in_analysis_tab: true +profile_name: Putative copy-number alterations from GISTIC +profile_description: Putative copy-number from GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +data_filename: data_cna.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_mrna_seq_fpkm.txt b/crdc/gdc/aml_target_gdc/meta_mrna_seq_fpkm.txt new file mode 100644 index 0000000000..6ea9088c21 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_mrna_seq_fpkm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_fpkm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (FPKM) +profile_description: mRNA expression from capture (RNA Seq FPKM) +data_filename: data_mrna_seq_fpkm.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt b/crdc/gdc/aml_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..b1b4062618 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_fpkm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression fpkm Zscores +profile_description: mRNA expression from capture (RNA Seq FPKM) zscores +data_filename: data_mrna_seq_fpkm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_mrna_seq_read_counts.txt b/crdc/gdc/aml_target_gdc/meta_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..5c8996cf71 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_mrna_seq_read_counts.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: rna_seq_mrna +show_profile_in_analysis_tab: false +profile_name: mRNA expression +profile_description: Expression levels +data_filename: data_mrna_seq_read_counts.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt b/crdc/gdc/aml_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..b92a523b96 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_read_counts_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression Zscores +profile_description: mRNA expression from capture read count zscores +data_filename: data_mrna_seq_read_counts_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_mrna_seq_tpm.txt b/crdc/gdc/aml_target_gdc/meta_mrna_seq_tpm.txt new file mode 100644 index 0000000000..d6f8fd91e3 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_mrna_seq_tpm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_tpm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (TPM) +profile_description: mRNA expression from capture (RNA Seq TPM) +data_filename: data_mrna_seq_tpm.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/aml_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..d87d3eb863 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_tpm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression tpm Zscores +profile_description: mRNA expression from capture (RNA Seq TPM) zscores +data_filename: data_mrna_seq_tpm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_mutations.txt b/crdc/gdc/aml_target_gdc/meta_mutations.txt new file mode 100644 index 0000000000..c5e8cc5c8a --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +data_filename: data_mutations.txt +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutation data. +profile_name: Mutations \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_study.txt b/crdc/gdc/aml_target_gdc/meta_study.txt new file mode 100644 index 0000000000..fb418aaff3 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: aml +cancer_study_identifier: aml_target_gdc +name: Acute Myeloid Leukemia (TARGET, GDC) +short_name: AML +description: TARGET Acute Myeloid Leukemia. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +reference_genome: hg38 +groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_timeline_status.txt b/crdc/gdc/aml_target_gdc/meta_timeline_status.txt new file mode 100644 index 0000000000..194442e233 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/meta_timeline_status.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: aml_target_gdc +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_timeline_status.txt \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/validation_reports/aml_target_gdc-validation.html b/crdc/gdc/aml_target_gdc/validation_reports/aml_target_gdc-validation.html new file mode 100644 index 0000000000..766e4a0c55 --- /dev/null +++ b/crdc/gdc/aml_target_gdc/validation_reports/aml_target_gdc-validation.html @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6dc345d426708abb8175e20d0724a470de8bd9f6d2c36415fd1f5d3370b56b36 +size 3550985 diff --git a/crdc/gdc/bll_target_gdc/README.md b/crdc/gdc/bll_target_gdc/README.md new file mode 100644 index 0000000000..62aad53666 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/README.md @@ -0,0 +1,149 @@ +# Comments & assumptions made during curation + +## General + +- Study is updated once every 3 months with latest data from [ISB-CGC BigQuery tables](https://isb-cgc.appspot.com/bq_meta_search/) + - The ISB-CGC tables allow easy access to data collected from multiple NCI-CRDC repositories including the GDC, PDC, and others. The TARGET data in this study comes from the GDC and is accessed through these tables. +- Reference genome used: hg38 +- TARGET started using the hg38 genome as of GDC release 32. For more information, refer to the [GDC release notes](https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-320). + +- Only tumor sample data is included (no normal samples) +- [GDC project webpage](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P2) + +## Clinical data + +- **Patient data:** Retrieved from `isb-cgc-bq.TARGET_versioned.clinical_gdc_r40`. ISB-CGC data was created in April 2024. +- **Sample data:** Retrieved from `isb-cgc-bq.TARGET_versioned.per_sample_file_metadata_hg38_gdc_r40`. ISB-CGC data was created in April 2024. + +### Survival data + +Survival fields are calculated from the clinical data and added as new columns in the clinical file. + +- `OS_STATUS` is converted from `demo__vital_status` +- `OS_MONTHS` is converted from `demo__days_to_death`, falls back to `diag__days_to_last_follow_up` + + + + +### Timeline data + +- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +- For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. + +- Birth timeline events are removed, as they (1) push other events to the far right of the graph and (2) can potentially be used to identify the patient. + +The following status values are supported in `data_timeline_status.txt`: + +- `__time0__` +- `demo__days_to_death` +- `diag__days_to_last_follow_up` +### Other transformations + +- `"not reported"` values are replaced with blanks. +- If a clinical field is missing for the entire study, the column is removed from the data file. +- `RACE`, `ETHNICITY`, and `SEX` are capitalized. +- `AGE` is converted from days to years. + +## CNA data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.copy_number_gene_level_hg38_gdc_r36`. ISB-CGC data was created in March 2023. +- Transformations + - Copy number values from the BigQuery tables are converted from [ASCAT](https://www.pnas.org/doi/10.1073/pnas.1009843107https://www.pnas.org/doi/10.1073/pnas.1009843107) to GISTIC 2.0 using the following thresholds: + +| ASCAT Value | GISTIC Value | Meaning | +|---|---|---| +| X = 0 | -2 | Deep loss | +| X = 1 | -1 | Single-copy loss | +| X = 2 | 0 | Diploid | +| 2 < X < 7 | 1 | Low-level gain | +| 7 ≤ X | 2 | Amplification | + +Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on the cBioPortal website. As a result these conversion thresholds affect how many samples show up in the CNA chart, which can be inconsistent with legacy versions of this study. We chose ASCAT ≥ 7 as the amplification threshold because it resulted in the least deviation from our legacy studies. + + + +## mRNA Expression data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.RNAseq_hg38_gdc_r35`. ISB-CGC data was created in December 2022. +- The `unstranded`, `tpm_unstranded`, and `fpkm_uq_unstranded` columns are pulled and each mapped to their own data file. + - The regular FPKM values are excluded because [FPKM-UQ provides a more stable metric](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#upper-quartile-fpkm). +- Transformations: see [Genomic data transformations](#genomic-data-transformations) + + + +## Mutation data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.masked_somatic_mutation_hg38_gdc_r40`. ISB-CGC data was created in July 2024. +- The MAF is annotated with Genome Nexus in order to avoid issues with the isoform mapping. Parameters used: + - Endpoint: https://grch38.genomenexus.org/ + - Isoform override: mskcc + - Replace gene symbols and Entrez IDs + - Post interval size: 500 +- Mutation data may be missing for some samples-- this reflects a lack of data availability in ISB-CGC. + +## Expression data transformations (CNA / mRNA) + +- Ensembl gene IDs are mapped to Entrez IDs using the [Genome Nexus hg38 canonical transcript file](https://github.com/genome-nexus/genome-nexus-importer/blob/master/data/grch38_ensembl95/export/ensembl_biomart_canonical_transcripts_per_hgnc.txt). Any genes that cannot be converted using this file are dropped. + - Prior to conversion, we also filter out a small number of duplicate Ensembl genes. These genes have copies containing data for both the X and the Y chromosomes. +- If a sample has multiple aliquots, it has to be condensed to 1 before it can imported into cBioPortal. This is done by choosing the aliquot ID with the highest sort value (eg. highest plate number), following [the same policy](https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844334036/FAQ#FAQ-replicateFilteringQ%3AWhatdoyoudowhenmultiplealiquotbarcodesexistforagivensample%2Fportion%2Fanalytecombination%3F) used by GDAC used to condense aliquot data in their studies. + +## Post-processing steps + + - Samples that lack any genomic data are removed from the clinical sample file. + - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - Case lists are generated under `case_lists/` using a curation-provided script. + - The validator script is run and the HTML report is saved under `validation_reports/`. + +## List of remapped columns + +### Clinical patient + +| Original | cBioPortal | +|---|---| +| submitter_id | PATIENT_ID | +| case_id | OTHER_PATIENT_ID | +| demo__ethnicity | ETHNICITY | +| demo__gender | SEX | +| demo__race | RACE | +| demo__vital_status | VITAL_STATUS | +| diag__age_at_diagnosis | AGE | +| diag__classification_of_tumor | TUMOR_CLASSIFICATION | +| diag__cog_neuroblastoma_risk_group | COG_NEUROBLASTOMA_RISK_GROUP | +| diag__icd_10_code | ICD_10 | +| diag__inss_stage | INSS_STAGE | +| diag__last_known_disease_status | DISEASE_STATUS | +| diag__metastasis_at_diagnosis | METASTASIS_AT_DIAGNOSIS | +| diag__morphology | MORPHOLOGY | +| diag__path__necrosis_percent | PATHOLOGY_NECROSIS_PERCENT | +| diag__primary_diagnosis | PRIMARY_DIAGNOSIS | +| diag__site_of_resection_or_biopsy | BIOPSY_SITE | +| diag__year_of_diagnosis | YEAR_OF_DIAGNOSIS | +| disease_type | DISEASE_TYPE | +| index_date | INDEX_DATE | +| primary_site | PRIMARY_SITE_PATIENT | +| proj__name | PROJECT_NAME | +| proj__project_id | PROJECT_ID | + + +### Clinical sample + +| Original | cBioPortal | +|---|---| +| case_barcode | PATIENT_ID | +| sample_barcode | SAMPLE_ID | +| sample_gdc_id | OTHER_SAMPLE_ID | +| sample_type_name | SAMPLE_TYPE | +| primary_site | PRIMARY_SITE | +| days_to_collection | DAYS_TO_COLLECTION | +| days_to_sample_procurement | DAYS_TO_SPECIMEN_COLLECTION | +| is_ffpe | IS_FFPE | + + + +### Mutation + +| Original | cBioPortal | +|---|---| +| sample_barcode_tumor | Tumor_Sample_Barcode | +| sample_barcode_normal | Matched_Norm_Sample_Barcode | \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/case_lists/cases_all.txt b/crdc/gdc/bll_target_gdc/case_lists/cases_all.txt new file mode 100644 index 0000000000..6c95c0e978 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: bll_target_gdc +stable_id: bll_target_gdc_all +case_list_name: All samples +case_list_description: All samples (921 samples) +case_list_category: all_cases_in_study +case_list_ids: TARGET-10-PARDWE-03A TARGET-10-PANUHA-09A TARGET-10-PARWID-09A TARGET-10-PARDWN-09B TARGET-10-PAPESW-09A TARGET-10-PAPGWN-09A TARGET-10-PARTEF-09A TARGET-10-PAPERU-09A TARGET-10-PANIEU-09A TARGET-10-PANZYY-09A TARGET-10-PAPLTZ-09A TARGET-10-PARDUM-09A TARGET-10-PAUBCT-09A TARGET-10-PAREJA-09A TARGET-10-PAPFZX-09A TARGET-10-PATBTX-09A TARGET-10-PARTAY-09A TARGET-10-PARUYH-09A TARGET-10-PARFTR-03A TARGET-10-PAUBXP-09A TARGET-10-PANLGK-03B TARGET-10-PASXUC-09A TARGET-10-PANKDT-03A TARGET-10-PAPNNX-03A TARGET-10-PATALJ-09A TARGET-10-PARDFB-09A TARGET-10-PAPLDM-09A TARGET-10-PANTUZ-09A TARGET-10-PANWYM-09A TARGET-10-PATMYZ-09A TARGET-10-PARLFI-09A TARGET-10-PARBKP-09A TARGET-10-PAUBCB-09A TARGET-10-PARGBK-09A TARGET-10-PARLEK-03A TARGET-10-PAPEZL-09A TARGET-10-PAPDVG-09A TARGET-10-PAPIIB-09A TARGET-10-PARSSV-09A TARGET-10-PAPCUI-09A TARGET-10-PARNXJ-09A TARGET-10-PANWDN-09A TARGET-10-PAPAVR-09A TARGET-10-PARAFH-09A TARGET-10-PASUGC-09A TARGET-10-PAPJIB-09A TARGET-10-PARCHB-03A TARGET-10-PAPJIB-03A TARGET-10-PASLAB-09A TARGET-10-PARMMA-09A TARGET-10-PAPCRU-03A TARGET-10-PATVDA-03A TARGET-10-PARATY-09A TARGET-10-PATLHS-09A TARGET-10-PANXZK-09A TARGET-10-PARANN-09A TARGET-10-PAPBFN-09A TARGET-10-PAPIJD-09A TARGET-10-PASMGZ-09B TARGET-10-PAPHXJ-09A TARGET-10-PATEYS-09A TARGET-10-PARNSH-03A TARGET-10-PAPZTL-09A TARGET-10-PANVUD-09A TARGET-10-PAPHED-09A TARGET-10-PAPAXK-09B TARGET-10-PATNIA-09A TARGET-10-PARTIK-09A TARGET-10-PANURW-09A TARGET-10-PARMKM-03A TARGET-10-PAPZPJ-09A TARGET-10-PARUFL-09B TARGET-10-PATAAH-09B TARGET-10-PAPCED-09A TARGET-10-PARLMI-09A TARGET-10-PAPERM-09A TARGET-10-PATLMA-03A TARGET-10-PARBSP-09A TARGET-10-PARSTB-09A TARGET-10-PANSBR-09A TARGET-10-PARAUE-09A TARGET-10-PATXNR-09A TARGET-10-PARNDY-09A TARGET-10-PARJPL-09A TARGET-10-PARDDW-09A TARGET-10-PARJXW-09A TARGET-10-PARRJV-09A TARGET-10-PASSSR-09A TARGET-10-PARLST-09A TARGET-10-PARPZJ-03A TARGET-10-PARDXG-09A TARGET-10-PATWXC-09A TARGET-10-PARIAD-03A TARGET-10-PARXMC-09A TARGET-10-PAPZTD-09A TARGET-10-PARGUZ-09A TARGET-10-PAPHNM-09A TARGET-10-PAPZRA-09A TARGET-10-PATHJF-09A TARGET-10-PARSNX-09A TARGET-10-PARCZY-09A TARGET-10-PASKRN-03A TARGET-10-PAPCRD-09A TARGET-10-PARJZZ-03A TARGET-10-PARMRF-09A TARGET-10-PATEFF-09A TARGET-10-PANWFB-09A TARGET-10-PARWDM-09B TARGET-10-PATLHH-09A TARGET-10-PARKFN-09A TARGET-10-PASKTG-09A TARGET-10-PASTSR-09B TARGET-10-PATHGY-09A TARGET-10-PAREYJ-09A TARGET-10-PARNEH-09A TARGET-10-PASHDV-09A TARGET-10-PAPIJM-09A TARGET-10-PASSRP-09A TARGET-10-PAREST-09A TARGET-10-PAPDDA-09A TARGET-10-PAPDYE-09A TARGET-10-PAPJXI-09A TARGET-10-PARGML-03A TARGET-10-PATRHL-09A TARGET-10-PAPGFP-09A TARGET-10-PASPDS-09A TARGET-10-PARABL-09A TARGET-10-PANVAW-09A TARGET-10-PAPHRV-09A TARGET-10-PATJBC-09A TARGET-10-PATRAB-09A TARGET-10-PANWZG-09A TARGET-10-PARDLZ-09A TARGET-10-PARBPX-09A TARGET-10-PARPZI-09A TARGET-10-PASILW-09A TARGET-10-PAPHZT-09A TARGET-10-PARFIZ-09A TARGET-10-PANSIZ-09A TARGET-10-PATWHB-09A TARGET-10-PARGGI-09A TARGET-10-PARMKK-09A TARGET-10-PAPKNJ-09B TARGET-10-PAPTAT-09B TARGET-10-PANZUI-09A TARGET-10-PATRXL-09A TARGET-10-PATMXN-09A TARGET-10-PASKXN-09A TARGET-10-PAPDKD-09A TARGET-10-PASTDU-09A TARGET-10-PATYCH-09A TARGET-10-PAREPB-09A TARGET-10-PASLZM-03A TARGET-10-PATSLH-09A TARGET-10-PATMRE-09A TARGET-10-PAPCNP-09A TARGET-10-PAPRCS-09A TARGET-10-PASKAY-09A TARGET-10-PARUCT-09A TARGET-10-PARXCD-09B TARGET-10-PARLBP-09A TARGET-10-PATDDZ-09A TARGET-10-PATIKN-03A TARGET-10-PARJLA-09B TARGET-10-PARCTN-09A TARGET-10-PASSPP-09A TARGET-10-PATHFE-09A TARGET-10-PAPART-09A TARGET-10-PAUACG-09A TARGET-10-PANTTB-09A TARGET-10-PANKGK-09A TARGET-10-PAPAZA-09A TARGET-10-PAPIHU-09A TARGET-10-PANSBK-03B TARGET-10-PASHUP-09A TARGET-10-PATPDA-09A TARGET-10-PAREWE-09A TARGET-10-PASMNV-09A TARGET-10-PARAGW-09A TARGET-10-PAPHNR-09A TARGET-10-PAPHEK-03A TARGET-10-PAPBCK-09A TARGET-10-PAREUH-09A TARGET-10-PARNSW-09A TARGET-10-PAPMYD-03A TARGET-10-PARAZN-09A TARGET-10-PAPHHP-09A TARGET-10-PAPVTA-09A TARGET-10-PARFDW-09A TARGET-10-PATCDM-09A TARGET-10-PATYMP-09A TARGET-10-PATTEE-03A TARGET-10-PARLPA-09A TARGET-10-PARDAK-09A TARGET-10-PAPBLU-09A TARGET-10-PARUIT-09A TARGET-10-PAPFWH-09A TARGET-10-PANWJR-09A TARGET-10-PASLZM-40A TARGET-10-PARCWB-09A TARGET-10-PAPHYV-09A TARGET-10-PARYGI-03A TARGET-10-PAPCRJ-09A TARGET-10-PARBIX-03A TARGET-10-PARAKF-03A TARGET-10-PAPBYM-09A TARGET-10-PANWDS-09A TARGET-10-PASZEW-09A TARGET-10-PAPZRB-09A TARGET-10-PARSET-09A TARGET-10-PARDLR-09A TARGET-10-PARPXV-09A TARGET-10-PAPGNC-03A TARGET-10-PARTJL-09A TARGET-10-PARTID-09A TARGET-10-PAPZNK-09A TARGET-10-PAPERW-09A TARGET-10-PANTBB-09A TARGET-10-PAPNFY-03A TARGET-10-PAPFHH-09A TARGET-10-PAPFNV-09A TARGET-10-PAPFFW-09A TARGET-10-PANXSF-09A TARGET-10-PARPNM-03A TARGET-10-PARJNL-09A TARGET-10-PAPLUG-09A TARGET-10-PASRCV-09A TARGET-10-PAPHMH-09A TARGET-10-PASYWF-03A TARGET-10-PARUKW-09A TARGET-10-PARAYM-09A TARGET-10-PATKWU-09A TARGET-10-PAPZPZ-09A TARGET-10-PANSXG-09A TARGET-10-PAPFHX-09A TARGET-10-PAPAZD-09A TARGET-10-PAPRFE-09A TARGET-10-PANTZE-09B TARGET-10-PARGLW-09A TARGET-10-PAPEJN-09A TARGET-10-PARURK-09A TARGET-10-PARTJJ-09A TARGET-10-PASRMM-09A TARGET-10-PASYAJ-09A TARGET-10-PARWMF-09A TARGET-10-PANVFF-09A TARGET-10-PANVDH-09A TARGET-10-PATNAM-09A TARGET-10-PASXMF-09A TARGET-10-PARBKG-09A TARGET-10-PASYIS-09A TARGET-10-PAPZVI-09A TARGET-10-PARDSP-09A TARGET-10-PASDYK-03A TARGET-10-PATLGU-09A TARGET-10-PARJBB-09A TARGET-10-PATXKW-03A TARGET-10-PATBYK-09A TARGET-10-PARUAT-09B TARGET-10-PATZSL-09A TARGET-10-PANZZI-09A TARGET-10-PATDGZ-09A TARGET-10-PARUYE-03A TARGET-10-PARDCY-09A TARGET-10-PARXLS-09A TARGET-10-PARCBK-09A TARGET-10-PARCVB-09A TARGET-10-PAUAZV-09A TARGET-10-PANWYH-09B TARGET-10-PARVBY-09A TARGET-10-PAPAKJ-09A TARGET-10-PASZIY-09A TARGET-10-PASRSV-03B TARGET-10-PANSYA-09A TARGET-10-PARUYU-09A TARGET-10-PAPJHR-09A TARGET-10-PARJRT-09A TARGET-10-PARUBK-03A TARGET-10-PAPNMY-09A TARGET-10-PARBGL-09B TARGET-10-PASTPT-09A TARGET-10-PANFNZ-03A TARGET-10-PARHSD-09A TARGET-10-PARPRW-03A TARGET-10-PANWDL-09A TARGET-10-PARRYW-09A TARGET-10-PANZJL-09A TARGET-10-PANVIX-09A TARGET-10-PAPHPX-03B TARGET-10-PANXLR-09A TARGET-10-PARETV-09A TARGET-10-PASWSR-09A TARGET-10-PATPGE-09A TARGET-10-PANWES-09A TARGET-10-PARNAF-03A TARGET-10-PANDWE-03A TARGET-10-PATBGC-09A TARGET-10-PASKGG-09A TARGET-10-PAPAPX-09A TARGET-10-PAPCVI-09A TARGET-10-PANDBX-09B TARGET-10-PARFLV-09A TARGET-10-PARVWD-09A TARGET-10-PARFDB-09A TARGET-10-PATFYZ-09A TARGET-10-PARBRV-09A TARGET-10-PAPAGK-09A TARGET-10-PASLBB-09A TARGET-10-PAPDBX-09A TARGET-10-PAPDSW-09A TARGET-10-PATITY-09A TARGET-10-PASJMK-09A TARGET-10-PANATY-09B TARGET-10-PASSZA-09A TARGET-10-PARSKV-09A TARGET-10-PARCFM-09A TARGET-10-PAPIGV-09A TARGET-10-PARCDZ-09A TARGET-10-PARSHV-09A TARGET-10-PARENT-09A TARGET-10-PATTHR-09A TARGET-10-PATMVH-09A TARGET-10-PATDMN-09A TARGET-10-PARWNW-09A TARGET-10-PAPESZ-09A TARGET-10-PATDBU-09A TARGET-10-PATDLG-09A TARGET-10-PAPEZR-09A TARGET-10-PARYAJ-09B TARGET-10-PAPBAN-09A TARGET-10-PARPRW-09A TARGET-10-PAPAGB-09A TARGET-10-PASJLN-09A TARGET-10-PARPHB-09A TARGET-10-PARDDM-09A TARGET-10-PAPKNC-09A TARGET-10-PARUBU-09A TARGET-10-PATZWA-03A TARGET-10-PANSTA-09A TARGET-10-PAPDUF-09A TARGET-10-PARRVI-09A TARGET-10-PAMXHJ-09A TARGET-10-PAPECF-09A TARGET-10-PANVIB-09A TARGET-10-PARUYU-03B TARGET-10-PAPHAM-09A TARGET-10-PAREZM-09A TARGET-10-PARGJH-09A TARGET-10-PARVCG-09A TARGET-10-PARMMV-09A TARGET-10-PAMXSP-09A TARGET-10-PANVCM-09A TARGET-10-PARFJM-09A TARGET-10-PARJNR-09A TARGET-10-PASTLP-09A TARGET-10-PAUAFN-09A TARGET-10-PAPAGS-09A TARGET-10-PAPDCS-09A TARGET-10-PAREBH-09A TARGET-10-PATWYL-09A TARGET-10-PAPCUR-09A TARGET-10-PASHUI-09A TARGET-10-PARCUW-09A TARGET-10-PARDVD-09A TARGET-10-PARGHW-03A TARGET-10-PAKSWW-03A TARGET-10-PASXIL-09A TARGET-10-PAPMVB-09A TARGET-10-PAREHN-09A TARGET-10-PATXNK-09A TARGET-10-PARSZH-09A TARGET-10-PAPCVR-09A TARGET-10-PARGFX-03A TARGET-10-PASVPZ-09A TARGET-10-PARWRJ-09B TARGET-10-PANRDC-03A TARGET-10-PASPBU-09A TARGET-10-PARTAK-09A TARGET-10-PATFVG-09A TARGET-10-PATDKT-09A TARGET-10-PATMAF-09A TARGET-10-PATKGP-09A TARGET-10-PAPFUF-09A TARGET-10-PANUXS-09A TARGET-10-PASTYT-09B TARGET-10-PAPFHR-09A TARGET-10-PARBBV-09A TARGET-10-PARJMY-09A TARGET-10-PANVKF-09A TARGET-10-PAPLDL-03A TARGET-10-PATWYZ-09A TARGET-10-PARAJY-09A TARGET-10-PANIEU-03A TARGET-10-PARFXJ-09A TARGET-10-PANJPG-09A TARGET-10-PARLTX-09A TARGET-10-PAPAGV-09A TARGET-10-PASWZJ-09A TARGET-10-PARESP-09A TARGET-10-PAPGMT-09A TARGET-10-PARDBN-09A TARGET-10-PARETH-09A TARGET-10-PARDLP-09A TARGET-10-PANUSN-03A TARGET-10-PARZYX-09B TARGET-10-PATGBY-09A TARGET-10-PARBYS-09A TARGET-10-PAPFXN-09A TARGET-10-PARABU-09A TARGET-10-PATCTI-09A TARGET-10-PASFKA-09A TARGET-10-PARBXX-09A TARGET-10-PANZBY-03A TARGET-10-PASFLK-09A TARGET-10-PARCHU-09A TARGET-10-PATZYR-03A TARGET-10-PAPHLH-09A TARGET-10-PARENU-09A TARGET-10-PARMWH-09A TARGET-10-PARNGI-09A TARGET-10-PARMFF-09A TARGET-10-PARPGL-09A TARGET-10-PAREWZ-09A TARGET-10-PARFDL-09A TARGET-10-PARNSP-09A TARGET-10-PAPFZF-09A TARGET-10-PARBWN-09A TARGET-10-PASILP-09B TARGET-10-PARTWH-09A TARGET-10-PATXSK-09A TARGET-10-PARBRK-03A TARGET-10-PANSPW-09A TARGET-10-PARVAK-09A TARGET-10-PASKIC-09A TARGET-10-PAPAPC-09A TARGET-10-PAPHZT-09B TARGET-10-PANXDB-03A TARGET-10-PARLDF-09A TARGET-10-PARPDP-09A TARGET-10-PAREAA-09A TARGET-10-PARHBI-09A TARGET-10-PARSKH-09A TARGET-10-PASEVJ-09B TARGET-10-PAPCSZ-09A TARGET-10-PASYSJ-09A TARGET-10-PARMUC-03A TARGET-10-PASIZE-09B TARGET-10-PAPCJR-09A TARGET-10-PAPIHH-09A TARGET-10-PARWVN-03A TARGET-10-PAREPF-09A TARGET-10-PARDEP-09A TARGET-10-PAREYW-09A TARGET-10-PARHEA-09A TARGET-10-PANWKP-09A TARGET-10-PATEVL-09A TARGET-10-PAPERN-09A TARGET-10-PATDFE-09A TARGET-10-PARACE-09A TARGET-10-PARCUM-09A TARGET-10-PARDDV-09A TARGET-10-PATSIY-09A TARGET-10-PARBDP-09A TARGET-10-PASJJR-09A TARGET-10-PARDST-09A TARGET-10-PARIZN-09A TARGET-10-PAUAJA-09A TARGET-10-PARDFN-09A TARGET-10-PARBVI-09A TARGET-10-PARFIH-09A TARGET-10-PANKAK-09A TARGET-10-PAPJHB-09A TARGET-10-PARSJG-09A TARGET-10-PARMIH-09A TARGET-10-PATGXS-09A TARGET-10-PAUBLL-09A TARGET-10-PARMSB-09A TARGET-10-PASKHT-03A TARGET-10-PASCIU-03A TARGET-10-PAKSWW-60A TARGET-10-PARAXH-09A TARGET-10-PARDXI-03A TARGET-10-PASUBW-09A TARGET-10-PAPICC-09A TARGET-10-PARUNW-09B TARGET-10-PASSEF-09A TARGET-10-PATHWV-09A TARGET-10-PAPZUE-03A TARGET-10-PARUGP-09A TARGET-10-PANTLF-03A TARGET-10-PARDLJ-09A TARGET-10-PAPBSY-09A TARGET-10-PANWJM-09A TARGET-10-PASNEH-09A TARGET-10-PATEMI-09A TARGET-10-PATAXS-09A TARGET-10-PARGMW-09A TARGET-10-PASVIN-09A TARGET-10-PARBTA-09A TARGET-10-PASUWG-03B TARGET-10-PAPBVD-09A TARGET-10-PAREKH-09A TARGET-10-PARKLK-09A TARGET-10-PARTZE-09A TARGET-10-PARCVT-09A TARGET-10-PARFAP-09A TARGET-10-PARJYV-09A TARGET-10-PARFSF-09A TARGET-10-PASFHR-09A TARGET-10-PARVHY-09A TARGET-10-PAPDLN-09A TARGET-10-PARPGW-09A TARGET-10-PARFWD-03B TARGET-10-PAPHDN-09A TARGET-10-PARDWM-09A TARGET-10-PANTVC-09A TARGET-10-PANTSM-09A TARGET-10-PAPIGX-09A TARGET-10-PASINX-09A TARGET-10-PANSUL-09A TARGET-10-PANZPJ-09A TARGET-10-PARRKK-09A TARGET-10-PATKYI-09A TARGET-10-PARRSR-09A TARGET-10-PANUUF-09A TARGET-10-PARNJB-09A TARGET-10-PANXGD-09A TARGET-10-PARBGG-09A TARGET-10-PANVTB-09A TARGET-10-PAPHDX-09A TARGET-10-PASXZH-09B TARGET-10-PARMEG-09A TARGET-10-PATRNA-09A TARGET-10-PARBNY-09A TARGET-10-PATZVD-09A TARGET-10-PATGLV-09A TARGET-10-PARIYD-09A TARGET-10-PATBDJ-09A TARGET-10-PAPFPZ-09A TARGET-10-PARLSU-09A TARGET-10-PAREIE-09A TARGET-10-PAPANB-09A TARGET-10-PANSHK-09A TARGET-10-PANZGN-09A TARGET-10-PATWNL-09A TARGET-10-PANYZE-09A TARGET-10-PARGJY-09A TARGET-10-PAPSPN-09A TARGET-10-PARWLP-09A TARGET-10-PARTPW-09A TARGET-10-PARFDG-09A TARGET-10-PARAPE-09B TARGET-10-PAREJZ-09A TARGET-10-PAPGLS-09A TARGET-10-PAPAXH-09A TARGET-10-PATENL-09A TARGET-10-PASMIC-09A TARGET-10-PANWKM-09A TARGET-10-PATMTV-09A TARGET-10-PARBND-09A TARGET-10-PARBSW-09A TARGET-10-PASDYM-09B TARGET-10-PATCZN-09A TARGET-10-PARPFF-09A TARGET-10-PASIIY-09A TARGET-10-PANUSL-09A TARGET-10-PAPEFH-09A TARGET-10-PANVGZ-09A TARGET-10-PATYWV-09A TARGET-10-PARDRS-09A TARGET-10-PARJZZ-09A TARGET-10-PAPBES-03A TARGET-10-PASWFN-09A TARGET-10-PARSKY-09A TARGET-10-PARNBN-09A TARGET-10-PAPBCI-09A TARGET-10-PASLMB-03B TARGET-10-PATELK-03B TARGET-10-PARGBR-09A TARGET-10-PASLCJ-03B TARGET-10-PAPSPG-03A TARGET-10-PAPEMZ-09A TARGET-10-PANTSM-03A TARGET-10-PAUBTC-09A TARGET-10-PARUGV-09A TARGET-10-PARASN-09A TARGET-10-PARSLL-09B TARGET-10-PATGKE-09A TARGET-10-PAPGYC-09A TARGET-10-PARCLU-09A TARGET-10-PANXDR-09A TARGET-10-PAPHWE-09A TARGET-10-PAPDRP-09A TARGET-10-PAPFKA-09A TARGET-10-PANWJS-09A TARGET-10-PANSDA-09A TARGET-10-PARKZX-09A TARGET-10-PANVDV-09A TARGET-10-PASWXB-09A TARGET-10-PAPHCA-09A TARGET-10-PASUIN-09A TARGET-10-PASREU-09B TARGET-10-PANKMB-09A TARGET-10-PARVMR-09A TARGET-10-PANXGM-09A TARGET-10-PASYGM-03A TARGET-10-PAREWM-09A TARGET-10-PAPAMH-09A TARGET-10-PATRUN-09A TARGET-10-PAPZUW-09A TARGET-10-PARTZJ-09A TARGET-10-PANCVR-03A TARGET-10-PANYGB-09A TARGET-10-PASUSV-09A TARGET-10-PATBRV-09A TARGET-10-PASFXA-03A TARGET-10-PASZJW-03A TARGET-10-PARNIZ-09A TARGET-10-PAPDUV-09A TARGET-10-PARPPV-09A TARGET-10-PATJZK-09A TARGET-10-PAPBPC-09A TARGET-10-PARUKK-09A TARGET-10-PARCVM-03A TARGET-10-PARSUV-09A TARGET-10-PARCKD-09A TARGET-10-PANGIF-03A TARGET-10-PATBNT-09A TARGET-10-PANTXA-09A TARGET-10-PARERS-09A TARGET-10-PARBRX-09A TARGET-10-PANSIA-09A TARGET-10-PANYEJ-09A TARGET-10-PATEIT-09A TARGET-10-PASTXU-09A TARGET-10-PATGMP-09A TARGET-10-PAPEMC-09A TARGET-10-PARFTR-09A TARGET-10-PATCUK-09A TARGET-10-PARGFL-09A TARGET-10-PARILG-09A TARGET-10-PARNDB-09A TARGET-10-PARXVS-09A TARGET-10-PAPDMU-09A TARGET-10-PARLAF-09A TARGET-10-PARPYH-09A TARGET-10-PAPCXR-09A TARGET-10-PASJYI-09A TARGET-10-PARBCW-09A TARGET-10-PARDRI-09A TARGET-10-PANLIC-09A TARGET-10-PARUCI-09A TARGET-10-PASTLM-03B TARGET-10-PARPUL-09A TARGET-10-PARMYP-09A TARGET-10-PARPYS-09A TARGET-10-PATDRC-03A TARGET-10-PATXAL-09A TARGET-10-PARSJH-09A TARGET-10-PASXUU-09A TARGET-10-PANEUH-09A TARGET-10-PARBHI-09A TARGET-10-PARBLL-09A TARGET-10-PARPZR-09A TARGET-10-PAPGGT-03A TARGET-10-PAPHBW-09A TARGET-10-PASMHF-09A TARGET-10-PATGWP-09A TARGET-10-PANVJI-09A TARGET-10-PANVXF-09A TARGET-10-PAPAGK-03A TARGET-10-PARDKG-09A TARGET-10-PARFHH-09A TARGET-10-PARNMV-09A TARGET-10-PATEVE-09B TARGET-10-PASKSY-09A TARGET-10-PARACA-09A TARGET-10-PARJNX-09A TARGET-10-PARVEI-09A TARGET-10-PANTWC-09A TARGET-10-PARDXS-09A TARGET-10-PAPFBX-09A TARGET-10-PATLPN-03A TARGET-10-PASWNU-09A TARGET-10-PAPGKP-09A TARGET-10-PAPILF-09A TARGET-10-PARGLE-09A TARGET-10-PARBRK-09A TARGET-10-PARHAN-09A TARGET-10-PARKFU-09A TARGET-10-PARHFF-09A TARGET-10-PATLNZ-09A TARGET-10-PANWGG-09A TARGET-10-PANXLP-09A TARGET-10-PATAYT-09A TARGET-10-PARLJA-09A TARGET-10-PARRVK-09A TARGET-10-PAREAL-09A TARGET-10-PASYCN-09A TARGET-10-PAPBZK-09A TARGET-10-PARAFI-09A TARGET-10-PATIBE-09A TARGET-10-PANXTP-09A TARGET-10-PATFWF-09A TARGET-10-PANWVW-09A TARGET-10-PAPFTJ-09A TARGET-10-PAPFIX-09A TARGET-10-PARJLF-09A TARGET-10-PAUBPY-09A TARGET-10-PARKLL-09A TARGET-10-PAPETC-09A TARGET-10-PASYHN-09A TARGET-10-PANXAM-09A TARGET-10-PARLTU-09A TARGET-10-PANVKH-09A TARGET-10-PATGZA-09A TARGET-10-PATGVX-09A TARGET-10-PAPZTS-09A TARGET-10-PATCDM-40A TARGET-10-PATFJD-09A TARGET-10-PAPZNK-03A TARGET-10-PATSIL-09A TARGET-10-PATWIJ-09A TARGET-10-PASGFH-09A TARGET-10-PARFKD-09A TARGET-10-PARIIA-09A TARGET-10-PATZYC-09A TARGET-10-PARDFH-09A TARGET-10-PATHRF-09A TARGET-10-PANVIC-03A TARGET-10-PARFPJ-09A TARGET-10-PASXSI-09A TARGET-10-PASPPN-09A TARGET-10-PAPDHA-09A TARGET-10-PANWHJ-09A TARGET-10-PANJWJ-09A TARGET-10-PAPHIG-09A TARGET-10-PANZEG-03A TARGET-10-PATEAK-09A TARGET-10-PAPADT-09A TARGET-10-PATCDZ-09A TARGET-10-PATLNS-09A TARGET-10-PAPIYG-03B TARGET-10-PAPAMS-09A TARGET-10-PARPIF-09A TARGET-10-PAPAIZ-09A TARGET-10-PARHLM-09A TARGET-10-PARDEY-09A TARGET-10-PASHXL-09A TARGET-10-PARETC-09A TARGET-10-PASNJI-09B TARGET-10-PANTRY-09A TARGET-10-PATPWF-03A TARGET-10-PARDNF-09A TARGET-10-PATBDK-09A TARGET-10-PAPDKR-09A TARGET-10-PARRMU-09A TARGET-10-PAPIGD-09A TARGET-10-PAUCDY-09A TARGET-10-PARCBE-09A TARGET-10-PARFEH-09A TARGET-10-PAPCPB-09A TARGET-10-PARUBX-09A TARGET-10-PANUYZ-09A TARGET-10-PARTSC-09A TARGET-10-PASSXJ-03A TARGET-10-PATEHZ-03A TARGET-10-PASRYW-03B TARGET-10-PAPGEE-09A TARGET-10-PAPAGW-09A TARGET-10-PARENW-09A TARGET-10-PAPHYM-09A TARGET-10-PARMWZ-09A TARGET-10-PAUCDC-09A TARGET-10-PAPHJF-09A TARGET-10-PARGBT-09A TARGET-10-PATCJJ-09B TARGET-10-PASTHE-09A TARGET-10-PARTGW-09A TARGET-10-PARAKF-09A TARGET-10-PARTKL-09A TARGET-10-PARMXF-03A TARGET-10-PARFJK-09A TARGET-10-PATFJP-09A TARGET-10-PATLRZ-09A TARGET-10-PAPILG-09A TARGET-10-PARTBP-09A TARGET-10-PARMSP-09A TARGET-10-PARHES-09A TARGET-10-PANWYH-09A TARGET-10-PAPZZJ-09A TARGET-10-PASRWZ-03B TARGET-10-PASXLT-09A TARGET-10-PAPEJL-09A TARGET-10-PAREGC-03A TARGET-10-PAPBAI-09A TARGET-10-PATGYH-09A TARGET-10-PAPEFH-03A TARGET-10-PARKEN-03A TARGET-10-PAPDKJ-09A TARGET-10-PARCDX-09A TARGET-10-PANWHW-09A TARGET-10-PATFRM-09A TARGET-10-PARJWB-09A TARGET-10-PARLPB-09A TARGET-10-PANZXZ-03A TARGET-10-PARJAY-09A TARGET-10-PARKEU-09A TARGET-10-PAPESB-09A TARGET-10-PARDEG-09A TARGET-10-PARSGM-09A TARGET-10-PAPNNX-09A TARGET-10-PANPJI-09A TARGET-10-PATYJK-09A TARGET-10-PAPFAT-09A TARGET-10-PANGIF-09A TARGET-10-PASNTZ-09A TARGET-10-PAPFZL-09A TARGET-10-PAPHYN-09B TARGET-10-PAPFBR-09A TARGET-10-PARNMF-03A TARGET-10-PASXFY-09B TARGET-10-PARCDS-09A TARGET-10-PATRGV-09A TARGET-10-PAPIHT-09A TARGET-10-PASWXZ-09A TARGET-10-PARXHT-03A TARGET-10-PAPTLM-09A TARGET-10-PARASZ-09A TARGET-10-PAREGE-09A TARGET-10-PATCKV-09A TARGET-10-PARCKV-09A TARGET-10-PARTLY-09A TARGET-10-PANPJW-09A TARGET-10-PARERM-09A TARGET-10-PARCMG-03A TARGET-10-PARPET-09A TARGET-10-PASKCL-09B TARGET-10-PANVUU-09A TARGET-10-PAUBRD-09A TARGET-10-PANRWG-09A TARGET-10-PARIBB-09A TARGET-10-PANXXD-09A TARGET-10-PAPEJM-09A TARGET-10-PARBLS-09A TARGET-10-PAPGFD-09A TARGET-10-PARNLW-09A TARGET-10-PARWXF-03B TARGET-10-PARHBT-09A TARGET-10-PARPYJ-09A TARGET-10-PANWIM-09A TARGET-10-PARCCM-09A TARGET-10-PARPGJ-09A TARGET-10-PANWEZ-09B TARGET-10-PAPIRZ-09A TARGET-10-PAPBZK-03A TARGET-10-PASXLZ-09A TARGET-10-PATSDS-03A TARGET-10-PAUAYB-09A TARGET-10-PAPEWB-09A TARGET-10-PAPIIX-09A TARGET-10-PANXEE-09A TARGET-10-PAPAGF-09A TARGET-10-PARGKD-09A TARGET-10-PAREEX-09A TARGET-10-PARDMI-09A TARGET-10-PATKVD-09A TARGET-10-PASIGB-03B TARGET-10-PAPGLD-09A TARGET-10-PATJLT-09A TARGET-10-PARDHK-09A TARGET-10-PAREIV-09A TARGET-10-PAPIEW-09A TARGET-10-PAREKM-09A TARGET-10-PANRYM-09A TARGET-10-PAPSPN-03A TARGET-10-PANTCR-09A TARGET-10-PASHNK-09A TARGET-10-PAPDUX-09A TARGET-10-PANFNZ-09A TARGET-10-PARJSR-09A TARGET-10-PANZFN-09A TARGET-10-PARDEJ-09A TARGET-10-PARSGC-03A TARGET-10-PATWJU-09A TARGET-10-PATZFF-09A TARGET-10-PARASC-09A TARGET-10-PANVMT-09A TARGET-10-PASKAD-09A TARGET-10-PAPDFS-09A TARGET-10-PARSRI-09A TARGET-10-PATCNI-09A TARGET-10-PAPZST-09A TARGET-10-PANTTZ-09B TARGET-10-PAPEJA-09A TARGET-10-PAPZXI-09A TARGET-10-PAPHGD-09A TARGET-10-PARAPT-09A TARGET-10-PARARJ-09A TARGET-10-PARUEU-09A TARGET-10-PASSHC-09A TARGET-10-PARUBN-09A TARGET-10-PAPBZW-09A TARGET-10-PARXMV-03A TARGET-10-PATHBG-09A TARGET-10-PARFFC-03A TARGET-10-PARPNM-09A TARGET-10-PANKRG-03A TARGET-10-PANWSP-09A TARGET-10-PANXCX-09A TARGET-10-PAREGZ-09A TARGET-10-PATITB-09A TARGET-10-PAPESY-09A TARGET-10-PARTGB-09A TARGET-10-PARCLW-09A TARGET-10-PARCDV-09A TARGET-10-PAPRMM-09B TARGET-10-PANTYP-09A TARGET-10-PARDBT-09A TARGET-10-PARCAX-09A TARGET-10-PARBYU-09A diff --git a/crdc/gdc/bll_target_gdc/case_lists/cases_cna.txt b/crdc/gdc/bll_target_gdc/case_lists/cases_cna.txt new file mode 100644 index 0000000000..76c6a27412 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: bll_target_gdc +stable_id: bll_target_gdc_cna +case_list_name: Samples with CNA data +case_list_description: Samples with CNA data (293 samples) +case_list_category: all_cases_with_cna_data +case_list_ids: TARGET-10-PARWID-09A TARGET-10-PASSEF-09A TARGET-10-PANIEU-09A TARGET-10-PATHWV-09A TARGET-10-PAUBCT-09A TARGET-10-PATBTX-09A TARGET-10-PASNEH-09A TARGET-10-PAUBXP-09A TARGET-10-PASXUC-09A TARGET-10-PATEMI-09A TARGET-10-PATALJ-09A TARGET-10-PATAXS-09A TARGET-10-PASVIN-09A TARGET-10-PAPLDM-09A TARGET-10-PATMYZ-09A TARGET-10-PARKLK-09A TARGET-10-PAUBCB-09A TARGET-10-PASFHR-09A TARGET-10-PARVHY-09A TARGET-10-PARNXJ-09A TARGET-10-PASINX-09A TARGET-10-PARRKK-09A TARGET-10-PATKYI-09A TARGET-10-PASUGC-09A TARGET-10-PANUUF-09A TARGET-10-PARNJB-09A TARGET-10-PASLAB-09A TARGET-10-PATVDA-03A TARGET-10-PATRNA-09A TARGET-10-PATLHS-09A TARGET-10-PATZVD-09A TARGET-10-PATGLV-09A TARGET-10-PARIYD-09A TARGET-10-PATBDJ-09A TARGET-10-PATEYS-09A TARGET-10-PATNIA-09A TARGET-10-PARMKM-03A TARGET-10-PANURW-09A TARGET-10-PATWNL-09A TARGET-10-PARWLP-09A TARGET-10-PATLMA-03A TARGET-10-PANSBR-09A TARGET-10-PARTPW-09A TARGET-10-PATXNR-09A TARGET-10-PARJPL-09A TARGET-10-PARJXW-09A TARGET-10-PATENL-09A TARGET-10-PASMIC-09A TARGET-10-PATMTV-09A TARGET-10-PASSSR-09A TARGET-10-PARLST-09A TARGET-10-PATCZN-09A TARGET-10-PASIIY-09A TARGET-10-PATWXC-09A TARGET-10-PATYWV-09A TARGET-10-PAPBES-03A TARGET-10-PASWFN-09A TARGET-10-PARNBN-09A TARGET-10-PATHJF-09A TARGET-10-PARSNX-09A TARGET-10-PASKRN-03A TARGET-10-PARMRF-09A TARGET-10-PATEFF-09A TARGET-10-PARWDM-09B TARGET-10-PATLHH-09A TARGET-10-PAUBTC-09A TARGET-10-PASKTG-09A TARGET-10-PARNEH-09A TARGET-10-PATHGY-09A TARGET-10-PASHDV-09A TARGET-10-PATGKE-09A TARGET-10-PAPIJM-09A TARGET-10-PASSRP-09A TARGET-10-PANXDR-09A TARGET-10-PATRHL-09A TARGET-10-PANSDA-09A TARGET-10-PASPDS-09A TARGET-10-PASWXB-09A TARGET-10-PATJBC-09A TARGET-10-PATRAB-09A TARGET-10-PASILW-09A TARGET-10-PASUIN-09A TARGET-10-PANKMB-09A TARGET-10-PARVMR-09A TARGET-10-PARMKK-09A TARGET-10-PATWHB-09A TARGET-10-PATRXL-09A TARGET-10-PATMXN-09A TARGET-10-PATRUN-09A TARGET-10-PASKXN-09A TARGET-10-PASTDU-09A TARGET-10-PATYCH-09A TARGET-10-PATSLH-09A TARGET-10-PATMRE-09A TARGET-10-PASUSV-09A TARGET-10-PASZJW-03A TARGET-10-PATBRV-09A TARGET-10-PATDDZ-09A TARGET-10-PATIKN-03A TARGET-10-PATJZK-09A TARGET-10-PASSPP-09A TARGET-10-PATHFE-09A TARGET-10-PARCVM-03A TARGET-10-PAUACG-09A TARGET-10-PANKGK-09A TARGET-10-PATBNT-09A TARGET-10-PASHUP-09A TARGET-10-PANSIA-09A TARGET-10-PATPDA-09A TARGET-10-PASMNV-09A TARGET-10-PATEIT-09A TARGET-10-PASTXU-09A TARGET-10-PATGMP-09A TARGET-10-PATCUK-09A TARGET-10-PARGFL-09A TARGET-10-PATCDM-09A TARGET-10-PATYMP-09A TARGET-10-PARXVS-09A TARGET-10-PAPFWH-09A TARGET-10-PAPCXR-09A TARGET-10-PARYGI-03A TARGET-10-PASJYI-09A TARGET-10-PASZEW-09A TARGET-10-PARPUL-09A TARGET-10-PARSET-09A TARGET-10-PATDRC-03A TARGET-10-PATXAL-09A TARGET-10-PASXUU-09A TARGET-10-PANEUH-09A TARGET-10-PAPGGT-03A TARGET-10-PASMHF-09A TARGET-10-PATGWP-09A TARGET-10-PARNMV-09A TARGET-10-PASRCV-09A TARGET-10-PASYWF-03A TARGET-10-PARUKW-09A TARGET-10-PASKSY-09A TARGET-10-PARJNX-09A TARGET-10-PARAYM-09A TARGET-10-PARVEI-09A TARGET-10-PATKWU-09A TARGET-10-PATLPN-03A TARGET-10-PASWNU-09A TARGET-10-PATLNZ-09A TARGET-10-PASRMM-09A TARGET-10-PASYAJ-09A TARGET-10-PARWMF-09A TARGET-10-PATAYT-09A TARGET-10-PARLJA-09A TARGET-10-PATNAM-09A TARGET-10-PASXMF-09A TARGET-10-PASYIS-09A TARGET-10-PASYCN-09A TARGET-10-PATLGU-09A TARGET-10-PATIBE-09A TARGET-10-PATXKW-03A TARGET-10-PATFWF-09A TARGET-10-PATBYK-09A TARGET-10-PATZSL-09A TARGET-10-PATDGZ-09A TARGET-10-PAUBPY-09A TARGET-10-PASYHN-09A TARGET-10-PARXLS-09A TARGET-10-PARCBK-09A TARGET-10-PAUAZV-09A TARGET-10-PASZIY-09A TARGET-10-PATGZA-09A TARGET-10-PATGVX-09A TARGET-10-PATFJD-09A TARGET-10-PATSIL-09A TARGET-10-PATWIJ-09A TARGET-10-PASTPT-09A TARGET-10-PASGFH-09A TARGET-10-PATZYC-09A TARGET-10-PANZJL-09A TARGET-10-PATPGE-09A TARGET-10-PASWSR-09A TARGET-10-PATHRF-09A TARGET-10-PARFPJ-09A TARGET-10-PASXSI-09A TARGET-10-PASPPN-09A TARGET-10-PANJWJ-09A TARGET-10-PATBGC-09A TARGET-10-PASKGG-09A TARGET-10-PATEAK-09A TARGET-10-PATCDZ-09A TARGET-10-PATLNS-09A TARGET-10-PATFYZ-09A TARGET-10-PASLBB-09A TARGET-10-PASHXL-09A TARGET-10-PATPWF-03A TARGET-10-PATITY-09A TARGET-10-PASJMK-09A TARGET-10-PATBDK-09A TARGET-10-PASSZA-09A TARGET-10-PAUCDY-09A TARGET-10-PATTHR-09A TARGET-10-PATDMN-09A TARGET-10-PARWNW-09A TARGET-10-PATEHZ-03A TARGET-10-PATMVH-09A TARGET-10-PATDBU-09A TARGET-10-PATDLG-09A TARGET-10-PAUCDC-09A TARGET-10-PARPHB-09A TARGET-10-PASJLN-09A TARGET-10-PASTHE-09A TARGET-10-PATZWA-03A TARGET-10-PATFJP-09A TARGET-10-PAMXHJ-09A TARGET-10-PATLRZ-09A TARGET-10-PARTBP-09A TARGET-10-PARHES-09A TARGET-10-PASXLT-09A TARGET-10-PATGYH-09A TARGET-10-PARMMV-09A TARGET-10-PATFRM-09A TARGET-10-PASTLP-09A TARGET-10-PAUAFN-09A TARGET-10-PARJAY-09A TARGET-10-PATWYL-09A TARGET-10-PATYJK-09A TARGET-10-PANGIF-09A TARGET-10-PASNTZ-09A TARGET-10-PASXIL-09A TARGET-10-PATXNK-09A TARGET-10-PATRGV-09A TARGET-10-PASWXZ-09A TARGET-10-PASVPZ-09A TARGET-10-PARXHT-03A TARGET-10-PANRDC-03A TARGET-10-PARASZ-09A TARGET-10-PARTLY-09A TARGET-10-PASPBU-09A TARGET-10-PATCKV-09A TARGET-10-PATFVG-09A TARGET-10-PANPJW-09A TARGET-10-PARPET-09A TARGET-10-PATDKT-09A TARGET-10-PATKGP-09A TARGET-10-PATMAF-09A TARGET-10-PAUBRD-09A TARGET-10-PANRWG-09A TARGET-10-PARHBT-09A TARGET-10-PARPYJ-09A TARGET-10-PATWYZ-09A TARGET-10-PARFXJ-09A TARGET-10-PASWZJ-09A TARGET-10-PAPBZK-03A TARGET-10-PASXLZ-09A TARGET-10-PATGBY-09A TARGET-10-PATSDS-03A TARGET-10-PAPEWB-09A TARGET-10-PASFKA-09A TARGET-10-PAUAYB-09A TARGET-10-PASFLK-09A TARGET-10-PATZYR-03A TARGET-10-PATKVD-09A TARGET-10-PATJLT-09A TARGET-10-PARMFF-09A TARGET-10-PARFDL-09A TARGET-10-PANRYM-09A TARGET-10-PARNSP-09A TARGET-10-PASHNK-09A TARGET-10-PANFNZ-09A TARGET-10-PATXSK-09A TARGET-10-PASKIC-09A TARGET-10-PATWJU-09A TARGET-10-PATZFF-09A TARGET-10-PARHBI-09A TARGET-10-PASKAD-09A TARGET-10-PATCNI-09A TARGET-10-PASYSJ-09A TARGET-10-PARMUC-03A TARGET-10-PAPHGD-09A TARGET-10-PARUEU-09A TARGET-10-PASSHC-09A TARGET-10-PATEVL-09A TARGET-10-PARXMV-03A TARGET-10-PATDFE-09A TARGET-10-PATHBG-09A TARGET-10-PANKRG-03A TARGET-10-PATSIY-09A TARGET-10-PASJJR-09A TARGET-10-PAREGZ-09A TARGET-10-PARIZN-09A TARGET-10-PAUAJA-09A TARGET-10-PATITB-09A TARGET-10-PARFIH-09A TARGET-10-PARSJG-09A TARGET-10-PARMIH-09A TARGET-10-PATGXS-09A TARGET-10-PAUBLL-09A diff --git a/crdc/gdc/bll_target_gdc/case_lists/cases_cnaseq.txt b/crdc/gdc/bll_target_gdc/case_lists/cases_cnaseq.txt new file mode 100644 index 0000000000..4ad743a7cd --- /dev/null +++ b/crdc/gdc/bll_target_gdc/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: bll_target_gdc +stable_id: bll_target_gdc_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (248 samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: TARGET-10-PATLNZ-09A TARGET-10-PARWID-09A TARGET-10-PASYAJ-09A TARGET-10-PARWMF-09A TARGET-10-PATAYT-09A TARGET-10-PARLJA-09A TARGET-10-PATNAM-09A TARGET-10-PASXMF-09A TARGET-10-PASYIS-09A TARGET-10-PASSEF-09A TARGET-10-PASYCN-09A TARGET-10-PATHWV-09A TARGET-10-PATLGU-09A TARGET-10-PATIBE-09A TARGET-10-PATXKW-03A TARGET-10-PATBTX-09A TARGET-10-PATBYK-09A TARGET-10-PASNEH-09A TARGET-10-PATZSL-09A TARGET-10-PAUBXP-09A TARGET-10-PATDGZ-09A TARGET-10-PAUBPY-09A TARGET-10-PASXUC-09A TARGET-10-PATALJ-09A TARGET-10-PATAXS-09A TARGET-10-PARXLS-09A TARGET-10-PARCBK-09A TARGET-10-PASYHN-09A TARGET-10-PAUAZV-09A TARGET-10-PASVIN-09A TARGET-10-PATMYZ-09A TARGET-10-PARKLK-09A TARGET-10-PASZIY-09A TARGET-10-PATGZA-09A TARGET-10-PATGVX-09A TARGET-10-PATFJD-09A TARGET-10-PATSIL-09A TARGET-10-PASFHR-09A TARGET-10-PARVHY-09A TARGET-10-PATWIJ-09A TARGET-10-PASTPT-09A TARGET-10-PASGFH-09A TARGET-10-PATZYC-09A TARGET-10-PARNXJ-09A TARGET-10-PATPGE-09A TARGET-10-PASINX-09A TARGET-10-PATHRF-09A TARGET-10-PARFPJ-09A TARGET-10-PARRKK-09A TARGET-10-PASXSI-09A TARGET-10-PASPPN-09A TARGET-10-PATKYI-09A TARGET-10-PATBGC-09A TARGET-10-PASKGG-09A TARGET-10-PATEAK-09A TARGET-10-PASUGC-09A TARGET-10-PATCDZ-09A TARGET-10-PARNJB-09A TARGET-10-PASLAB-09A TARGET-10-PATLNS-09A TARGET-10-PATFYZ-09A TARGET-10-PATVDA-03A TARGET-10-PATRNA-09A TARGET-10-PATLHS-09A TARGET-10-PATZVD-09A TARGET-10-PASLBB-09A TARGET-10-PATGLV-09A TARGET-10-PARIYD-09A TARGET-10-PASHXL-09A TARGET-10-PATBDJ-09A TARGET-10-PATPWF-03A TARGET-10-PATITY-09A TARGET-10-PASJMK-09A TARGET-10-PATBDK-09A TARGET-10-PASSZA-09A TARGET-10-PATNIA-09A TARGET-10-PARMKM-03A TARGET-10-PATWNL-09A TARGET-10-PAUCDY-09A TARGET-10-PARWLP-09A TARGET-10-PATLMA-03A TARGET-10-PATTHR-09A TARGET-10-PATDMN-09A TARGET-10-PARWNW-09A TARGET-10-PATMVH-09A TARGET-10-PATEHZ-03A TARGET-10-PARTPW-09A TARGET-10-PATDBU-09A TARGET-10-PATDLG-09A TARGET-10-PARJPL-09A TARGET-10-PAUCDC-09A TARGET-10-PARJXW-09A TARGET-10-PARPHB-09A TARGET-10-PASJLN-09A TARGET-10-PATENL-09A TARGET-10-PASMIC-09A TARGET-10-PASTHE-09A TARGET-10-PATZWA-03A TARGET-10-PATMTV-09A TARGET-10-PASSSR-09A TARGET-10-PARLST-09A TARGET-10-PATCZN-09A TARGET-10-PATFJP-09A TARGET-10-PATLRZ-09A TARGET-10-PASIIY-09A TARGET-10-PARTBP-09A TARGET-10-PARHES-09A TARGET-10-PATWXC-09A TARGET-10-PATYWV-09A TARGET-10-PASXLT-09A TARGET-10-PASWFN-09A TARGET-10-PARNBN-09A TARGET-10-PATHJF-09A TARGET-10-PATGYH-09A TARGET-10-PARSNX-09A TARGET-10-PARMMV-09A TARGET-10-PASKRN-03A TARGET-10-PATFRM-09A TARGET-10-PASTLP-09A TARGET-10-PAUAFN-09A TARGET-10-PARMRF-09A TARGET-10-PATEFF-09A TARGET-10-PARJAY-09A TARGET-10-PARWDM-09B TARGET-10-PATWYL-09A TARGET-10-PATLHH-09A TARGET-10-PAUBTC-09A TARGET-10-PATYJK-09A TARGET-10-PASKTG-09A TARGET-10-PASNTZ-09A TARGET-10-PASXIL-09A TARGET-10-PARNEH-09A TARGET-10-PATHGY-09A TARGET-10-PASHDV-09A TARGET-10-PATGKE-09A TARGET-10-PATXNK-09A TARGET-10-PATRGV-09A TARGET-10-PASWXZ-09A TARGET-10-PATRHL-09A TARGET-10-PASVPZ-09A TARGET-10-PARXHT-03A TARGET-10-PASPDS-09A TARGET-10-PARASZ-09A TARGET-10-PASPBU-09A TARGET-10-PARTLY-09A TARGET-10-PATCKV-09A TARGET-10-PATFVG-09A TARGET-10-PATJBC-09A TARGET-10-PATRAB-09A TARGET-10-PATDKT-09A TARGET-10-PATMAF-09A TARGET-10-PATKGP-09A TARGET-10-PASWXB-09A TARGET-10-PARPET-09A TARGET-10-PASILW-09A TARGET-10-PAUBRD-09A TARGET-10-PASUIN-09A TARGET-10-PARVMR-09A TARGET-10-PARMKK-09A TARGET-10-PATWHB-09A TARGET-10-PARHBT-09A TARGET-10-PATRXL-09A TARGET-10-PATMXN-09A TARGET-10-PARPYJ-09A TARGET-10-PATWYZ-09A TARGET-10-PASKXN-09A TARGET-10-PASTDU-09A TARGET-10-PATYCH-09A TARGET-10-PARFXJ-09A TARGET-10-PATSLH-09A TARGET-10-PATMRE-09A TARGET-10-PASZJW-03A TARGET-10-PATBRV-09A TARGET-10-PATDDZ-09A TARGET-10-PATGBY-09A TARGET-10-PATIKN-03A TARGET-10-PASXLZ-09A TARGET-10-PATSDS-03A TARGET-10-PATJZK-09A TARGET-10-PASSPP-09A TARGET-10-PASFKA-09A TARGET-10-PAUAYB-09A TARGET-10-PASFLK-09A TARGET-10-PATHFE-09A TARGET-10-PARCVM-03A TARGET-10-PAUACG-09A TARGET-10-PATKVD-09A TARGET-10-PATBNT-09A TARGET-10-PATJLT-09A TARGET-10-PARMFF-09A TARGET-10-PASHUP-09A TARGET-10-PATPDA-09A TARGET-10-PASMNV-09A TARGET-10-PARFDL-09A TARGET-10-PATEIT-09A TARGET-10-PARNSP-09A TARGET-10-PASTXU-09A TARGET-10-PATGMP-09A TARGET-10-PASHNK-09A TARGET-10-PATCUK-09A TARGET-10-PATXSK-09A TARGET-10-PARGFL-09A TARGET-10-PATCDM-09A TARGET-10-PATYMP-09A TARGET-10-PASKIC-09A TARGET-10-PARXVS-09A TARGET-10-PATWJU-09A TARGET-10-PATZFF-09A TARGET-10-PARYGI-03A TARGET-10-PASJYI-09A TARGET-10-PARHBI-09A TARGET-10-PASKAD-09A TARGET-10-PASZEW-09A TARGET-10-PATCNI-09A TARGET-10-PASYSJ-09A TARGET-10-PARSET-09A TARGET-10-PARMUC-03A TARGET-10-PARPUL-09A TARGET-10-PATDRC-03A TARGET-10-PATXAL-09A TARGET-10-PASXUU-09A TARGET-10-PARUEU-09A TARGET-10-PATEVL-09A TARGET-10-PATDFE-09A TARGET-10-PARXMV-03A TARGET-10-PATHBG-09A TARGET-10-PATGWP-09A TARGET-10-PATSIY-09A TARGET-10-PASJJR-09A TARGET-10-PARNMV-09A TARGET-10-PASRCV-09A TARGET-10-PARIZN-09A TARGET-10-PAREGZ-09A TARGET-10-PAUAJA-09A TARGET-10-PASYWF-03A TARGET-10-PARUKW-09A TARGET-10-PASKSY-09A TARGET-10-PARJNX-09A TARGET-10-PARAYM-09A TARGET-10-PATKWU-09A TARGET-10-PARFIH-09A TARGET-10-PARVEI-09A TARGET-10-PATITB-09A TARGET-10-PATLPN-03A TARGET-10-PARSJG-09A TARGET-10-PASWNU-09A TARGET-10-PARMIH-09A TARGET-10-PAUBLL-09A diff --git a/crdc/gdc/bll_target_gdc/case_lists/cases_sequenced.txt b/crdc/gdc/bll_target_gdc/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..6d006b6183 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: bll_target_gdc +stable_id: bll_target_gdc_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (719 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: TARGET-10-PARDWE-03A TARGET-10-PARWID-09A TARGET-10-PAPGWN-09A TARGET-10-PARTEF-09A TARGET-10-PAPERU-09A TARGET-10-PANZYY-09A TARGET-10-PARDUM-09A TARGET-10-PAREJA-09A TARGET-10-PAPFZX-09A TARGET-10-PATBTX-09A TARGET-10-PARTAY-09A TARGET-10-PARUYH-09A TARGET-10-PARFTR-03A TARGET-10-PAUBXP-09A TARGET-10-PASXUC-09A TARGET-10-PAPNNX-03A TARGET-10-PATALJ-09A TARGET-10-PARDFB-09A TARGET-10-PANTUZ-09A TARGET-10-PANWYM-09A TARGET-10-PATMYZ-09A TARGET-10-PARLFI-09A TARGET-10-PARBKP-09A TARGET-10-PARGBK-09A TARGET-10-PAPEZL-09A TARGET-10-PAPDVG-09A TARGET-10-PAPIIB-09A TARGET-10-PARSSV-09A TARGET-10-PAPCUI-09A TARGET-10-PARNXJ-09A TARGET-10-PANWDN-09A TARGET-10-PAPAVR-09A TARGET-10-PARAFH-09A TARGET-10-PASUGC-09A TARGET-10-PARMMA-09A TARGET-10-PASLAB-09A TARGET-10-PAPJIB-03A TARGET-10-PAPCRU-03A TARGET-10-PARATY-09A TARGET-10-PATVDA-03A TARGET-10-PATLHS-09A TARGET-10-PANXZK-09A TARGET-10-PARANN-09A TARGET-10-PAPIJD-09A TARGET-10-PAPHXJ-09A TARGET-10-PAPZTL-09A TARGET-10-PANVUD-09A TARGET-10-PAPHED-09A TARGET-10-PATNIA-09A TARGET-10-PAPZPJ-09A TARGET-10-PARMKM-03A TARGET-10-PARTIK-09A TARGET-10-PAPCED-09A TARGET-10-PARLMI-09A TARGET-10-PAPERM-09A TARGET-10-PATLMA-03A TARGET-10-PARBSP-09A TARGET-10-PARSTB-09A TARGET-10-PARAUE-09A TARGET-10-PARNDY-09A TARGET-10-PARJPL-09A TARGET-10-PARDDW-09A TARGET-10-PARJXW-09A TARGET-10-PARRJV-09A TARGET-10-PASSSR-09A TARGET-10-PARLST-09A TARGET-10-PARDXG-09A TARGET-10-PATWXC-09A TARGET-10-PARIAD-03A TARGET-10-PAPZTD-09A TARGET-10-PARGUZ-09A TARGET-10-PAPHNM-09A TARGET-10-PAPZRA-09A TARGET-10-PATHJF-09A TARGET-10-PARSNX-09A TARGET-10-PARCZY-09A TARGET-10-PASKRN-03A TARGET-10-PAPCRD-09A TARGET-10-PARJZZ-03A TARGET-10-PARMRF-09A TARGET-10-PATEFF-09A TARGET-10-PARWDM-09B TARGET-10-PATLHH-09A TARGET-10-PARKFN-09A TARGET-10-PASKTG-09A TARGET-10-PAREYJ-09A TARGET-10-PARNEH-09A TARGET-10-PATHGY-09A TARGET-10-PASHDV-09A TARGET-10-PAREST-09A TARGET-10-PAPDYE-09A TARGET-10-PAPDDA-09A TARGET-10-PATRHL-09A TARGET-10-PARABL-09A TARGET-10-PANVAW-09A TARGET-10-PASPDS-09A TARGET-10-PAPHRV-09A TARGET-10-PATJBC-09A TARGET-10-PATRAB-09A TARGET-10-PANWZG-09A TARGET-10-PARDLZ-09A TARGET-10-PARBPX-09A TARGET-10-PARPZI-09A TARGET-10-PASILW-09A TARGET-10-PARFIZ-09A TARGET-10-PANSIZ-09A TARGET-10-PARGGI-09A TARGET-10-PARMKK-09A TARGET-10-PATWHB-09A TARGET-10-PANZUI-09A TARGET-10-PATRXL-09A TARGET-10-PATMXN-09A TARGET-10-PAPDKD-09A TARGET-10-PASKXN-09A TARGET-10-PASTDU-09A TARGET-10-PAREPB-09A TARGET-10-PASLZM-03A TARGET-10-PAPCNP-09A TARGET-10-PATSLH-09A TARGET-10-PATMRE-09A TARGET-10-PATYCH-09A TARGET-10-PARUCT-09A TARGET-10-PARLBP-09A TARGET-10-PATDDZ-09A TARGET-10-PATIKN-03A TARGET-10-PARCTN-09A TARGET-10-PASSPP-09A TARGET-10-PAPART-09A TARGET-10-PATHFE-09A TARGET-10-PANTTB-09A TARGET-10-PAPAZA-09A TARGET-10-PAPIHU-09A TARGET-10-PAUACG-09A TARGET-10-PASHUP-09A TARGET-10-PATPDA-09A TARGET-10-PAREWE-09A TARGET-10-PASMNV-09A TARGET-10-PARAGW-09A TARGET-10-PAPHNR-09A TARGET-10-PAPBCK-09A TARGET-10-PAREUH-09A TARGET-10-PARNSW-09A TARGET-10-PARAZN-09A TARGET-10-PAPHHP-09A TARGET-10-PARFDW-09A TARGET-10-PATCDM-09A TARGET-10-PATYMP-09A TARGET-10-PARLPA-09A TARGET-10-PARDAK-09A TARGET-10-PAPBLU-09A TARGET-10-PARUIT-09A TARGET-10-PANWJR-09A TARGET-10-PARCWB-09A TARGET-10-PAPHYV-09A TARGET-10-PAPCRJ-09A TARGET-10-PARYGI-03A TARGET-10-PARBIX-03A TARGET-10-PARAKF-03A TARGET-10-PAPBYM-09A TARGET-10-PANWDS-09A TARGET-10-PASZEW-09A TARGET-10-PAPZRB-09A TARGET-10-PARSET-09A TARGET-10-PARDLR-09A 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TARGET-10-PASJLN-09A TARGET-10-PARUBU-09A TARGET-10-PANSTA-09A TARGET-10-PATZWA-03A TARGET-10-PARRVI-09A TARGET-10-PANVIB-09A TARGET-10-PAPHAM-09A TARGET-10-PAREZM-09A TARGET-10-PARGJH-09A TARGET-10-PARVCG-09A TARGET-10-PARMMV-09A TARGET-10-PANVCM-09A TARGET-10-PARFJM-09A TARGET-10-PARJNR-09A TARGET-10-PAPDCS-09A TARGET-10-PASTLP-09A TARGET-10-PAPAGS-09A TARGET-10-PAREBH-09A TARGET-10-PAUAFN-09A TARGET-10-PATWYL-09A TARGET-10-PARCUW-09A TARGET-10-PARDVD-09A TARGET-10-PARGHW-03A TARGET-10-PAKSWW-03A TARGET-10-PASXIL-09A TARGET-10-PAREHN-09A TARGET-10-PATXNK-09A TARGET-10-PAPCVR-09A TARGET-10-PARGFX-03A TARGET-10-PASVPZ-09A TARGET-10-PASPBU-09A TARGET-10-PARTAK-09A TARGET-10-PATFVG-09A TARGET-10-PATDKT-09A TARGET-10-PATMAF-09A TARGET-10-PATKGP-09A TARGET-10-PAPFUF-09A TARGET-10-PANUXS-09A TARGET-10-PAPFHR-09A TARGET-10-PARBBV-09A TARGET-10-PARJMY-09A TARGET-10-PANVKF-09A TARGET-10-PAPLDL-03A TARGET-10-PATWYZ-09A TARGET-10-PARAJY-09A TARGET-10-PARFXJ-09A TARGET-10-PARLTX-09A TARGET-10-PAPAGV-09A TARGET-10-PAPGMT-09A TARGET-10-PARDBN-09A TARGET-10-PARDLP-09A TARGET-10-PARESP-09A TARGET-10-PARETH-09A TARGET-10-PARBYS-09A TARGET-10-PATGBY-09A TARGET-10-PARABU-09A TARGET-10-PANZBY-03A TARGET-10-PARBXX-09A TARGET-10-PARCHU-09A TARGET-10-PASFKA-09A TARGET-10-PASFLK-09A TARGET-10-PAPHLH-09A TARGET-10-PARENU-09A TARGET-10-PARMWH-09A TARGET-10-PARNGI-09A TARGET-10-PARMFF-09A TARGET-10-PARPGL-09A TARGET-10-PAREWZ-09A TARGET-10-PARFDL-09A TARGET-10-PARNSP-09A TARGET-10-PAPFZF-09A TARGET-10-PARBWN-09A TARGET-10-PARTWH-09A TARGET-10-PATXSK-09A TARGET-10-PARBRK-03A TARGET-10-PARVAK-09A TARGET-10-PASKIC-09A TARGET-10-PAPAPC-09A TARGET-10-PARLDF-09A TARGET-10-PARPDP-09A TARGET-10-PAREAA-09A TARGET-10-PARHBI-09A TARGET-10-PARSKH-09A TARGET-10-PAPCSZ-09A TARGET-10-PASYSJ-09A TARGET-10-PARMUC-03A TARGET-10-PAPCJR-09A TARGET-10-PAPIHH-09A TARGET-10-PAREPF-09A TARGET-10-PARDEP-09A TARGET-10-PAREYW-09A TARGET-10-PARHEA-09A TARGET-10-PANWKP-09A TARGET-10-PAPERN-09A TARGET-10-PATDFE-09A TARGET-10-PARACE-09A TARGET-10-PATEVL-09A TARGET-10-PARCUM-09A TARGET-10-PARDDV-09A TARGET-10-PARBDP-09A TARGET-10-PASJJR-09A TARGET-10-PATSIY-09A TARGET-10-PARDST-09A TARGET-10-PARIZN-09A TARGET-10-PAUAJA-09A TARGET-10-PARDFN-09A TARGET-10-PARFIH-09A TARGET-10-PARSJG-09A TARGET-10-PARMIH-09A TARGET-10-PAUBLL-09A TARGET-10-PARMSB-09A TARGET-10-PAKSWW-60A TARGET-10-PARAXH-09A TARGET-10-PARDXI-03A TARGET-10-PAPICC-09A TARGET-10-PASSEF-09A TARGET-10-PATHWV-09A TARGET-10-PAPZUE-03A TARGET-10-PANTLF-03A TARGET-10-PARDLJ-09A TARGET-10-PANWJM-09A TARGET-10-PASNEH-09A TARGET-10-PATAXS-09A TARGET-10-PARGMW-09A TARGET-10-PASVIN-09A TARGET-10-PARBTA-09A TARGET-10-PAPBVD-09A TARGET-10-PAREKH-09A TARGET-10-PARKLK-09A TARGET-10-PARTZE-09A TARGET-10-PARCVT-09A TARGET-10-PARFAP-09A TARGET-10-PARJYV-09A TARGET-10-PARFSF-09A TARGET-10-PARPGW-09A TARGET-10-PARVHY-09A TARGET-10-PAPDLN-09A TARGET-10-PASFHR-09A TARGET-10-PAPHDN-09A TARGET-10-PARDWM-09A TARGET-10-PANTVC-09A TARGET-10-PASINX-09A TARGET-10-PARRKK-09A TARGET-10-PATKYI-09A TARGET-10-PARRSR-09A TARGET-10-PARNJB-09A TARGET-10-PANXGD-09A TARGET-10-PARBGG-09A TARGET-10-PANVTB-09A TARGET-10-PAPHDX-09A TARGET-10-PARMEG-09A TARGET-10-PATRNA-09A TARGET-10-PARBNY-09A TARGET-10-PATZVD-09A TARGET-10-PATGLV-09A TARGET-10-PARIYD-09A TARGET-10-PAPFPZ-09A TARGET-10-PARLSU-09A TARGET-10-PAREIE-09A TARGET-10-PATBDJ-09A TARGET-10-PAPANB-09A TARGET-10-PANSHK-09A TARGET-10-PANZGN-09A TARGET-10-PATWNL-09A TARGET-10-PANYZE-09A TARGET-10-PARGJY-09A TARGET-10-PARWLP-09A TARGET-10-PARTPW-09A TARGET-10-PARFDG-09A TARGET-10-PAREJZ-09A TARGET-10-PAPGLS-09A TARGET-10-PAPAXH-09A TARGET-10-PATENL-09A TARGET-10-PASMIC-09A TARGET-10-PANWKM-09A TARGET-10-PARBND-09A TARGET-10-PARBSW-09A TARGET-10-PATMTV-09A TARGET-10-PATCZN-09A TARGET-10-PARPFF-09A TARGET-10-PASIIY-09A TARGET-10-PANUSL-09A TARGET-10-PANVGZ-09A TARGET-10-PATYWV-09A TARGET-10-PARDRS-09A TARGET-10-PASWFN-09A TARGET-10-PARNBN-09A TARGET-10-PARSKY-09A TARGET-10-PARGBR-09A TARGET-10-PAPSPG-03A TARGET-10-PAPEMZ-09A TARGET-10-PANTSM-03A TARGET-10-PAUBTC-09A TARGET-10-PARUGV-09A TARGET-10-PARASN-09A TARGET-10-PATGKE-09A TARGET-10-PARCLU-09A TARGET-10-PAPHWE-09A TARGET-10-PAPDRP-09A TARGET-10-PAPFKA-09A TARGET-10-PANWJS-09A TARGET-10-PARKZX-09A TARGET-10-PANVDV-09A TARGET-10-PASWXB-09A TARGET-10-PAPHCA-09A TARGET-10-PASUIN-09A TARGET-10-PARVMR-09A TARGET-10-PANXGM-09A TARGET-10-PAREWM-09A TARGET-10-PAPAMH-09A TARGET-10-PAPZUW-09A TARGET-10-PARTZJ-09A TARGET-10-PANYGB-09A TARGET-10-PAPDUV-09A TARGET-10-PASFXA-03A TARGET-10-PASZJW-03A TARGET-10-PARPPV-09A TARGET-10-PARNIZ-09A TARGET-10-PATBRV-09A TARGET-10-PATJZK-09A TARGET-10-PAPBPC-09A TARGET-10-PARUKK-09A TARGET-10-PARCVM-03A TARGET-10-PARSUV-09A TARGET-10-PARCKD-09A TARGET-10-PATBNT-09A TARGET-10-PANTXA-09A TARGET-10-PARBRX-09A TARGET-10-PARERS-09A TARGET-10-PATEIT-09A TARGET-10-PASTXU-09A TARGET-10-PATGMP-09A TARGET-10-PAPEMC-09A TARGET-10-PATCUK-09A TARGET-10-PARGFL-09A TARGET-10-PARILG-09A TARGET-10-PARNDB-09A TARGET-10-PARXVS-09A TARGET-10-PAPDMU-09A TARGET-10-PARPYH-09A TARGET-10-PASJYI-09A TARGET-10-PARBCW-09A TARGET-10-PARDRI-09A TARGET-10-PARUCI-09A TARGET-10-PARMYP-09A TARGET-10-PARPUL-09A TARGET-10-PARPYS-09A TARGET-10-PATDRC-03A TARGET-10-PARSJH-09A TARGET-10-PATXAL-09A TARGET-10-PASXUU-09A TARGET-10-PARBHI-09A TARGET-10-PARBLL-09A TARGET-10-PARPZR-09A TARGET-10-PAPHBW-09A TARGET-10-PARDKG-09A TARGET-10-PANVJI-09A TARGET-10-PANVXF-09A TARGET-10-PAPAGK-03A TARGET-10-PARFHH-09A TARGET-10-PARNMV-09A TARGET-10-PATGWP-09A TARGET-10-PASKSY-09A TARGET-10-PARJNX-09A TARGET-10-PANTWC-09A TARGET-10-PARVEI-09A TARGET-10-PARDXS-09A TARGET-10-PAPFBX-09A TARGET-10-PATLPN-03A TARGET-10-PASWNU-09A TARGET-10-PAPGKP-09A TARGET-10-PAPILF-09A TARGET-10-PARGLE-09A TARGET-10-PARHAN-09A TARGET-10-PARKFU-09A TARGET-10-PARHFF-09A TARGET-10-PATLNZ-09A TARGET-10-PANWGG-09A TARGET-10-PANXLP-09A TARGET-10-PATAYT-09A TARGET-10-PARLJA-09A TARGET-10-PARRVK-09A TARGET-10-PAREAL-09A TARGET-10-PASYCN-09A TARGET-10-PARAFI-09A TARGET-10-PATIBE-09A TARGET-10-PANXTP-09A TARGET-10-PAPFTJ-09A TARGET-10-PAPFIX-09A TARGET-10-PARJLF-09A TARGET-10-PAUBPY-09A TARGET-10-PARKLL-09A TARGET-10-PAPETC-09A TARGET-10-PASYHN-09A TARGET-10-PANXAM-09A TARGET-10-PARLTU-09A TARGET-10-PANVKH-09A TARGET-10-PATGZA-09A TARGET-10-PAPZTS-09A TARGET-10-PATCDM-40A TARGET-10-PATGVX-09A TARGET-10-PAPZNK-03A TARGET-10-PATFJD-09A TARGET-10-PATSIL-09A TARGET-10-PATWIJ-09A TARGET-10-PARFKD-09A TARGET-10-PARIIA-09A TARGET-10-PASGFH-09A TARGET-10-PATZYC-09A TARGET-10-PARDFH-09A TARGET-10-PATHRF-09A TARGET-10-PANVIC-03A TARGET-10-PARFPJ-09A TARGET-10-PASXSI-09A TARGET-10-PASPPN-09A TARGET-10-PAPDHA-09A TARGET-10-PAPHIG-09A TARGET-10-PANZEG-03A TARGET-10-PAPADT-09A TARGET-10-PATCDZ-09A TARGET-10-PATEAK-09A TARGET-10-PATLNS-09A TARGET-10-PAPAMS-09A TARGET-10-PARPIF-09A TARGET-10-PARHLM-09A TARGET-10-PARDEY-09A TARGET-10-PARETC-09A TARGET-10-PASHXL-09A TARGET-10-PANTRY-09A TARGET-10-PATPWF-03A TARGET-10-PARDNF-09A TARGET-10-PATBDK-09A TARGET-10-PAPDKR-09A TARGET-10-PARRMU-09A TARGET-10-PAPIGD-09A TARGET-10-PARCBE-09A TARGET-10-PARFEH-09A TARGET-10-PARUBX-09A TARGET-10-PAPCPB-09A TARGET-10-PAUCDY-09A TARGET-10-PANUYZ-09A TARGET-10-PARTSC-09A TARGET-10-PATEHZ-03A TARGET-10-PAPGEE-09A TARGET-10-PAPAGW-09A TARGET-10-PARENW-09A TARGET-10-PAPHYM-09A TARGET-10-PARMWZ-09A TARGET-10-PAUCDC-09A TARGET-10-PAPHJF-09A TARGET-10-PARGBT-09A TARGET-10-PASTHE-09A TARGET-10-PARTGW-09A TARGET-10-PARFJK-09A TARGET-10-PATFJP-09A TARGET-10-PAPILG-09A TARGET-10-PATLRZ-09A TARGET-10-PARMSP-09A TARGET-10-PARTBP-09A TARGET-10-PARHES-09A TARGET-10-PANWYH-09A TARGET-10-PAPZZJ-09A TARGET-10-PASXLT-09A TARGET-10-PAPEJL-09A TARGET-10-PAREGC-03A TARGET-10-PAPBAI-09A TARGET-10-PATGYH-09A TARGET-10-PAPEFH-03A TARGET-10-PARKEN-03A TARGET-10-PARCDX-09A TARGET-10-PARJWB-09A TARGET-10-PATFRM-09A TARGET-10-PARLPB-09A TARGET-10-PARJAY-09A TARGET-10-PARKEU-09A TARGET-10-PAPESB-09A TARGET-10-PARDEG-09A TARGET-10-PARSGM-09A TARGET-10-PATYJK-09A TARGET-10-PAPFAT-09A TARGET-10-PASNTZ-09A TARGET-10-PAPFZL-09A TARGET-10-PAPFBR-09A TARGET-10-PARCDS-09A TARGET-10-PATRGV-09A TARGET-10-PAPIHT-09A TARGET-10-PASWXZ-09A TARGET-10-PARXHT-03A TARGET-10-PARASZ-09A TARGET-10-PAREGE-09A TARGET-10-PARCKV-09A TARGET-10-PARTLY-09A TARGET-10-PATCKV-09A TARGET-10-PARERM-09A TARGET-10-PARCMG-03A TARGET-10-PANVUU-09A TARGET-10-PARPET-09A TARGET-10-PASKCL-09B TARGET-10-PAUBRD-09A TARGET-10-PANXXD-09A TARGET-10-PAPEJM-09A TARGET-10-PARIBB-09A TARGET-10-PARBLS-09A TARGET-10-PAPGFD-09A TARGET-10-PARNLW-09A TARGET-10-PARHBT-09A TARGET-10-PARPYJ-09A TARGET-10-PANWIM-09A TARGET-10-PARCCM-09A TARGET-10-PARPGJ-09A TARGET-10-PAPIIX-09A TARGET-10-PANXEE-09A TARGET-10-PAPAGF-09A TARGET-10-PARGKD-09A TARGET-10-PASXLZ-09A TARGET-10-PATSDS-03A TARGET-10-PAUAYB-09A TARGET-10-PAREEX-09A TARGET-10-PARDMI-09A TARGET-10-PATKVD-09A TARGET-10-PAPGLD-09A TARGET-10-PATJLT-09A TARGET-10-PARDHK-09A TARGET-10-PAREIV-09A TARGET-10-PAPIEW-09A TARGET-10-PAREKM-09A TARGET-10-PAPSPN-03A TARGET-10-PANTCR-09A TARGET-10-PASHNK-09A TARGET-10-PAPDUX-09A TARGET-10-PANZFN-09A TARGET-10-PARDEJ-09A TARGET-10-PATWJU-09A TARGET-10-PATZFF-09A TARGET-10-PARASC-09A TARGET-10-PANVMT-09A TARGET-10-PASKAD-09A TARGET-10-PAPDFS-09A TARGET-10-PARSRI-09A TARGET-10-PATCNI-09A TARGET-10-PAPEJA-09A TARGET-10-PAPZXI-09A TARGET-10-PARAPT-09A TARGET-10-PARUBN-09A TARGET-10-PAPBZW-09A TARGET-10-PARUEU-09A TARGET-10-PARFFC-03A TARGET-10-PARXMV-03A TARGET-10-PATHBG-09A TARGET-10-PANWSP-09A TARGET-10-PANXCX-09A TARGET-10-PAREGZ-09A TARGET-10-PATITB-09A TARGET-10-PAPESY-09A TARGET-10-PARTGB-09A TARGET-10-PARCLW-09A TARGET-10-PARCDV-09A TARGET-10-PANTYP-09A TARGET-10-PARDBT-09A TARGET-10-PARCAX-09A TARGET-10-PARBYU-09A diff --git a/crdc/gdc/bll_target_gdc/data_clinical_patient.txt b/crdc/gdc/bll_target_gdc/data_clinical_patient.txt new file mode 100644 index 0000000000..3a0ffc4dff --- /dev/null +++ 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b/crdc/gdc/bll_target_gdc/data_mrna_seq_fpkm.txt new file mode 100644 index 0000000000..5f91cf0cfa --- /dev/null +++ b/crdc/gdc/bll_target_gdc/data_mrna_seq_fpkm.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:eef35d9caf6b4e659c9c0f7e45bcc11246df3a7b7ada519e1fd08a42102cb737 +size 112808740 diff --git a/crdc/gdc/bll_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt b/crdc/gdc/bll_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..a9290e06b6 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d9afebea8a2d9f888545301540eb0d46e999e9dc5f314e0a09f8b2fb19f1a969 +size 138958705 diff --git a/crdc/gdc/bll_target_gdc/data_mrna_seq_read_counts.txt b/crdc/gdc/bll_target_gdc/data_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..6ce85e4a3f --- /dev/null +++ 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sha256:f8301fefcd8bfe63110eb68ed1701eba0ba16ba8b816b6d507dcb706baf6aa35 +size 114550953 diff --git a/crdc/gdc/bll_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/bll_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..19e3ac8881 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e1842c01805788b26f58891daafde9ca6b6d283876ff74c90a650c1e369b37ab +size 138632365 diff --git a/crdc/gdc/bll_target_gdc/data_mutations.txt b/crdc/gdc/bll_target_gdc/data_mutations.txt new file mode 100644 index 0000000000..0df58d6fb2 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:59627d24c66bbebd522f68001dea7ff8620302a6a6b411c5fb2a24be25e19a8a +size 4604514 diff --git a/crdc/gdc/bll_target_gdc/data_timeline_status.txt b/crdc/gdc/bll_target_gdc/data_timeline_status.txt new file mode 100644 index 0000000000..be4edb578f --- /dev/null +++ b/crdc/gdc/bll_target_gdc/data_timeline_status.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e6afdbb91cc0aa598373f304411c5774e2995ab51479469af7589de87d0e17d6 +size 47076 diff --git a/crdc/gdc/bll_target_gdc/meta_clinical_patient.txt b/crdc/gdc/bll_target_gdc/meta_clinical_patient.txt new file mode 100644 index 0000000000..8586df1c5c --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_clinical_sample.txt b/crdc/gdc/bll_target_gdc/meta_clinical_sample.txt new file mode 100644 index 0000000000..7cc7db81a3 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_cna.txt b/crdc/gdc/bll_target_gdc/meta_cna.txt new file mode 100644 index 0000000000..d87c79186b --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +stable_id: cna +show_profile_in_analysis_tab: true +profile_name: Putative copy-number alterations from GISTIC +profile_description: Putative copy-number from GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +data_filename: data_cna.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_mrna_seq_fpkm.txt b/crdc/gdc/bll_target_gdc/meta_mrna_seq_fpkm.txt new file mode 100644 index 0000000000..1196dbe38e --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_mrna_seq_fpkm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_fpkm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (FPKM) +profile_description: mRNA expression from capture (RNA Seq FPKM) +data_filename: data_mrna_seq_fpkm.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt b/crdc/gdc/bll_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..e10dcfc226 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_fpkm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression fpkm Zscores +profile_description: mRNA expression from capture (RNA Seq FPKM) zscores +data_filename: data_mrna_seq_fpkm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_mrna_seq_read_counts.txt b/crdc/gdc/bll_target_gdc/meta_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..c7b6f019fb --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_mrna_seq_read_counts.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: rna_seq_mrna +show_profile_in_analysis_tab: false +profile_name: mRNA expression +profile_description: Expression levels +data_filename: data_mrna_seq_read_counts.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt b/crdc/gdc/bll_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..85c00526b4 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_read_counts_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression Zscores +profile_description: mRNA expression from capture read count zscores +data_filename: data_mrna_seq_read_counts_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_mrna_seq_tpm.txt b/crdc/gdc/bll_target_gdc/meta_mrna_seq_tpm.txt new file mode 100644 index 0000000000..0955a4c66d --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_mrna_seq_tpm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_tpm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (TPM) +profile_description: mRNA expression from capture (RNA Seq TPM) +data_filename: data_mrna_seq_tpm.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/bll_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..cd7012c964 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_tpm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression tpm Zscores +profile_description: mRNA expression from capture (RNA Seq TPM) zscores +data_filename: data_mrna_seq_tpm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_mutations.txt b/crdc/gdc/bll_target_gdc/meta_mutations.txt new file mode 100644 index 0000000000..f8794e4584 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +data_filename: data_mutations.txt +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutation data. +profile_name: Mutations \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_study.txt b/crdc/gdc/bll_target_gdc/meta_study.txt new file mode 100644 index 0000000000..ab2f0de0ff --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: bll +cancer_study_identifier: bll_target_gdc +name: B-Lymphoblastic Leukemia/Lymphoma - Phase II (TARGET, GDC) +short_name: BLL +description: TARGET B-Lymphoblastic Leukemia/Lymphoma - Phase II. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +reference_genome: hg38 +groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_timeline_status.txt b/crdc/gdc/bll_target_gdc/meta_timeline_status.txt new file mode 100644 index 0000000000..8e8c51da94 --- /dev/null +++ b/crdc/gdc/bll_target_gdc/meta_timeline_status.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: bll_target_gdc +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_timeline_status.txt \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/validation_reports/bll_target_gdc-validation.html b/crdc/gdc/bll_target_gdc/validation_reports/bll_target_gdc-validation.html new file mode 100644 index 0000000000..e09051d0ad --- /dev/null +++ b/crdc/gdc/bll_target_gdc/validation_reports/bll_target_gdc-validation.html @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:353aeb106e9258dfd0dd10baa4f6e47accab08d54877e8adec5a394a7927bbb7 +size 4909442 diff --git a/crdc/gdc/nbl_target_gdc/README.md b/crdc/gdc/nbl_target_gdc/README.md new file mode 100644 index 0000000000..e4eca551d5 --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/README.md @@ -0,0 +1,149 @@ +# Comments & assumptions made during curation + +## General + +- Study is updated once every 3 months with latest data from [ISB-CGC BigQuery tables](https://isb-cgc.appspot.com/bq_meta_search/) + - The ISB-CGC tables allow easy access to data collected from multiple NCI-CRDC repositories including the GDC, PDC, and others. The TARGET data in this study comes from the GDC and is accessed through these tables. +- Reference genome used: hg38 +- TARGET started using the hg38 genome as of GDC release 32. For more information, refer to the [GDC release notes](https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-320). + +- Only tumor sample data is included (no normal samples) +- [GDC project webpage](https://portal.gdc.cancer.gov/projects/TARGET-NBL) + +## Clinical data + +- **Patient data:** Retrieved from `isb-cgc-bq.TARGET_versioned.clinical_gdc_r40`. ISB-CGC data was created in April 2024. +- **Sample data:** Retrieved from `isb-cgc-bq.TARGET_versioned.per_sample_file_metadata_hg38_gdc_r40`. ISB-CGC data was created in April 2024. + +### Survival data + +Survival fields are calculated from the clinical data and added as new columns in the clinical file. + +- `OS_STATUS` is converted from `demo__vital_status` +- `OS_MONTHS` is converted from `demo__days_to_death`, falls back to `diag__days_to_last_follow_up` + + + + +### Timeline data + +- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +- For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. + +- Birth timeline events are removed, as they (1) push other events to the far right of the graph and (2) can potentially be used to identify the patient. + +The following status values are supported in `data_timeline_status.txt`: + +- `__time0__` +- `demo__days_to_death` +- `diag__days_to_last_follow_up` +### Other transformations + +- `"not reported"` values are replaced with blanks. +- If a clinical field is missing for the entire study, the column is removed from the data file. +- `RACE`, `ETHNICITY`, and `SEX` are capitalized. +- `AGE` is converted from days to years. + +## CNA data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.copy_number_gene_level_hg38_gdc_r36`. ISB-CGC data was created in March 2023. +- Transformations + - Copy number values from the BigQuery tables are converted from [ASCAT](https://www.pnas.org/doi/10.1073/pnas.1009843107https://www.pnas.org/doi/10.1073/pnas.1009843107) to GISTIC 2.0 using the following thresholds: + +| ASCAT Value | GISTIC Value | Meaning | +|---|---|---| +| X = 0 | -2 | Deep loss | +| X = 1 | -1 | Single-copy loss | +| X = 2 | 0 | Diploid | +| 2 < X < 7 | 1 | Low-level gain | +| 7 ≤ X | 2 | Amplification | + +Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on the cBioPortal website. As a result these conversion thresholds affect how many samples show up in the CNA chart, which can be inconsistent with legacy versions of this study. We chose ASCAT ≥ 7 as the amplification threshold because it resulted in the least deviation from our legacy studies. + + + +## mRNA Expression data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.RNAseq_hg38_gdc_r35`. ISB-CGC data was created in December 2022. +- The `unstranded`, `tpm_unstranded`, and `fpkm_uq_unstranded` columns are pulled and each mapped to their own data file. + - The regular FPKM values are excluded because [FPKM-UQ provides a more stable metric](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#upper-quartile-fpkm). +- Transformations: see [Genomic data transformations](#genomic-data-transformations) + + + +## Mutation data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.masked_somatic_mutation_hg38_gdc_r40`. ISB-CGC data was created in July 2024. +- The MAF is annotated with Genome Nexus in order to avoid issues with the isoform mapping. Parameters used: + - Endpoint: https://grch38.genomenexus.org/ + - Isoform override: mskcc + - Replace gene symbols and Entrez IDs + - Post interval size: 500 +- Mutation data may be missing for some samples-- this reflects a lack of data availability in ISB-CGC. + +## Expression data transformations (CNA / mRNA) + +- Ensembl gene IDs are mapped to Entrez IDs using the [Genome Nexus hg38 canonical transcript file](https://github.com/genome-nexus/genome-nexus-importer/blob/master/data/grch38_ensembl95/export/ensembl_biomart_canonical_transcripts_per_hgnc.txt). Any genes that cannot be converted using this file are dropped. + - Prior to conversion, we also filter out a small number of duplicate Ensembl genes. These genes have copies containing data for both the X and the Y chromosomes. +- If a sample has multiple aliquots, it has to be condensed to 1 before it can imported into cBioPortal. This is done by choosing the aliquot ID with the highest sort value (eg. highest plate number), following [the same policy](https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844334036/FAQ#FAQ-replicateFilteringQ%3AWhatdoyoudowhenmultiplealiquotbarcodesexistforagivensample%2Fportion%2Fanalytecombination%3F) used by GDAC used to condense aliquot data in their studies. + +## Post-processing steps + + - Samples that lack any genomic data are removed from the clinical sample file. + - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - Case lists are generated under `case_lists/` using a curation-provided script. + - The validator script is run and the HTML report is saved under `validation_reports/`. + +## List of remapped columns + +### Clinical patient + +| Original | cBioPortal | +|---|---| +| submitter_id | PATIENT_ID | +| case_id | OTHER_PATIENT_ID | +| demo__ethnicity | ETHNICITY | +| demo__gender | SEX | +| demo__race | RACE | +| demo__vital_status | VITAL_STATUS | +| diag__age_at_diagnosis | AGE | +| diag__classification_of_tumor | TUMOR_CLASSIFICATION | +| diag__cog_neuroblastoma_risk_group | COG_NEUROBLASTOMA_RISK_GROUP | +| diag__icd_10_code | ICD_10 | +| diag__inss_stage | INSS_STAGE | +| diag__last_known_disease_status | DISEASE_STATUS | +| diag__metastasis_at_diagnosis | METASTASIS_AT_DIAGNOSIS | +| diag__morphology | MORPHOLOGY | +| diag__path__necrosis_percent | PATHOLOGY_NECROSIS_PERCENT | +| diag__primary_diagnosis | PRIMARY_DIAGNOSIS | +| diag__site_of_resection_or_biopsy | BIOPSY_SITE | +| diag__year_of_diagnosis | YEAR_OF_DIAGNOSIS | +| disease_type | DISEASE_TYPE | +| index_date | INDEX_DATE | +| primary_site | PRIMARY_SITE_PATIENT | +| proj__name | PROJECT_NAME | +| proj__project_id | PROJECT_ID | + + +### Clinical sample + +| Original | cBioPortal | +|---|---| +| case_barcode | PATIENT_ID | +| sample_barcode | SAMPLE_ID | +| sample_gdc_id | OTHER_SAMPLE_ID | +| sample_type_name | SAMPLE_TYPE | +| primary_site | PRIMARY_SITE | +| days_to_collection | DAYS_TO_COLLECTION | +| days_to_sample_procurement | DAYS_TO_SPECIMEN_COLLECTION | +| is_ffpe | IS_FFPE | + + + +### Mutation + +| Original | cBioPortal | +|---|---| +| sample_barcode_tumor | Tumor_Sample_Barcode | +| sample_barcode_normal | Matched_Norm_Sample_Barcode | \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/case_lists/cases_all.txt b/crdc/gdc/nbl_target_gdc/case_lists/cases_all.txt new file mode 100644 index 0000000000..4f6f9762a4 --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: nbl_target_gdc +stable_id: nbl_target_gdc_all +case_list_name: All samples +case_list_description: All samples (529 samples) +case_list_category: all_cases_in_study +case_list_ids: TARGET-30-PASMDM-01A TARGET-30-PATBHY-01A TARGET-30-PASUEA-01A TARGET-30-PALCBW-01A TARGET-30-PANLET-01A TARGET-30-PASEYW-01A TARGET-30-PAREAG-01A TARGET-30-PARACM-01A TARGET-30-PASNPG-02A TARGET-30-PALZZV-01A TARGET-30-PAKFUY-01A TARGET-30-PASCZY-01A TARGET-30-PAUKAP-01A TARGET-30-PAUGRP-01A TARGET-30-PARYEH-01A TARGET-30-PASXIE-01A TARGET-30-PAVAYF-01A TARGET-30-PASDRV-01A TARGET-30-PAUELT-01A TARGET-30-PATKHS-01A TARGET-30-PATPPU-01A TARGET-30-PASHFA-01A TARGET-30-PALJPX-01A TARGET-30-PATFES-01A TARGET-30-PATVDP-01A TARGET-30-PAKIPY-01A TARGET-30-PARACS-01A TARGET-30-PATNWL-01A TARGET-30-PASCJJ-01A TARGET-30-PARUCM-01A TARGET-30-PATMJV-09A TARGET-30-PATTPW-01A TARGET-30-PASVKL-09A TARGET-30-PASVYV-01A TARGET-30-PAIVHE-01A TARGET-30-PATHKB-01A TARGET-30-PARGHY-01A TARGET-30-PAVAGS-01A TARGET-30-PAUCGP-01A TARGET-30-PAUZSB-01A TARGET-30-PAUMBB-01A TARGET-30-PASYLD-01A TARGET-30-PATXHW-01A TARGET-30-PARURB-01A TARGET-30-PASGAP-02A TARGET-30-PARNNC-01A TARGET-30-PARETE-01A TARGET-30-PATFXV-01A TARGET-30-PASTKW-01A TARGET-30-PASFDJ-01A TARGET-30-PANNMS-01A TARGET-30-PANBJH-01A TARGET-30-PANWRR-01A TARGET-30-PATILE-01A TARGET-30-PARGZK-01A TARGET-30-PAUXIW-09A TARGET-30-PATVDY-09A TARGET-30-PATUPR-09A TARGET-30-PAUKRF-01A TARGET-30-PAMZMG-01A TARGET-30-PATHVK-01A TARGET-30-PALZRG-01A TARGET-30-PASJWG-01A TARGET-30-PATIYD-09A TARGET-30-PAUDDZ-01A TARGET-30-PASMNT-01A TARGET-30-PASMPT-01A TARGET-30-PAPREJ-01A TARGET-30-PAMEZH-01A TARGET-30-PAUDVA-09A TARGET-30-PASZKE-01A TARGET-30-PAUUGT-01A TARGET-30-PAKXDZ-01A TARGET-30-PATHJU-09A TARGET-30-PATTPC-01A TARGET-30-PASFDV-01A TARGET-30-PALUYS-01A TARGET-30-PARDIW-01A TARGET-30-PAUYDE-01A TARGET-30-PATXUG-01A TARGET-30-PATJZF-01A TARGET-30-PATEKG-01A TARGET-30-PAUDMU-01A TARGET-30-PAITEG-01A TARGET-30-PATZIG-01A TARGET-30-PATXXI-01A TARGET-30-PAUUHD-01A TARGET-30-PATXHC-01A TARGET-30-PATYPH-01A TARGET-30-PAIXNC-01A TARGET-30-PARZMY-06A TARGET-30-PAPTDH-01A TARGET-30-PATJHU-01A TARGET-30-PAPBJE-01A TARGET-30-PAPVFD-01A TARGET-30-PANBCI-01A TARGET-30-PATBPG-01A TARGET-30-PASBPN-01A TARGET-30-PAPLSD-01A TARGET-30-PANPVI-01A TARGET-30-PANRRW-01A TARGET-30-PALKUC-01A TARGET-30-PATYWX-01A TARGET-30-PAUIHH-01A TARGET-30-PASPXU-01A TARGET-30-PASLTC-01A TARGET-30-PATNRI-01A TARGET-30-PARASL-01A TARGET-30-PATNGD-01A TARGET-30-PAUCRL-01A TARGET-30-PAKYZS-01A TARGET-30-PASVSU-09A TARGET-30-PASXRG-01A TARGET-30-PARDVT-01A TARGET-30-PAUDDK-01A TARGET-30-PAIXNV-01A TARGET-30-PALNVP-01A TARGET-30-PANRHJ-01A TARGET-30-PARLTG-01A TARGET-30-PAPWFY-01A TARGET-30-PATFMU-01A TARGET-30-PAMMXF-01A TARGET-30-PAVCLI-01A TARGET-30-PASZGB-01A TARGET-30-PAKVUY-01A TARGET-30-PATSPZ-01A TARGET-30-PASUCB-01A TARGET-30-PATJZC-01A TARGET-30-PAUAKT-01A TARGET-30-PAMNYX-01A TARGET-30-PAKZRH-01A TARGET-30-PAPZYP-01A TARGET-30-PASGAP-01A TARGET-30-PARZCJ-01A TARGET-30-PAPEFE-01A TARGET-30-PASCDX-01A TARGET-30-PASFWL-01A TARGET-30-PANXJL-01A TARGET-30-PATWGC-01A TARGET-30-PASTXR-01A TARGET-30-PASCFC-01A TARGET-30-PASEGA-01A TARGET-30-PATTHA-01A TARGET-30-PATCEM-01A TARGET-30-PATCFL-01A TARGET-30-PARBAJ-01A TARGET-30-PASBGV-01A TARGET-30-PARVNT-01A TARGET-30-PASYPX-01A TARGET-30-PALUDH-01A TARGET-30-PATBAC-01A TARGET-30-PAPRMJ-01A TARGET-30-PAVCHH-01A TARGET-30-PASKSX-01A TARGET-30-PAUBRR-01A TARGET-30-PAUMUC-01A TARGET-30-PALXTB-01A TARGET-30-PATZRF-01A TARGET-30-PASMJG-01A TARGET-30-PAPTJB-01A TARGET-30-PASUTC-01A TARGET-30-PAPYNZ-01A TARGET-30-PANKFE-01A TARGET-30-PATTPL-01A TARGET-30-PASSRN-01A TARGET-30-PARSVF-01A TARGET-30-PAUHFW-01A TARGET-30-PATGJU-01A TARGET-30-PARBAJ-02A TARGET-30-PASEJZ-01A TARGET-30-PASJUU-01A TARGET-30-PATVWA-01A TARGET-30-PALAKE-01A TARGET-30-PAPUNH-01A TARGET-30-PATBMM-01A TARGET-30-PAPTAN-01A TARGET-30-PATYWM-01A TARGET-30-PATTMM-01A TARGET-30-PALXHW-01A TARGET-30-PATACA-01A TARGET-30-PALRSD-01A TARGET-30-PAUNTY-01A TARGET-30-PAUBWP-01A TARGET-30-PASBMW-01A TARGET-30-PATYIL-01A TARGET-30-PASALE-01A TARGET-30-PATUEH-01A TARGET-30-PANYGR-01A TARGET-30-PASYIP-01A TARGET-30-PAIFXV-01A TARGET-30-PAPVRN-01A TARGET-30-PALIIN-01A TARGET-30-PARAMT-01A TARGET-30-PAMMWD-01A TARGET-30-PAUBDC-01A TARGET-30-PAUMMZ-01A TARGET-30-PAVALS-01A TARGET-30-PASESX-01A TARGET-30-PASNZU-01A TARGET-30-PASNUI-01A TARGET-30-PATWTW-01A TARGET-30-PANZPV-01A TARGET-30-PASSRS-01A TARGET-30-PASEWZ-01A TARGET-30-PATTDY-01A TARGET-30-PAUICI-01A TARGET-30-PANUKV-01A TARGET-30-PARNNG-01A TARGET-30-PAKZRE-01A TARGET-30-PASWLY-01A TARGET-30-PATRJG-01A TARGET-30-PAUBGW-01A TARGET-30-PAUAZA-01A TARGET-30-PALNLU-01A TARGET-30-PARXLN-01A TARGET-30-PASXGP-01A TARGET-30-PASFNY-01A TARGET-30-PAILNU-01A TARGET-30-PARUTJ-01A TARGET-30-PARSRJ-01A TARGET-30-PATYMS-01A TARGET-30-PATAYJ-01A TARGET-30-PAUPRN-01A TARGET-30-PARVZT-01A TARGET-30-PATPET-01A TARGET-30-PARYSR-01A TARGET-30-PAUZAE-01A TARGET-30-PATGLU-01A TARGET-30-PAPUEB-01A TARGET-30-PAISSH-01A TARGET-30-PATNEA-01A TARGET-30-PAUBHV-01A TARGET-30-PASXCG-01A TARGET-30-PATZRU-01A TARGET-30-PASSWW-01A TARGET-30-PAUNWR-01A TARGET-30-PAPUJU-01A TARGET-30-PAPTLA-01A TARGET-30-PATVJX-01A TARGET-30-PATCJP-09A TARGET-30-PALAKM-01A TARGET-30-PATVDI-01A TARGET-30-PASLDM-01A TARGET-30-PATMFL-01A TARGET-30-PALFPI-01A TARGET-30-PATXWS-01A TARGET-30-PAPTFZ-01A TARGET-30-PATSJV-01A TARGET-30-PARVWL-01A TARGET-30-PASTGD-01A TARGET-30-PASPER-01A TARGET-30-PASLXS-01A TARGET-30-PATLKI-01A TARGET-30-PATNRK-09A TARGET-30-PARVLK-01A TARGET-30-PAUZRC-01A TARGET-30-PASNEF-01A TARGET-30-PAURPL-01A TARGET-30-PARGKK-01A TARGET-30-PATMPC-01A TARGET-30-PAUBSW-01A TARGET-30-PAPBGH-01A TARGET-30-PATSRD-01A TARGET-30-PAMDAL-01A TARGET-30-PANGXK-01A TARGET-30-PAUFPG-01A TARGET-30-PASKFV-01A TARGET-30-PATWMX-01A TARGET-30-PATESI-01A TARGET-30-PAUWYM-01A TARGET-30-PAKGKH-01A TARGET-30-PARPGU-01A TARGET-30-PAUGWT-01A TARGET-30-PASSNN-01A TARGET-30-PATGWT-01A TARGET-30-PASFGG-01A TARGET-30-PASCIX-09A TARGET-30-PASSII-01A TARGET-30-PATECM-01A TARGET-30-PAITCI-01A TARGET-30-PASJZC-01A TARGET-30-PALBFW-01A TARGET-30-PAPZYZ-01A TARGET-30-PATXKG-01A TARGET-30-PASTCN-01A TARGET-30-PASDYT-01A TARGET-30-PARHUX-01A TARGET-30-PARZIP-01A TARGET-30-PAIWRB-01A TARGET-30-PARJEN-01A TARGET-30-PANJLH-01A TARGET-30-PASXNN-01A TARGET-30-PAULVH-01A TARGET-30-PASNPG-01A TARGET-30-PARJMX-01A TARGET-30-PAUIWS-01A TARGET-30-PATWNB-01A TARGET-30-PARDYU-01A TARGET-30-PATXHT-01A TARGET-30-PAIPGU-01A TARGET-30-PAUCKF-01A TARGET-30-PATXDV-01A TARGET-30-PAUCFI-01A TARGET-30-PASZST-01A TARGET-30-PASPBZ-01A TARGET-30-PAUHSJ-01A TARGET-30-PAVEZM-01A TARGET-30-PASWIJ-01A TARGET-30-PASYJF-01A TARGET-30-PATBKX-01A TARGET-30-PANUIF-01A TARGET-30-PATLXP-01A TARGET-30-PASYTP-01A TARGET-30-PAMBAC-01A TARGET-30-PARYNK-01A TARGET-30-PATYMK-01A TARGET-30-PAIXRK-01A TARGET-30-PATXXF-01A TARGET-30-PASVRU-01A TARGET-30-PATCKU-01A TARGET-30-PARUCL-01A TARGET-30-PATKSX-01A TARGET-30-PASWFB-01A TARGET-30-PAUIFL-01A TARGET-30-PASFEV-01A TARGET-30-PAMUTD-01A TARGET-30-PARZKK-09A TARGET-30-PATSKE-01A TARGET-30-PATHUU-01A TARGET-30-PATNKP-02A TARGET-30-PASRFS-01A TARGET-30-PAUKLK-01A TARGET-30-PASAAN-01A TARGET-30-PARMDD-01A TARGET-30-PATNCI-01A TARGET-30-PARACR-01A TARGET-30-PAKJRE-01A TARGET-30-PASTKC-01A TARGET-30-PAUTLP-01A TARGET-30-PAPCTS-01A TARGET-30-PASZPI-01A TARGET-30-PAUHIK-01A TARGET-30-PASZYY-01A TARGET-30-PAULNF-01A TARGET-30-PASUYG-01A TARGET-30-PAUFFP-01A TARGET-30-PASXHE-01A TARGET-30-PAUTVX-01A TARGET-30-PARYVD-01A TARGET-30-PALXMM-01A TARGET-30-PAPKWN-01A TARGET-30-PAHYWC-01A TARGET-30-PASAJU-01A TARGET-30-PAIXIF-01A TARGET-30-PAMCXF-01A TARGET-30-PAMYCE-01A TARGET-30-PARJVP-01A TARGET-30-PAIMDT-01A TARGET-30-PATUNX-01A TARGET-30-PATRUX-09A TARGET-30-PARRLH-01A TARGET-30-PAMZGT-01A TARGET-30-PASLRM-01A TARGET-30-PASTMW-09A TARGET-30-PAVDBS-01A TARGET-30-PAPICY-01A TARGET-30-PATDXG-01A TARGET-30-PATSDR-01A TARGET-30-PARNTS-01A TARGET-30-PAMVLG-01A TARGET-30-PASEWX-01A TARGET-30-PATYCM-01A TARGET-30-PATINJ-01A TARGET-30-PATMSR-01A TARGET-30-PALVKK-01A TARGET-30-PALSAE-01A TARGET-30-PAPZFW-01A TARGET-30-PARHAM-02A TARGET-30-PASNML-01A TARGET-30-PASRSG-01A TARGET-30-PARKGJ-01A TARGET-30-PAUJPC-01A TARGET-30-PAUDIK-01A TARGET-30-PAUEYW-09A TARGET-30-PAUXUP-01A TARGET-30-PASYYM-01A TARGET-30-PATDXC-01A TARGET-30-PATVSU-01A TARGET-30-PALEVG-01A TARGET-30-PASRWE-01A TARGET-30-PARABJ-01A TARGET-30-PALZSL-01A TARGET-30-PARVVM-09A TARGET-30-PARKZF-01A TARGET-30-PANZRV-01A TARGET-30-PARXXC-01A TARGET-30-PATVTL-01A TARGET-30-PASCWD-01A TARGET-30-PAMBMJ-01A TARGET-30-PASPVZ-09A TARGET-30-PARUPT-01A TARGET-30-PARCRR-01A TARGET-30-PAUPWX-01A TARGET-30-PATHYK-01A TARGET-30-PASSWB-01A TARGET-30-PAPSMC-01A TARGET-30-PASGEE-01A TARGET-30-PAVCGD-01A TARGET-30-PATVYZ-01A TARGET-30-PALHVD-01A TARGET-30-PAPTLV-01A TARGET-30-PASAFG-01A TARGET-30-PAKHHB-01A TARGET-30-PARBLH-01A TARGET-30-PARXPD-01A TARGET-30-PATJIN-01A TARGET-30-PATLLI-01A TARGET-30-PARMLF-01A TARGET-30-PARZBH-01A TARGET-30-PASLIH-01A TARGET-30-PASNVM-01A TARGET-30-PASPGB-01A TARGET-30-PAIFCS-01A TARGET-30-PARDCK-01A TARGET-30-PATMSI-01A TARGET-30-PATWWJ-01A TARGET-30-PATDFU-01A TARGET-30-PALETP-01A TARGET-30-PATUWG-01A TARGET-30-PATLCM-01A TARGET-30-PAPBZI-01A TARGET-30-PARKNP-01A TARGET-30-PARYXW-01A TARGET-30-PATPYK-01A TARGET-30-PANBSP-01A TARGET-30-PAPHPE-01A TARGET-30-PATYIL-02A TARGET-30-PAKZRF-01A TARGET-30-PARFRE-01A TARGET-30-PAUXFZ-01A TARGET-30-PAPUWY-01A TARGET-30-PATRMB-01A TARGET-30-PAUJLH-01A TARGET-30-PARUPN-01A TARGET-30-PATDWN-01A TARGET-30-PATYMZ-01A TARGET-30-PASWYR-01A TARGET-30-PALTEG-01A TARGET-30-PASFGD-01A TARGET-30-PAPNEP-01A TARGET-30-PASYMX-01A TARGET-30-PAICGF-01A TARGET-30-PATWGR-01A TARGET-30-PASFIC-01A TARGET-30-PARSBI-01A TARGET-30-PASLAE-01A TARGET-30-PASGUT-01A TARGET-30-PAPVXS-01A TARGET-30-PATYEJ-01A TARGET-30-PASTGH-09A TARGET-30-PAVETV-01A TARGET-30-PARKAG-01A TARGET-30-PAMVRA-01A TARGET-30-PALWVJ-01A TARGET-30-PAUTKP-01A TARGET-30-PASWVY-01A TARGET-30-PAPTCR-01A TARGET-30-PAUGVZ-01A TARGET-30-PATUZF-01A TARGET-30-PATPXJ-01A TARGET-30-PANIPC-06A TARGET-30-PATZBH-01A TARGET-30-PASKPC-01A TARGET-30-PAURCG-01A TARGET-30-PAUATG-01A TARGET-30-PANBMJ-01A TARGET-30-PARMPP-01A TARGET-30-PAUGIP-01A TARGET-30-PAUDDK-02A TARGET-30-PARFWB-01A TARGET-30-PASUML-01A TARGET-30-PATEPF-01A TARGET-30-PATBJI-01A TARGET-30-PASXRJ-01A TARGET-30-PASTSI-01A TARGET-30-PASFDU-01A TARGET-30-PANRVJ-01A TARGET-30-PAKHCF-01A TARGET-30-PATCDJ-01A TARGET-30-PATYDC-01A TARGET-30-PARZHA-01A TARGET-30-PARBGP-01A TARGET-30-PASMET-01A TARGET-30-PAPPKJ-01A TARGET-30-PAPKXS-01A TARGET-30-PAPRPR-01A TARGET-30-PAUFUS-01A TARGET-30-PASCTR-01A TARGET-30-PATRHD-01A TARGET-30-PALWIP-01A TARGET-30-PALPGG-01A TARGET-30-PAUDFR-01A TARGET-30-PAUDBX-01A TARGET-30-PALTYB-01A TARGET-30-PATPHR-01A TARGET-30-PAVCJZ-01A TARGET-30-PANYBL-01A TARGET-30-PAUBFU-01A TARGET-30-PARUTX-01A TARGET-30-PANZVU-01A TARGET-30-PAPBJT-01A TARGET-30-PAUKNU-01A TARGET-30-PATFCY-01A TARGET-30-PATISU-01A TARGET-30-PATNPW-01A TARGET-30-PASCEW-09A TARGET-30-PAPRXW-01A TARGET-30-PAUXSZ-01A TARGET-30-PAUPIC-01A TARGET-30-PAISNS-01A TARGET-30-PAINLN-01A TARGET-30-PATFIN-01A TARGET-30-PARHAM-01A TARGET-30-PAUJRW-01A TARGET-30-PAUGZD-01A TARGET-30-PANSBN-01A TARGET-30-PATMTX-01A TARGET-30-PAMNLH-01A TARGET-30-PASUMG-01A diff --git a/crdc/gdc/nbl_target_gdc/case_lists/cases_sequenced.txt b/crdc/gdc/nbl_target_gdc/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..649c604e34 --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: nbl_target_gdc +stable_id: nbl_target_gdc_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (471 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: TARGET-30-PATBHY-01A TARGET-30-PASUEA-01A TARGET-30-PANLET-01A TARGET-30-PAREAG-01A TARGET-30-PAVAYF-01A TARGET-30-PASDRV-01A TARGET-30-PATPPU-01A TARGET-30-PATFES-01A TARGET-30-PATVDP-01A TARGET-30-PATNWL-01A TARGET-30-PASVKL-09A TARGET-30-PASVYV-01A TARGET-30-PAIVHE-01A TARGET-30-PARGHY-01A TARGET-30-PAVAGS-01A TARGET-30-PAUZSB-01A TARGET-30-PAUMBB-01A TARGET-30-PASYLD-01A 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--- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_clinical_sample.txt b/crdc/gdc/nbl_target_gdc/meta_clinical_sample.txt new file mode 100644 index 0000000000..03797e16ed --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_mrna_seq_fpkm.txt b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_fpkm.txt new file mode 100644 index 0000000000..400dbc6cfe --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_fpkm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_fpkm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (FPKM) +profile_description: mRNA expression from capture (RNA Seq FPKM) +data_filename: data_mrna_seq_fpkm.txt \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..0083964d0e --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_fpkm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression fpkm Zscores +profile_description: mRNA expression from capture (RNA Seq FPKM) zscores +data_filename: data_mrna_seq_fpkm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_mrna_seq_read_counts.txt b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..05e9133938 --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_read_counts.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: rna_seq_mrna +show_profile_in_analysis_tab: false +profile_name: mRNA expression +profile_description: Expression levels +data_filename: data_mrna_seq_read_counts.txt \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..d2eef62d82 --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_read_counts_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression Zscores +profile_description: mRNA expression from capture read count zscores +data_filename: data_mrna_seq_read_counts_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_mrna_seq_tpm.txt b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_tpm.txt new file mode 100644 index 0000000000..1f70badba5 --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_tpm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_tpm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (TPM) +profile_description: mRNA expression from capture (RNA Seq TPM) +data_filename: data_mrna_seq_tpm.txt \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..c7601c1e41 --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_tpm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression tpm Zscores +profile_description: mRNA expression from capture (RNA Seq TPM) zscores +data_filename: data_mrna_seq_tpm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_mutations.txt b/crdc/gdc/nbl_target_gdc/meta_mutations.txt new file mode 100644 index 0000000000..2e342b0dcd --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +data_filename: data_mutations.txt +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutation data. +profile_name: Mutations \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_study.txt b/crdc/gdc/nbl_target_gdc/meta_study.txt new file mode 100644 index 0000000000..9c24f0ba3b --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: nbl +cancer_study_identifier: nbl_target_gdc +name: Neuroblastoma (TARGET, GDC) +short_name: NBL +description: TARGET Neuroblastoma. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +reference_genome: hg38 +groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_timeline_status.txt b/crdc/gdc/nbl_target_gdc/meta_timeline_status.txt new file mode 100644 index 0000000000..1a38016aec --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/meta_timeline_status.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: nbl_target_gdc +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_timeline_status.txt \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/validation_reports/nbl_target_gdc-validation.html b/crdc/gdc/nbl_target_gdc/validation_reports/nbl_target_gdc-validation.html new file mode 100644 index 0000000000..464f4afe4e --- /dev/null +++ b/crdc/gdc/nbl_target_gdc/validation_reports/nbl_target_gdc-validation.html @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:78de3736c53b5852cae39f0e2f08cbcbfd81ca3cb0d99043cdd54fbf479d236f +size 3377705 diff --git a/crdc/gdc/os_target_gdc/README.md b/crdc/gdc/os_target_gdc/README.md new file mode 100644 index 0000000000..f3f0557abd --- /dev/null +++ b/crdc/gdc/os_target_gdc/README.md @@ -0,0 +1,149 @@ +# Comments & assumptions made during curation + +## General + +- Study is updated once every 3 months with latest data from [ISB-CGC BigQuery tables](https://isb-cgc.appspot.com/bq_meta_search/) + - The ISB-CGC tables allow easy access to data collected from multiple NCI-CRDC repositories including the GDC, PDC, and others. The TARGET data in this study comes from the GDC and is accessed through these tables. +- Reference genome used: hg38 +- TARGET started using the hg38 genome as of GDC release 32. For more information, refer to the [GDC release notes](https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-320). + +- Only tumor sample data is included (no normal samples) +- [GDC project webpage](https://portal.gdc.cancer.gov/projects/TARGET-OS) + +## Clinical data + +- **Patient data:** Retrieved from `isb-cgc-bq.TARGET_versioned.clinical_gdc_r40`. ISB-CGC data was created in April 2024. +- **Sample data:** Retrieved from `isb-cgc-bq.TARGET_versioned.per_sample_file_metadata_hg38_gdc_r40`. ISB-CGC data was created in April 2024. + +### Survival data + +Survival fields are calculated from the clinical data and added as new columns in the clinical file. + +- `OS_STATUS` is converted from `demo__vital_status` +- `OS_MONTHS` is converted from `demo__days_to_death`, falls back to `diag__days_to_last_follow_up` + + + + +### Timeline data + +- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +- For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. + +- Birth timeline events are removed, as they (1) push other events to the far right of the graph and (2) can potentially be used to identify the patient. + +The following status values are supported in `data_timeline_status.txt`: + +- `__time0__` +- `demo__days_to_death` +- `diag__days_to_last_follow_up` +### Other transformations + +- `"not reported"` values are replaced with blanks. +- If a clinical field is missing for the entire study, the column is removed from the data file. +- `RACE`, `ETHNICITY`, and `SEX` are capitalized. +- `AGE` is converted from days to years. + +## CNA data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.copy_number_gene_level_hg38_gdc_r36`. ISB-CGC data was created in March 2023. +- Transformations + - Copy number values from the BigQuery tables are converted from [ASCAT](https://www.pnas.org/doi/10.1073/pnas.1009843107https://www.pnas.org/doi/10.1073/pnas.1009843107) to GISTIC 2.0 using the following thresholds: + +| ASCAT Value | GISTIC Value | Meaning | +|---|---|---| +| X = 0 | -2 | Deep loss | +| X = 1 | -1 | Single-copy loss | +| X = 2 | 0 | Diploid | +| 2 < X < 7 | 1 | Low-level gain | +| 7 ≤ X | 2 | Amplification | + +Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on the cBioPortal website. As a result these conversion thresholds affect how many samples show up in the CNA chart, which can be inconsistent with legacy versions of this study. We chose ASCAT ≥ 7 as the amplification threshold because it resulted in the least deviation from our legacy studies. + + + +## mRNA Expression data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.RNAseq_hg38_gdc_r35`. ISB-CGC data was created in December 2022. +- The `unstranded`, `tpm_unstranded`, and `fpkm_uq_unstranded` columns are pulled and each mapped to their own data file. + - The regular FPKM values are excluded because [FPKM-UQ provides a more stable metric](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#upper-quartile-fpkm). +- Transformations: see [Genomic data transformations](#genomic-data-transformations) + + + +## Mutation data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.masked_somatic_mutation_hg38_gdc_r40`. ISB-CGC data was created in July 2024. +- The MAF is annotated with Genome Nexus in order to avoid issues with the isoform mapping. Parameters used: + - Endpoint: https://grch38.genomenexus.org/ + - Isoform override: mskcc + - Replace gene symbols and Entrez IDs + - Post interval size: 500 +- Mutation data may be missing for some samples-- this reflects a lack of data availability in ISB-CGC. + +## Expression data transformations (CNA / mRNA) + +- Ensembl gene IDs are mapped to Entrez IDs using the [Genome Nexus hg38 canonical transcript file](https://github.com/genome-nexus/genome-nexus-importer/blob/master/data/grch38_ensembl95/export/ensembl_biomart_canonical_transcripts_per_hgnc.txt). Any genes that cannot be converted using this file are dropped. + - Prior to conversion, we also filter out a small number of duplicate Ensembl genes. These genes have copies containing data for both the X and the Y chromosomes. +- If a sample has multiple aliquots, it has to be condensed to 1 before it can imported into cBioPortal. This is done by choosing the aliquot ID with the highest sort value (eg. highest plate number), following [the same policy](https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844334036/FAQ#FAQ-replicateFilteringQ%3AWhatdoyoudowhenmultiplealiquotbarcodesexistforagivensample%2Fportion%2Fanalytecombination%3F) used by GDAC used to condense aliquot data in their studies. + +## Post-processing steps + + - Samples that lack any genomic data are removed from the clinical sample file. + - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - Case lists are generated under `case_lists/` using a curation-provided script. + - The validator script is run and the HTML report is saved under `validation_reports/`. + +## List of remapped columns + +### Clinical patient + +| Original | cBioPortal | +|---|---| +| submitter_id | PATIENT_ID | +| case_id | OTHER_PATIENT_ID | +| demo__ethnicity | ETHNICITY | +| demo__gender | SEX | +| demo__race | RACE | +| demo__vital_status | VITAL_STATUS | +| diag__age_at_diagnosis | AGE | +| diag__classification_of_tumor | TUMOR_CLASSIFICATION | +| diag__cog_neuroblastoma_risk_group | COG_NEUROBLASTOMA_RISK_GROUP | +| diag__icd_10_code | ICD_10 | +| diag__inss_stage | INSS_STAGE | +| diag__last_known_disease_status | DISEASE_STATUS | +| diag__metastasis_at_diagnosis | METASTASIS_AT_DIAGNOSIS | +| diag__morphology | MORPHOLOGY | +| diag__path__necrosis_percent | PATHOLOGY_NECROSIS_PERCENT | +| diag__primary_diagnosis | PRIMARY_DIAGNOSIS | +| diag__site_of_resection_or_biopsy | BIOPSY_SITE | +| diag__year_of_diagnosis | YEAR_OF_DIAGNOSIS | +| disease_type | DISEASE_TYPE | +| index_date | INDEX_DATE | +| primary_site | PRIMARY_SITE_PATIENT | +| proj__name | PROJECT_NAME | +| proj__project_id | PROJECT_ID | + + +### Clinical sample + +| Original | cBioPortal | +|---|---| +| case_barcode | PATIENT_ID | +| sample_barcode | SAMPLE_ID | +| sample_gdc_id | OTHER_SAMPLE_ID | +| sample_type_name | SAMPLE_TYPE | +| primary_site | PRIMARY_SITE | +| days_to_collection | DAYS_TO_COLLECTION | +| days_to_sample_procurement | DAYS_TO_SPECIMEN_COLLECTION | +| is_ffpe | IS_FFPE | + + + +### Mutation + +| Original | cBioPortal | +|---|---| +| sample_barcode_tumor | Tumor_Sample_Barcode | +| sample_barcode_normal | Matched_Norm_Sample_Barcode | \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/case_lists/cases_all.txt b/crdc/gdc/os_target_gdc/case_lists/cases_all.txt new file mode 100644 index 0000000000..774cb9393d --- /dev/null +++ b/crdc/gdc/os_target_gdc/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: os_target_gdc +stable_id: os_target_gdc_all +case_list_name: All samples +case_list_description: All samples (159 samples) +case_list_category: all_cases_in_study +case_list_ids: TARGET-40-PASRNE-01A TARGET-40-PARVXK-01A TARGET-40-NAAHBI-01A TARGET-40-NAAHBY-01A TARGET-40-NAASJK-01A TARGET-40-NAAHBJ-01A TARGET-40-PATJVI-01A TARGET-40-PALHRL-01A TARGET-40-PARGTM-01A TARGET-40-PANGRW-01A TARGET-40-PASUUH-01A TARGET-40-NAAWDT-01A TARGET-40-PANVJJ-01A TARGET-40-PAMHYN-01A TARGET-40-0A4I48-01A TARGET-40-PAPXWB-01A TARGET-40-PAUHGA-01A TARGET-40-PALKDP-01A TARGET-40-0A4I3S-01A TARGET-40-PALWWX-01A TARGET-40-NAAHBZ-01A TARGET-40-0A4I4E-01A TARGET-40-PATAWV-01A TARGET-40-NAAEDH-06A TARGET-40-PALIXF-01A TARGET-40-NAAWHH-01A TARGET-40-NAAECZ-01A TARGET-40-NAAHBY-02A TARGET-40-NAAWGC-01A TARGET-40-PAMLKS-01A TARGET-40-PANPUM-01A TARGET-40-0A4I9K-01A TARGET-40-NAAEDH-08A TARGET-40-NAAGJV-01A TARGET-40-NAAHDL-01A TARGET-40-PAUXPZ-01A TARGET-40-PASKZZ-01A TARGET-40-PAMJXS-01A TARGET-40-PANZHX-01A TARGET-40-NAAGJY-01A TARGET-40-0A4HX8-01A TARGET-40-NAAGJT-01A TARGET-40-PASYUK-01A TARGET-40-0A4I4O-01A TARGET-40-0A4I65-01A TARGET-40-PAVCLP-01A TARGET-40-PAMTCM-01A TARGET-40-0A4I0U-01A TARGET-40-0A4I0W-01A TARGET-40-PARKAF-01A TARGET-40-PAUBIT-01A TARGET-40-PAVLIB-01A TARGET-40-NAAGJK-01A TARGET-40-NAAGKC-01A TARGET-40-PAUTWB-01A TARGET-40-NAAHBS-01A TARGET-40-0A4HMC-01A TARGET-40-NAAWEW-01A TARGET-40-PASNZV-01A TARGET-40-PAVXDP-01A TARGET-40-PATMPU-01A TARGET-40-PANSEN-01A TARGET-40-0A4I0Q-01A TARGET-40-PAUUML-01A TARGET-40-PAPWWC-01A TARGET-40-NAAGJU-01A TARGET-40-NAAWDK-01A TARGET-40-0A4I42-01A TARGET-40-NAAWGR-01A TARGET-40-NAAWGJ-01A TARGET-40-PALKGN-01A TARGET-40-PARBGW-01A TARGET-40-PAVDSN-01A TARGET-40-0A4HXS-01A TARGET-40-NAAHDI-01A TARGET-40-0A4I0S-01A TARGET-40-NAAWEZ-01A TARGET-40-0A4I3W-01A TARGET-40-PANXSC-01A TARGET-40-PAVDTY-01A TARGET-40-PASEFS-01A TARGET-40-PAKUZU-01A TARGET-40-PAPKWD-01A TARGET-40-NAAHBP-02A TARGET-40-NAASJI-01A TARGET-40-NAAHBP-01A TARGET-40-PAVCHD-01A TARGET-40-NAAHDF-02A TARGET-40-PATKSS-01A TARGET-40-NAAGJR-01A TARGET-40-0A4I6O-01A TARGET-40-NAAGKG-01A TARGET-40-NAAGJP-01A TARGET-40-PATEEM-01A TARGET-40-PAMYYJ-01A TARGET-40-PAPNVD-01A TARGET-40-NAAEDB-01A TARGET-40-NAAGKM-01A TARGET-40-PATPBS-01A TARGET-40-NAAGKL-01A TARGET-40-PATUXZ-01A TARGET-40-NAAIBW-01A TARGET-40-PANMIG-01A TARGET-40-PARDAX-01A TARGET-40-PAPFLB-01A TARGET-40-PAPIJR-01A TARGET-40-PANZZJ-01A TARGET-40-NAAEDI-06A TARGET-40-PAVECB-01A TARGET-40-NAAHBU-01A TARGET-40-PALFYN-01A TARGET-40-PAVPHS-01A TARGET-40-PATMXR-01A TARGET-40-NAAWHG-01A TARGET-40-PANFZN-01A TARGET-40-0A4I4A-01A TARGET-40-0A4HLD-01A TARGET-40-0A4I4M-01A TARGET-40-PAPXGT-01A TARGET-40-NAAHBU-02A TARGET-40-NAAHDE-02A TARGET-40-0A4I8O-01A TARGET-40-NAAGJM-01A TARGET-40-PAUVUL-01A TARGET-40-PAMRHD-01A TARGET-40-PAUKXW-01A TARGET-40-PAVUKR-01A TARGET-40-PASEBY-01A TARGET-40-PARFTG-01A TARGET-40-PAVALD-01A TARGET-40-PAKFVX-01A TARGET-40-NAAEDH-01A TARGET-40-NAAGJX-01A TARGET-40-NAAWFT-01A TARGET-40-0A4I8U-01A TARGET-40-NAAVMJ-01A TARGET-40-0A4HY5-01A TARGET-40-NAAGJS-01A TARGET-40-PATMIF-01A TARGET-40-PAMHLF-01A TARGET-40-PANGPE-01A TARGET-40-PALECC-01A TARGET-40-NAAEDA-01A TARGET-40-0A4HXO-01A TARGET-40-PASSLM-01A TARGET-40-NAAEDI-08A TARGET-40-PALZGU-01A TARGET-40-NAAIBU-01A TARGET-40-PAKZZK-01A TARGET-40-PAUJZR-01A TARGET-40-0A4I5B-01A TARGET-40-PAMEKS-01A TARGET-40-PAKXLD-01A TARGET-40-NAAWGG-01A TARGET-40-PAUTYB-01A TARGET-40-PARJXU-01A TARGET-40-PAPVYW-01A TARGET-40-PAUYTT-01A TARGET-40-PASFCV-01A diff --git a/crdc/gdc/os_target_gdc/case_lists/cases_cna.txt b/crdc/gdc/os_target_gdc/case_lists/cases_cna.txt new file mode 100644 index 0000000000..518c4c2ccb --- /dev/null +++ b/crdc/gdc/os_target_gdc/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: os_target_gdc +stable_id: os_target_gdc_cna +case_list_name: Samples with CNA data +case_list_description: Samples with CNA data (81 samples) +case_list_category: all_cases_with_cna_data +case_list_ids: TARGET-40-PASRNE-01A TARGET-40-PAMYYJ-01A TARGET-40-PAPNVD-01A TARGET-40-PATJVI-01A TARGET-40-PALHRL-01A TARGET-40-PANGRW-01A TARGET-40-PATPBS-01A TARGET-40-PASUUH-01A TARGET-40-PATUXZ-01A TARGET-40-PANVJJ-01A TARGET-40-PAMHYN-01A TARGET-40-0A4I48-01A TARGET-40-PANMIG-01A TARGET-40-PARDAX-01A TARGET-40-PALKDP-01A TARGET-40-0A4I3S-01A TARGET-40-PALWWX-01A TARGET-40-0A4I4E-01A TARGET-40-PAPFLB-01A TARGET-40-PATAWV-01A TARGET-40-PAPIJR-01A TARGET-40-PAVECB-01A TARGET-40-PALFYN-01A TARGET-40-PAMLKS-01A TARGET-40-PANPUM-01A TARGET-40-PATMXR-01A TARGET-40-0A4I9K-01A TARGET-40-0A4HLD-01A TARGET-40-PAUXPZ-01A TARGET-40-0A4I4M-01A TARGET-40-PASKZZ-01A TARGET-40-PANZHX-01A TARGET-40-PAPXGT-01A TARGET-40-0A4HX8-01A TARGET-40-PASYUK-01A TARGET-40-0A4I4O-01A TARGET-40-0A4I65-01A TARGET-40-PAUVUL-01A TARGET-40-PAMRHD-01A TARGET-40-PAVCLP-01A TARGET-40-PASEBY-01A TARGET-40-0A4I0W-01A TARGET-40-PARKAF-01A TARGET-40-PAUBIT-01A TARGET-40-PARFTG-01A TARGET-40-PAVALD-01A TARGET-40-PAKFVX-01A TARGET-40-PAUTWB-01A TARGET-40-0A4HMC-01A TARGET-40-0A4I8U-01A TARGET-40-PASNZV-01A TARGET-40-0A4HY5-01A TARGET-40-PATMIF-01A TARGET-40-PATMPU-01A TARGET-40-PAMHLF-01A TARGET-40-PANSEN-01A TARGET-40-0A4I0Q-01A TARGET-40-PANGPE-01A TARGET-40-PALECC-01A TARGET-40-PASSLM-01A TARGET-40-PAUUML-01A TARGET-40-0A4I42-01A TARGET-40-PALZGU-01A TARGET-40-PAKZZK-01A TARGET-40-PALKGN-01A TARGET-40-PARBGW-01A TARGET-40-0A4HXS-01A TARGET-40-0A4I5B-01A TARGET-40-PAMEKS-01A TARGET-40-PAKXLD-01A TARGET-40-PANXSC-01A TARGET-40-PAVDTY-01A TARGET-40-PASEFS-01A TARGET-40-PAUTYB-01A TARGET-40-PAKUZU-01A TARGET-40-PARJXU-01A TARGET-40-PAPVYW-01A TARGET-40-PATKSS-01A TARGET-40-PAUYTT-01A TARGET-40-0A4I6O-01A TARGET-40-PASFCV-01A diff --git a/crdc/gdc/os_target_gdc/case_lists/cases_cnaseq.txt b/crdc/gdc/os_target_gdc/case_lists/cases_cnaseq.txt new file mode 100644 index 0000000000..c6fea6d5e8 --- /dev/null +++ b/crdc/gdc/os_target_gdc/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: os_target_gdc +stable_id: os_target_gdc_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (66 samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: TARGET-40-PASRNE-01A TARGET-40-PASEBY-01A TARGET-40-0A4I0W-01A TARGET-40-PAMYYJ-01A TARGET-40-PAPNVD-01A TARGET-40-PARKAF-01A TARGET-40-PARFTG-01A TARGET-40-PATJVI-01A TARGET-40-PALHRL-01A TARGET-40-PAKFVX-01A TARGET-40-PANGRW-01A TARGET-40-PATPBS-01A TARGET-40-PASUUH-01A TARGET-40-PATUXZ-01A TARGET-40-PANVJJ-01A TARGET-40-PAMHYN-01A TARGET-40-0A4I48-01A TARGET-40-PANMIG-01A TARGET-40-PARDAX-01A TARGET-40-0A4HMC-01A TARGET-40-0A4I8U-01A TARGET-40-PALKDP-01A TARGET-40-0A4I3S-01A TARGET-40-PASNZV-01A TARGET-40-0A4HY5-01A TARGET-40-PALWWX-01A TARGET-40-0A4I4E-01A TARGET-40-PAPFLB-01A TARGET-40-PATAWV-01A TARGET-40-PAPIJR-01A TARGET-40-PATMPU-01A TARGET-40-PATMIF-01A TARGET-40-PAMHLF-01A TARGET-40-PANSEN-01A TARGET-40-0A4I0Q-01A TARGET-40-PANGPE-01A TARGET-40-PALECC-01A TARGET-40-PASSLM-01A TARGET-40-PALFYN-01A TARGET-40-PALZGU-01A TARGET-40-PAMLKS-01A TARGET-40-PAKZZK-01A TARGET-40-PANPUM-01A TARGET-40-PATMXR-01A TARGET-40-0A4I9K-01A TARGET-40-PARBGW-01A TARGET-40-0A4HLD-01A TARGET-40-0A4HXS-01A TARGET-40-0A4I5B-01A TARGET-40-PASKZZ-01A TARGET-40-PAMEKS-01A TARGET-40-PANZHX-01A TARGET-40-PAPXGT-01A TARGET-40-PAKXLD-01A TARGET-40-0A4HX8-01A TARGET-40-PANXSC-01A TARGET-40-PASYUK-01A TARGET-40-0A4I4O-01A TARGET-40-0A4I65-01A TARGET-40-PASEFS-01A TARGET-40-PAKUZU-01A TARGET-40-PARJXU-01A TARGET-40-PAPVYW-01A TARGET-40-PAMRHD-01A TARGET-40-0A4I6O-01A TARGET-40-PASFCV-01A diff --git a/crdc/gdc/os_target_gdc/case_lists/cases_sequenced.txt b/crdc/gdc/os_target_gdc/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..56f9934be1 --- /dev/null +++ b/crdc/gdc/os_target_gdc/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: os_target_gdc +stable_id: os_target_gdc_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (143 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: TARGET-40-PASRNE-01A TARGET-40-PARVXK-01A TARGET-40-NAAHBI-01A TARGET-40-NAAHBY-01A TARGET-40-NAASJK-01A TARGET-40-NAAHBJ-01A TARGET-40-PATJVI-01A TARGET-40-PALHRL-01A TARGET-40-PARGTM-01A TARGET-40-PANGRW-01A TARGET-40-PASUUH-01A TARGET-40-NAAWDT-01A TARGET-40-PANVJJ-01A TARGET-40-PAPXWB-01A TARGET-40-PAUHGA-01A TARGET-40-PAMHYN-01A TARGET-40-0A4I48-01A TARGET-40-PALKDP-01A TARGET-40-0A4I3S-01A TARGET-40-PALWWX-01A TARGET-40-NAAHBZ-01A TARGET-40-0A4I4E-01A TARGET-40-PATAWV-01A TARGET-40-NAAEDH-06A TARGET-40-PALIXF-01A TARGET-40-NAAWHH-01A TARGET-40-NAAECZ-01A TARGET-40-NAAHBY-02A TARGET-40-NAAWGC-01A TARGET-40-PAMLKS-01A TARGET-40-PANPUM-01A TARGET-40-0A4I9K-01A TARGET-40-NAAEDH-08A TARGET-40-NAAGJV-01A TARGET-40-NAAHDL-01A TARGET-40-PASKZZ-01A TARGET-40-PAMJXS-01A TARGET-40-PANZHX-01A TARGET-40-NAAGJY-01A TARGET-40-0A4HX8-01A TARGET-40-NAAGJT-01A TARGET-40-PASYUK-01A TARGET-40-0A4I4O-01A TARGET-40-0A4I65-01A TARGET-40-PAMTCM-01A TARGET-40-0A4I0U-01A TARGET-40-0A4I0W-01A TARGET-40-PARKAF-01A TARGET-40-PAVLIB-01A TARGET-40-NAAGJK-01A TARGET-40-NAAGKC-01A TARGET-40-NAAHBS-01A TARGET-40-0A4HMC-01A TARGET-40-NAAWEW-01A TARGET-40-PASNZV-01A TARGET-40-PAVXDP-01A TARGET-40-PATMPU-01A TARGET-40-PANSEN-01A TARGET-40-0A4I0Q-01A TARGET-40-PAPWWC-01A TARGET-40-NAAGJU-01A TARGET-40-NAAWDK-01A TARGET-40-NAAWGR-01A TARGET-40-NAAWGJ-01A TARGET-40-PARBGW-01A TARGET-40-PAVDSN-01A TARGET-40-0A4HXS-01A TARGET-40-NAAHDI-01A TARGET-40-NAAWEZ-01A TARGET-40-0A4I3W-01A TARGET-40-PANXSC-01A TARGET-40-PASEFS-01A TARGET-40-PAKUZU-01A TARGET-40-NAASJI-01A TARGET-40-NAAHBP-01A TARGET-40-NAAHBP-02A TARGET-40-PAPKWD-01A TARGET-40-PAVCHD-01A TARGET-40-NAAHDF-02A TARGET-40-NAAGJR-01A TARGET-40-0A4I6O-01A TARGET-40-NAAGKG-01A TARGET-40-NAAGJP-01A TARGET-40-PATEEM-01A TARGET-40-PAMYYJ-01A TARGET-40-PAPNVD-01A TARGET-40-NAAEDB-01A TARGET-40-NAAGKM-01A TARGET-40-PATPBS-01A TARGET-40-NAAGKL-01A TARGET-40-PATUXZ-01A TARGET-40-NAAIBW-01A TARGET-40-PANMIG-01A TARGET-40-PARDAX-01A TARGET-40-PAPFLB-01A TARGET-40-PAPIJR-01A TARGET-40-PANZZJ-01A TARGET-40-NAAEDI-06A TARGET-40-NAAHBU-01A TARGET-40-PALFYN-01A TARGET-40-PAVPHS-01A TARGET-40-PATMXR-01A TARGET-40-NAAWHG-01A TARGET-40-PANFZN-01A TARGET-40-0A4HLD-01A TARGET-40-0A4I4A-01A TARGET-40-PAPXGT-01A TARGET-40-NAAHBU-02A TARGET-40-NAAHDE-02A TARGET-40-0A4I8O-01A TARGET-40-NAAGJM-01A TARGET-40-PAMRHD-01A TARGET-40-PAUKXW-01A TARGET-40-PAVUKR-01A TARGET-40-PASEBY-01A TARGET-40-PARFTG-01A TARGET-40-PAKFVX-01A TARGET-40-NAAEDH-01A TARGET-40-NAAGJX-01A TARGET-40-NAAWFT-01A TARGET-40-0A4I8U-01A TARGET-40-NAAVMJ-01A TARGET-40-0A4HY5-01A TARGET-40-NAAGJS-01A TARGET-40-PATMIF-01A TARGET-40-PAMHLF-01A TARGET-40-PANGPE-01A TARGET-40-PALECC-01A TARGET-40-NAAEDA-01A TARGET-40-0A4HXO-01A TARGET-40-PASSLM-01A TARGET-40-NAAEDI-08A TARGET-40-NAAIBU-01A TARGET-40-PALZGU-01A TARGET-40-PAKZZK-01A TARGET-40-PAUJZR-01A TARGET-40-0A4I5B-01A TARGET-40-PAMEKS-01A TARGET-40-PAKXLD-01A TARGET-40-NAAWGG-01A TARGET-40-PARJXU-01A TARGET-40-PAPVYW-01A TARGET-40-PASFCV-01A diff --git a/crdc/gdc/os_target_gdc/data_clinical_patient.txt b/crdc/gdc/os_target_gdc/data_clinical_patient.txt new 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a/crdc/gdc/os_target_gdc/data_mrna_seq_fpkm.txt b/crdc/gdc/os_target_gdc/data_mrna_seq_fpkm.txt new file mode 100644 index 0000000000..06d0a501c6 --- /dev/null +++ b/crdc/gdc/os_target_gdc/data_mrna_seq_fpkm.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2411e5fee3a207682f72fabc5d311f31302c6c62143191e5516a99a251ad2a62 +size 21937580 diff --git a/crdc/gdc/os_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt b/crdc/gdc/os_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..fc26324a7c --- /dev/null +++ b/crdc/gdc/os_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8788b79794a842919aad8c30a32e65b290af7ba212dc1e58dd3d55c3d9255eb2 +size 26874837 diff --git a/crdc/gdc/os_target_gdc/data_mrna_seq_read_counts.txt b/crdc/gdc/os_target_gdc/data_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..b5ebd025ce --- /dev/null +++ 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sha256:c29d10b763f85ee125d4060cbc25df1fd81a1ea55c06eada19075221cdb74558 +size 22361573 diff --git a/crdc/gdc/os_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/os_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..c9c4afabe7 --- /dev/null +++ b/crdc/gdc/os_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b3845e53fa17f3095667eea8903dca2a4e5c5c9909d8bfe32d0875aa3a6167b6 +size 26818680 diff --git a/crdc/gdc/os_target_gdc/data_mutations.txt b/crdc/gdc/os_target_gdc/data_mutations.txt new file mode 100644 index 0000000000..1e0d16362c --- /dev/null +++ b/crdc/gdc/os_target_gdc/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:789b0035d2226beda5a7c11b52aadf98715f89e595cb1c7fe6734c27af3ef8c7 +size 1281537 diff --git a/crdc/gdc/os_target_gdc/data_timeline_status.txt b/crdc/gdc/os_target_gdc/data_timeline_status.txt new file mode 100644 index 0000000000..c93130ebc7 --- /dev/null +++ b/crdc/gdc/os_target_gdc/data_timeline_status.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:25934baba4d20f036e687f17f2227c17be2556f06b3611874b3ba0106af3dc83 +size 13109 diff --git a/crdc/gdc/os_target_gdc/meta_clinical_patient.txt b/crdc/gdc/os_target_gdc/meta_clinical_patient.txt new file mode 100644 index 0000000000..9e1a4f98ec --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_clinical_sample.txt b/crdc/gdc/os_target_gdc/meta_clinical_sample.txt new file mode 100644 index 0000000000..fb6f598f95 --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_cna.txt b/crdc/gdc/os_target_gdc/meta_cna.txt new file mode 100644 index 0000000000..f6bf98dcd0 --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +stable_id: cna +show_profile_in_analysis_tab: true +profile_name: Putative copy-number alterations from GISTIC +profile_description: Putative copy-number from GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +data_filename: data_cna.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_mrna_seq_fpkm.txt b/crdc/gdc/os_target_gdc/meta_mrna_seq_fpkm.txt new file mode 100644 index 0000000000..0c6937228b --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_mrna_seq_fpkm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_fpkm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (FPKM) +profile_description: mRNA expression from capture (RNA Seq FPKM) +data_filename: data_mrna_seq_fpkm.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt b/crdc/gdc/os_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..285dcc9ec2 --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_fpkm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression fpkm Zscores +profile_description: mRNA expression from capture (RNA Seq FPKM) zscores +data_filename: data_mrna_seq_fpkm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_mrna_seq_read_counts.txt b/crdc/gdc/os_target_gdc/meta_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..572e08f099 --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_mrna_seq_read_counts.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: rna_seq_mrna +show_profile_in_analysis_tab: false +profile_name: mRNA expression +profile_description: Expression levels +data_filename: data_mrna_seq_read_counts.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt b/crdc/gdc/os_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..6ca5d5f37a --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_read_counts_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression Zscores +profile_description: mRNA expression from capture read count zscores +data_filename: data_mrna_seq_read_counts_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_mrna_seq_tpm.txt b/crdc/gdc/os_target_gdc/meta_mrna_seq_tpm.txt new file mode 100644 index 0000000000..828b8a60a1 --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_mrna_seq_tpm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_tpm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (TPM) +profile_description: mRNA expression from capture (RNA Seq TPM) +data_filename: data_mrna_seq_tpm.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/os_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..6c05058107 --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_tpm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression tpm Zscores +profile_description: mRNA expression from capture (RNA Seq TPM) zscores +data_filename: data_mrna_seq_tpm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_mutations.txt b/crdc/gdc/os_target_gdc/meta_mutations.txt new file mode 100644 index 0000000000..0a667a4553 --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +data_filename: data_mutations.txt +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutation data. +profile_name: Mutations \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_study.txt b/crdc/gdc/os_target_gdc/meta_study.txt new file mode 100644 index 0000000000..a42a077df0 --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: os +cancer_study_identifier: os_target_gdc +name: Osteosarcoma (TARGET, GDC) +short_name: OS +description: TARGET Osteosarcoma. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +reference_genome: hg38 +groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_timeline_status.txt b/crdc/gdc/os_target_gdc/meta_timeline_status.txt new file mode 100644 index 0000000000..c09776121d --- /dev/null +++ b/crdc/gdc/os_target_gdc/meta_timeline_status.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: os_target_gdc +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_timeline_status.txt \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/validation_reports/os_target_gdc-validation.html b/crdc/gdc/os_target_gdc/validation_reports/os_target_gdc-validation.html new file mode 100644 index 0000000000..ae634500a4 --- /dev/null +++ b/crdc/gdc/os_target_gdc/validation_reports/os_target_gdc-validation.html @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f3f6dd62005980cca4117bd76d1da60c845894001be769ae50f1def516a574d8 +size 3859973 diff --git a/crdc/gdc/wt_target_gdc/README.md b/crdc/gdc/wt_target_gdc/README.md new file mode 100644 index 0000000000..dd89847203 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/README.md @@ -0,0 +1,149 @@ +# Comments & assumptions made during curation + +## General + +- Study is updated once every 3 months with latest data from [ISB-CGC BigQuery tables](https://isb-cgc.appspot.com/bq_meta_search/) + - The ISB-CGC tables allow easy access to data collected from multiple NCI-CRDC repositories including the GDC, PDC, and others. The TARGET data in this study comes from the GDC and is accessed through these tables. +- Reference genome used: hg38 +- TARGET started using the hg38 genome as of GDC release 32. For more information, refer to the [GDC release notes](https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-320). + +- Only tumor sample data is included (no normal samples) +- [GDC project webpage](https://portal.gdc.cancer.gov/projects/TARGET-WT) + +## Clinical data + +- **Patient data:** Retrieved from `isb-cgc-bq.TARGET_versioned.clinical_gdc_r40`. ISB-CGC data was created in April 2024. +- **Sample data:** Retrieved from `isb-cgc-bq.TARGET_versioned.per_sample_file_metadata_hg38_gdc_r40`. ISB-CGC data was created in April 2024. + +### Survival data + +Survival fields are calculated from the clinical data and added as new columns in the clinical file. + +- `OS_STATUS` is converted from `demo__vital_status` +- `OS_MONTHS` is converted from `demo__days_to_death`, falls back to `diag__days_to_last_follow_up` + + + + +### Timeline data + +- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +- For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. + +- Birth timeline events are removed, as they (1) push other events to the far right of the graph and (2) can potentially be used to identify the patient. + +The following status values are supported in `data_timeline_status.txt`: + +- `__time0__` +- `demo__days_to_death` +- `diag__days_to_last_follow_up` +### Other transformations + +- `"not reported"` values are replaced with blanks. +- If a clinical field is missing for the entire study, the column is removed from the data file. +- `RACE`, `ETHNICITY`, and `SEX` are capitalized. +- `AGE` is converted from days to years. + +## CNA data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.copy_number_gene_level_hg38_gdc_r36`. ISB-CGC data was created in March 2023. +- Transformations + - Copy number values from the BigQuery tables are converted from [ASCAT](https://www.pnas.org/doi/10.1073/pnas.1009843107https://www.pnas.org/doi/10.1073/pnas.1009843107) to GISTIC 2.0 using the following thresholds: + +| ASCAT Value | GISTIC Value | Meaning | +|---|---|---| +| X = 0 | -2 | Deep loss | +| X = 1 | -1 | Single-copy loss | +| X = 2 | 0 | Diploid | +| 2 < X < 7 | 1 | Low-level gain | +| 7 ≤ X | 2 | Amplification | + +Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on the cBioPortal website. As a result these conversion thresholds affect how many samples show up in the CNA chart, which can be inconsistent with legacy versions of this study. We chose ASCAT ≥ 7 as the amplification threshold because it resulted in the least deviation from our legacy studies. + + + +## mRNA Expression data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.RNAseq_hg38_gdc_r35`. ISB-CGC data was created in December 2022. +- The `unstranded`, `tpm_unstranded`, and `fpkm_uq_unstranded` columns are pulled and each mapped to their own data file. + - The regular FPKM values are excluded because [FPKM-UQ provides a more stable metric](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#upper-quartile-fpkm). +- Transformations: see [Genomic data transformations](#genomic-data-transformations) + + + +## Mutation data + +- Retrieved from `isb-cgc-bq.TARGET_versioned.masked_somatic_mutation_hg38_gdc_r40`. ISB-CGC data was created in July 2024. +- The MAF is annotated with Genome Nexus in order to avoid issues with the isoform mapping. Parameters used: + - Endpoint: https://grch38.genomenexus.org/ + - Isoform override: mskcc + - Replace gene symbols and Entrez IDs + - Post interval size: 500 +- Mutation data may be missing for some samples-- this reflects a lack of data availability in ISB-CGC. + +## Expression data transformations (CNA / mRNA) + +- Ensembl gene IDs are mapped to Entrez IDs using the [Genome Nexus hg38 canonical transcript file](https://github.com/genome-nexus/genome-nexus-importer/blob/master/data/grch38_ensembl95/export/ensembl_biomart_canonical_transcripts_per_hgnc.txt). Any genes that cannot be converted using this file are dropped. + - Prior to conversion, we also filter out a small number of duplicate Ensembl genes. These genes have copies containing data for both the X and the Y chromosomes. +- If a sample has multiple aliquots, it has to be condensed to 1 before it can imported into cBioPortal. This is done by choosing the aliquot ID with the highest sort value (eg. highest plate number), following [the same policy](https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844334036/FAQ#FAQ-replicateFilteringQ%3AWhatdoyoudowhenmultiplealiquotbarcodesexistforagivensample%2Fportion%2Fanalytecombination%3F) used by GDAC used to condense aliquot data in their studies. + +## Post-processing steps + + - Samples that lack any genomic data are removed from the clinical sample file. + - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - Case lists are generated under `case_lists/` using a curation-provided script. + - The validator script is run and the HTML report is saved under `validation_reports/`. + +## List of remapped columns + +### Clinical patient + +| Original | cBioPortal | +|---|---| +| submitter_id | PATIENT_ID | +| case_id | OTHER_PATIENT_ID | +| demo__ethnicity | ETHNICITY | +| demo__gender | SEX | +| demo__race | RACE | +| demo__vital_status | VITAL_STATUS | +| diag__age_at_diagnosis | AGE | +| diag__classification_of_tumor | TUMOR_CLASSIFICATION | +| diag__cog_neuroblastoma_risk_group | COG_NEUROBLASTOMA_RISK_GROUP | +| diag__icd_10_code | ICD_10 | +| diag__inss_stage | INSS_STAGE | +| diag__last_known_disease_status | DISEASE_STATUS | +| diag__metastasis_at_diagnosis | METASTASIS_AT_DIAGNOSIS | +| diag__morphology | MORPHOLOGY | +| diag__path__necrosis_percent | PATHOLOGY_NECROSIS_PERCENT | +| diag__primary_diagnosis | PRIMARY_DIAGNOSIS | +| diag__site_of_resection_or_biopsy | BIOPSY_SITE | +| diag__year_of_diagnosis | YEAR_OF_DIAGNOSIS | +| disease_type | DISEASE_TYPE | +| index_date | INDEX_DATE | +| primary_site | PRIMARY_SITE_PATIENT | +| proj__name | PROJECT_NAME | +| proj__project_id | PROJECT_ID | + + +### Clinical sample + +| Original | cBioPortal | +|---|---| +| case_barcode | PATIENT_ID | +| sample_barcode | SAMPLE_ID | +| sample_gdc_id | OTHER_SAMPLE_ID | +| sample_type_name | SAMPLE_TYPE | +| primary_site | PRIMARY_SITE | +| days_to_collection | DAYS_TO_COLLECTION | +| days_to_sample_procurement | DAYS_TO_SPECIMEN_COLLECTION | +| is_ffpe | IS_FFPE | + + + +### Mutation + +| Original | cBioPortal | +|---|---| +| sample_barcode_tumor | Tumor_Sample_Barcode | +| sample_barcode_normal | Matched_Norm_Sample_Barcode | \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/case_lists/cases_all.txt b/crdc/gdc/wt_target_gdc/case_lists/cases_all.txt new file mode 100644 index 0000000000..7e5c063b23 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: wt_target_gdc +stable_id: wt_target_gdc_all +case_list_name: All samples +case_list_description: All samples (132 samples) +case_list_category: all_cases_in_study +case_list_ids: TARGET-50-PAJNRL-01A TARGET-50-PAKECR-01A TARGET-50-PAKSCC-01A TARGET-50-PAJMRL-01A TARGET-50-PAJNDU-01A TARGET-50-PAKFYV-01A TARGET-50-PAJMUF-01A TARGET-50-PAJMVU-01A TARGET-50-PALERC-01A TARGET-50-PALGVY-01A TARGET-50-PAECJB-01A TARGET-50-PAKVET-01A TARGET-50-CAAAAJ-01A TARGET-50-CAAAAL-01A TARGET-50-PAKNRX-01A TARGET-50-PAKZHF-01A TARGET-50-PALGLU-01A TARGET-50-PALEZT-01A TARGET-50-PAJNBN-01A TARGET-50-PAEAFB-01A TARGET-50-PAJMKI-01A TARGET-50-PAJNZI-01A TARGET-50-PAJLUJ-06A TARGET-50-PAKPDF-01A TARGET-50-PALDTE-01A TARGET-50-PAJNCJ-01A TARGET-50-PAJPDN-01A TARGET-50-PAJMKN-01A TARGET-50-PAKSDG-01A TARGET-50-PAJMMY-01A TARGET-50-PAJPAU-01A TARGET-50-PAKXXF-01A TARGET-50-CAAAAS-01A TARGET-50-PAJLSP-01A TARGET-50-PAJNTJ-02A TARGET-50-PAJLKR-01A TARGET-50-PAJMLI-01A TARGET-50-PAKZER-01A TARGET-50-PAKNXS-01A TARGET-50-PALKCW-01A TARGET-50-PAJNGH-01A TARGET-50-PAJMFU-01A TARGET-50-PAKULH-01A TARGET-50-PAJLTH-01A TARGET-50-PAJLIP-01A TARGET-50-PAJMJT-01A TARGET-50-PAJNTJ-01A TARGET-50-PAJMEN-01A TARGET-50-PAJNZU-01A TARGET-50-PAJNNC-01A TARGET-50-PAJMFY-01A TARGET-50-PAKMSV-01A TARGET-50-PAJNJJ-01A TARGET-50-PAJPEW-01A TARGET-50-PAJPDC-02A TARGET-50-PALFME-02A TARGET-50-PAKUIT-01A TARGET-50-PAKRCC-01A TARGET-50-PAJNAV-01A TARGET-50-PAJNVE-01A TARGET-50-PALGAZ-01A TARGET-50-PAJMEP-01A TARGET-50-PAKJGM-01A TARGET-50-PALFME-01A TARGET-50-PAKYLT-01A TARGET-50-PALLFB-01A TARGET-50-PAJPHA-01A TARGET-50-PAJNSL-01A TARGET-50-PAJMKJ-01A TARGET-50-PALJIP-01A TARGET-50-PAJLNJ-01A TARGET-50-PAKFME-01A TARGET-50-CAAAAQ-01A TARGET-50-CAAAAP-01A TARGET-50-PAJNCC-01A TARGET-50-PAJMSE-01A TARGET-50-PAJLTI-01A TARGET-50-PAJMIZ-01A TARGET-50-PAJNEC-01A TARGET-50-PAKKSE-01A TARGET-50-PAJMVC-01A TARGET-50-PAKGZX-01A TARGET-50-PAJPGY-01A TARGET-50-PAKGMU-01A TARGET-50-PAJMXF-01A TARGET-50-PAKWPM-01A TARGET-50-CAAAAR-01A TARGET-50-PAEBXA-01A TARGET-50-PALFRD-01A TARGET-50-PAKGED-01A TARGET-50-PAJMEL-01A TARGET-50-PAKXWB-01A TARGET-50-PAJNAA-01A TARGET-50-CAAAAA-01A TARGET-50-CAAAAM-01A TARGET-50-PAKMUB-01A TARGET-50-PAJNCZ-01A TARGET-50-CAAAAC-01A TARGET-50-PAKZFK-01A TARGET-50-PAJNZK-01A TARGET-50-PAJNYT-01A TARGET-50-PAKYFC-01A TARGET-50-PAJNZS-01A TARGET-50-CAAAAB-01A TARGET-50-PAJPCM-01A TARGET-50-CAAAAH-01A TARGET-50-PAJLWT-01A TARGET-50-PAKRVH-01A TARGET-50-PALJIP-02A TARGET-50-PAJNRH-01A TARGET-50-PAJLKC-01A TARGET-50-PALDWP-01A TARGET-50-PAKNTW-01A TARGET-50-PAKNAL-01A TARGET-50-PALKRS-01A TARGET-50-PAJPDC-01A TARGET-50-PAJNGH-02A TARGET-50-PALLCK-01A TARGET-50-PAJNVX-01A TARGET-50-PAJLLF-01A TARGET-50-PAKKNS-01A TARGET-50-PAJNUP-01A TARGET-50-CAAAAO-01A TARGET-50-PAJNNR-01A TARGET-50-PAJNUS-01A TARGET-50-PAJMLZ-01A TARGET-50-PADXAY-01A TARGET-50-PADZUB-01A TARGET-50-PAJLPX-01A TARGET-50-PAJNLT-01A TARGET-50-PAKRZW-01A TARGET-50-PAJPAR-01A diff --git a/crdc/gdc/wt_target_gdc/case_lists/cases_sequenced.txt b/crdc/gdc/wt_target_gdc/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..76f1568b94 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: wt_target_gdc +stable_id: wt_target_gdc_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (42 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: TARGET-50-PALFME-02A TARGET-50-PAJNVE-01A TARGET-50-PAKECR-01A TARGET-50-PAJMEP-01A TARGET-50-PAJPCM-01A TARGET-50-PAJNTJ-02A TARGET-50-PAJLKR-01A TARGET-50-PAKFYV-01A TARGET-50-PALFME-01A TARGET-50-PAKYLT-01A TARGET-50-PAJLWT-01A TARGET-50-PAJNGH-01A TARGET-50-PAJNRH-01A TARGET-50-PAJLKC-01A TARGET-50-PALJIP-01A TARGET-50-PAJLNJ-01A TARGET-50-CAAAAP-01A TARGET-50-PAJMSE-01A TARGET-50-PAJMVC-01A TARGET-50-PAKVET-01A TARGET-50-PAJPDC-01A TARGET-50-PAJMJT-01A TARGET-50-PAJNGH-02A TARGET-50-PAJNTJ-01A TARGET-50-PAJNVX-01A TARGET-50-PALLCK-01A TARGET-50-CAAAAR-01A TARGET-50-PAJNUP-01A TARGET-50-PAKKNS-01A TARGET-50-PAJPAR-01A TARGET-50-PAJNNC-01A TARGET-50-PALGLU-01A TARGET-50-PAJNNR-01A TARGET-50-PAKMSV-01A TARGET-50-PAKXWB-01A TARGET-50-PADXAY-01A TARGET-50-PAKPDF-01A TARGET-50-CAAAAA-01A TARGET-50-PADZUB-01A TARGET-50-PAJMKN-01A TARGET-50-PAJNLT-01A TARGET-50-PAJPDC-02A diff --git a/crdc/gdc/wt_target_gdc/data_clinical_patient.txt b/crdc/gdc/wt_target_gdc/data_clinical_patient.txt new file mode 100644 index 0000000000..9acaa91b2e --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4d9cb617f15bf0f48a8a2b8ddd5c4968774e8395382b948e497fd604c5b9287c +size 153034 diff --git a/crdc/gdc/wt_target_gdc/data_clinical_sample.txt b/crdc/gdc/wt_target_gdc/data_clinical_sample.txt new file mode 100644 index 0000000000..66749b9862 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2071e0c6dd9dccc3379da90e7a0727d58e799688ea188cba88b85738c4ee24ff +size 80542 diff --git a/crdc/gdc/wt_target_gdc/data_mrna_seq_fpkm.txt b/crdc/gdc/wt_target_gdc/data_mrna_seq_fpkm.txt new file mode 100644 index 0000000000..f15aaa666e --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_mrna_seq_fpkm.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:63ee5d3f27dab2b929bdb2636662732370288170d4982fce4e18e11b8f240fd1 +size 32843035 diff --git a/crdc/gdc/wt_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt b/crdc/gdc/wt_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..66530387bc --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:27fbfad1b090223c862c367230204fcb6f7f8c3a069f7b22a0282e9c8cc1f5bd +size 39394509 diff --git a/crdc/gdc/wt_target_gdc/data_mrna_seq_read_counts.txt b/crdc/gdc/wt_target_gdc/data_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..5787a31f14 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_mrna_seq_read_counts.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3783089cf3bc5832f40d2e35fb42c4810b85469c506f47b84f279d36727ffb9d +size 16837760 diff --git a/crdc/gdc/wt_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt b/crdc/gdc/wt_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..c0536be8f1 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:68c02c7b3fd2028e06423bce3521ba61006f6a38438358a2a79791f97c306745 +size 38475980 diff --git a/crdc/gdc/wt_target_gdc/data_mrna_seq_tpm.txt b/crdc/gdc/wt_target_gdc/data_mrna_seq_tpm.txt new file mode 100644 index 0000000000..da7ef03be5 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_mrna_seq_tpm.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fee3a64307fbd0ceb1fd6457a8d071ada71a260b9ec08fb23dccddbd56d82249 +size 33637928 diff --git a/crdc/gdc/wt_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/wt_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..574358f354 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fc6470be33997c88ca559080494754b939d900487f5e83a84d6cb8c036aa228e +size 39271581 diff --git a/crdc/gdc/wt_target_gdc/data_mutations.txt b/crdc/gdc/wt_target_gdc/data_mutations.txt new file mode 100644 index 0000000000..47766156ec --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4dae64aba718c19431a84f497f31dc58ae33226fc04cbba6cb4534cbdac49075 +size 123168 diff --git a/crdc/gdc/wt_target_gdc/data_timeline_status.txt b/crdc/gdc/wt_target_gdc/data_timeline_status.txt new file mode 100644 index 0000000000..ed1b834592 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/data_timeline_status.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3da2b108cabfbbcef69875aa3f83780805f43695d10806fec92d4d6945a1493d +size 33613 diff --git a/crdc/gdc/wt_target_gdc/meta_clinical_patient.txt b/crdc/gdc/wt_target_gdc/meta_clinical_patient.txt new file mode 100644 index 0000000000..6c89309364 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_clinical_sample.txt b/crdc/gdc/wt_target_gdc/meta_clinical_sample.txt new file mode 100644 index 0000000000..8aa2b52e0f --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_mrna_seq_fpkm.txt b/crdc/gdc/wt_target_gdc/meta_mrna_seq_fpkm.txt new file mode 100644 index 0000000000..6d06265c06 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_mrna_seq_fpkm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_fpkm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (FPKM) +profile_description: mRNA expression from capture (RNA Seq FPKM) +data_filename: data_mrna_seq_fpkm.txt \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt b/crdc/gdc/wt_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..ee41dc80ce --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_fpkm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression fpkm Zscores +profile_description: mRNA expression from capture (RNA Seq FPKM) zscores +data_filename: data_mrna_seq_fpkm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_mrna_seq_read_counts.txt b/crdc/gdc/wt_target_gdc/meta_mrna_seq_read_counts.txt new file mode 100644 index 0000000000..423d60d297 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_mrna_seq_read_counts.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: rna_seq_mrna +show_profile_in_analysis_tab: false +profile_name: mRNA expression +profile_description: Expression levels +data_filename: data_mrna_seq_read_counts.txt \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt b/crdc/gdc/wt_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..2261205c87 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_mrna_seq_read_counts_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_read_counts_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression Zscores +profile_description: mRNA expression from capture read count zscores +data_filename: data_mrna_seq_read_counts_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_mrna_seq_tpm.txt b/crdc/gdc/wt_target_gdc/meta_mrna_seq_tpm.txt new file mode 100644 index 0000000000..383cefddfe --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_mrna_seq_tpm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_tpm +show_profile_in_analysis_tab: false +profile_name: mRNA expression (TPM) +profile_description: mRNA expression from capture (RNA Seq TPM) +data_filename: data_mrna_seq_tpm.txt \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt b/crdc/gdc/wt_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..5f300aeeb4 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_tpm_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA expression tpm Zscores +profile_description: mRNA expression from capture (RNA Seq TPM) zscores +data_filename: data_mrna_seq_tpm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_mutations.txt b/crdc/gdc/wt_target_gdc/meta_mutations.txt new file mode 100644 index 0000000000..616ab1da69 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +data_filename: data_mutations.txt +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutation data. +profile_name: Mutations \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_study.txt b/crdc/gdc/wt_target_gdc/meta_study.txt new file mode 100644 index 0000000000..7085157844 --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: wt +cancer_study_identifier: wt_target_gdc +name: Wilms' Tumor (TARGET, GDC) +short_name: WT +description: TARGET Wilms' Tumor. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +reference_genome: hg38 +groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_timeline_status.txt b/crdc/gdc/wt_target_gdc/meta_timeline_status.txt new file mode 100644 index 0000000000..55344d5c2a --- /dev/null +++ b/crdc/gdc/wt_target_gdc/meta_timeline_status.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: wt_target_gdc +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_timeline_status.txt \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/validation_reports/wt_target_gdc-validation.html b/crdc/gdc/wt_target_gdc/validation_reports/wt_target_gdc-validation.html new file mode 100644 index 0000000000..7e9117758f --- /dev/null +++ b/crdc/gdc/wt_target_gdc/validation_reports/wt_target_gdc-validation.html @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3c65ea5be4386405b88b95634bcf78c3720c7c6b8345b104a431c0b39832c720 +size 3021601 From 6993710026560c4790c2026214142a891180c269 Mon Sep 17 00:00:00 2001 From: cbioportal import user Date: Fri, 29 Nov 2024 00:40:56 -0500 Subject: [PATCH 2/6] Add TARGET studies to CRDC README --- crdc/README.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/crdc/README.md b/crdc/README.md index 662b01088c..9b11a41c40 100644 --- a/crdc/README.md +++ b/crdc/README.md @@ -12,6 +12,7 @@ Supported programs: - [TCGA](https://www.cancer.gov/ccg/research/genome-sequencing/tcga) - [CPTAC](https://gdc.cancer.gov/about-gdc/contributed-genomic-data-cancer-research/clinical-proteomic-tumor-analysis-consortium-cptac) +- [TARGET](https://www.cancer.gov/ccg/research/genome-sequencing/target) ### TCGA @@ -73,3 +74,18 @@ Supported programs: - [`pancreas_cptac_gdc`](https://www.cbioportal.org/study/summary?id=pancreas_cptac_gdc): [Pancreatic Cancer](https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22pancreas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) - [`rcc_cptac_gdc`](https://www.cbioportal.org/study/summary?id=rcc_cptac_gdc): [Renal Cell Carcinoma](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22Adenomas%20and%20Adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22Kidney%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) - [`uec_cptac_gdc`](https://www.cbioportal.org/study/summary?id=uec_cptac_gdc): [Uterine Endometrioid Carcinoma](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22Adenomas%20and%20Adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22Uterus%2C%20NOS%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) + +### TARGET + +- **Cancer type mapping:** Each study corresponds to one or more TARGET projects. The TARGET project suffix is converted to an OncoTree code, which is used for the name of the study. + - **Example:** For the TARGET project `TARGET-ALL-P2`, the `ALL-P2` suffix is taken and converted to the Oncotree code `BLL`. The resulting cBioPortal study is `bll_target_gdc`. + - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/oncotree_mappings/target.txt) + +#### List of TARGET cBioPortal Studies + +- [`bll_target_gdc`](https://www.cbioportal.org/study/summary?id=bll_target_gdc): TARGET-ALL-P2, [Acute Lymphoblastic Leukemia - Phase II](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P2) +- [`alal_target_gdc`](https://www.cbioportal.org/study/summary?id=alal_target_gdc): TARGET-ALL-P3, [Acute Lymphoblastic Leukemia - Phase III](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P3) +- [`aml_target_gdc`](https://www.cbioportal.org/study/summary?id=aml_target_gdc): TARGET-AML, [Acute Myeloid Leukemia](https://portal.gdc.cancer.gov/projects/TARGET-AML) +- [`nbl_target_gdc`](https://www.cbioportal.org/study/summary?id=nbl_target_gdc): TARGET-NBL, [Neuroblastoma](https://portal.gdc.cancer.gov/projects/TARGET-NBL) +- [`os_target_gdc`](https://www.cbioportal.org/study/summary?id=os_target_gdc): TARGET-OS, [Osteosarcoma](https://portal.gdc.cancer.gov/projects/TARGET-OS) +- [`wt_target_gdc`](https://www.cbioportal.org/study/summary?id=wt_target_gdc): TARGET-WT, [Wilms' Tumor](https://portal.gdc.cancer.gov/projects/TARGET-WT) From e7415590f50d85dba79e195daaaf388c830f6ed3 Mon Sep 17 00:00:00 2001 From: cbioportal import user Date: Fri, 29 Nov 2024 11:35:19 -0500 Subject: [PATCH 3/6] Fix order of bll_target_gdc in README --- crdc/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/crdc/README.md b/crdc/README.md index 9b11a41c40..ece05e9d1d 100644 --- a/crdc/README.md +++ b/crdc/README.md @@ -83,9 +83,9 @@ Supported programs: #### List of TARGET cBioPortal Studies -- [`bll_target_gdc`](https://www.cbioportal.org/study/summary?id=bll_target_gdc): TARGET-ALL-P2, [Acute Lymphoblastic Leukemia - Phase II](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P2) - [`alal_target_gdc`](https://www.cbioportal.org/study/summary?id=alal_target_gdc): TARGET-ALL-P3, [Acute Lymphoblastic Leukemia - Phase III](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P3) - [`aml_target_gdc`](https://www.cbioportal.org/study/summary?id=aml_target_gdc): TARGET-AML, [Acute Myeloid Leukemia](https://portal.gdc.cancer.gov/projects/TARGET-AML) +- [`bll_target_gdc`](https://www.cbioportal.org/study/summary?id=bll_target_gdc): TARGET-ALL-P2, [Acute Lymphoblastic Leukemia - Phase II](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P2) - [`nbl_target_gdc`](https://www.cbioportal.org/study/summary?id=nbl_target_gdc): TARGET-NBL, [Neuroblastoma](https://portal.gdc.cancer.gov/projects/TARGET-NBL) - [`os_target_gdc`](https://www.cbioportal.org/study/summary?id=os_target_gdc): TARGET-OS, [Osteosarcoma](https://portal.gdc.cancer.gov/projects/TARGET-OS) - [`wt_target_gdc`](https://www.cbioportal.org/study/summary?id=wt_target_gdc): TARGET-WT, [Wilms' Tumor](https://portal.gdc.cancer.gov/projects/TARGET-WT) From ed09069e02962654d26171cc2846938357d6bcf6 Mon Sep 17 00:00:00 2001 From: cbioportal import user Date: Sat, 30 Nov 2024 11:03:50 -0500 Subject: [PATCH 4/6] Update study meta files in response to JJ feedback --- crdc/gdc/alal_target_gdc/meta_study.txt | 2 +- crdc/gdc/aml_target_gdc/meta_study.txt | 2 +- crdc/gdc/bll_target_gdc/meta_study.txt | 2 +- crdc/gdc/nbl_target_gdc/meta_study.txt | 2 +- crdc/gdc/os_target_gdc/meta_study.txt | 2 +- crdc/gdc/wt_target_gdc/meta_study.txt | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/crdc/gdc/alal_target_gdc/meta_study.txt b/crdc/gdc/alal_target_gdc/meta_study.txt index ce75b406e0..2f73e20fa4 100644 --- a/crdc/gdc/alal_target_gdc/meta_study.txt +++ b/crdc/gdc/alal_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: alal cancer_study_identifier: alal_target_gdc name: Acute Leukemias of Ambiguous Lineage - Phase III (TARGET, GDC) short_name: ALAL -description: TARGET Acute Leukemias of Ambiguous Lineage - Phase III. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +description: TARGET Acute Leukemias of Ambiguous Lineage - Phase III. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/meta_study.txt b/crdc/gdc/aml_target_gdc/meta_study.txt index fb418aaff3..05c30e1aa2 100644 --- a/crdc/gdc/aml_target_gdc/meta_study.txt +++ b/crdc/gdc/aml_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: aml cancer_study_identifier: aml_target_gdc name: Acute Myeloid Leukemia (TARGET, GDC) short_name: AML -description: TARGET Acute Myeloid Leukemia. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +description: TARGET Acute Myeloid Leukemia. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/meta_study.txt b/crdc/gdc/bll_target_gdc/meta_study.txt index ab2f0de0ff..1778bf774b 100644 --- a/crdc/gdc/bll_target_gdc/meta_study.txt +++ b/crdc/gdc/bll_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: bll cancer_study_identifier: bll_target_gdc name: B-Lymphoblastic Leukemia/Lymphoma - Phase II (TARGET, GDC) short_name: BLL -description: TARGET B-Lymphoblastic Leukemia/Lymphoma - Phase II. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +description: TARGET B-Lymphoblastic Leukemia/Lymphoma - Phase II. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/meta_study.txt b/crdc/gdc/nbl_target_gdc/meta_study.txt index 9c24f0ba3b..7ee68c073b 100644 --- a/crdc/gdc/nbl_target_gdc/meta_study.txt +++ b/crdc/gdc/nbl_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: nbl cancer_study_identifier: nbl_target_gdc name: Neuroblastoma (TARGET, GDC) short_name: NBL -description: TARGET Neuroblastoma. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +description: TARGET Neuroblastoma. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/meta_study.txt b/crdc/gdc/os_target_gdc/meta_study.txt index a42a077df0..bd3f529855 100644 --- a/crdc/gdc/os_target_gdc/meta_study.txt +++ b/crdc/gdc/os_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: os cancer_study_identifier: os_target_gdc name: Osteosarcoma (TARGET, GDC) short_name: OS -description: TARGET Osteosarcoma. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +description: TARGET Osteosarcoma. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/meta_study.txt b/crdc/gdc/wt_target_gdc/meta_study.txt index 7085157844..1fd5f8e8f7 100644 --- a/crdc/gdc/wt_target_gdc/meta_study.txt +++ b/crdc/gdc/wt_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: wt cancer_study_identifier: wt_target_gdc name: Wilms' Tumor (TARGET, GDC) short_name: WT -description: TARGET Wilms' Tumor. Source data from GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. Study README | GDC page +description: TARGET Wilms' Tumor. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file From f4a9b0790b82e82bcd68cbc2a074c33295e8607f Mon Sep 17 00:00:00 2001 From: cbioportal import user Date: Tue, 3 Dec 2024 14:08:45 -0500 Subject: [PATCH 5/6] Correct OncoTree capitalization --- crdc/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/crdc/README.md b/crdc/README.md index ece05e9d1d..666eb8939c 100644 --- a/crdc/README.md +++ b/crdc/README.md @@ -78,7 +78,7 @@ Supported programs: ### TARGET - **Cancer type mapping:** Each study corresponds to one or more TARGET projects. The TARGET project suffix is converted to an OncoTree code, which is used for the name of the study. - - **Example:** For the TARGET project `TARGET-ALL-P2`, the `ALL-P2` suffix is taken and converted to the Oncotree code `BLL`. The resulting cBioPortal study is `bll_target_gdc`. + - **Example:** For the TARGET project `TARGET-ALL-P2`, the `ALL-P2` suffix is taken and converted to the OncoTree code `BLL`. The resulting cBioPortal study is `bll_target_gdc`. - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/oncotree_mappings/target.txt) #### List of TARGET cBioPortal Studies From cb406e16e871a2eaa6b77555bc094e52d42ea390 Mon Sep 17 00:00:00 2001 From: cbioportal import user Date: Tue, 3 Dec 2024 14:14:32 -0500 Subject: [PATCH 6/6] Update README files to reflect new data transformations --- crdc/gdc/alal_target_gdc/README.md | 11 +++++++---- crdc/gdc/alal_target_gdc/meta_study.txt | 2 +- crdc/gdc/aml_target_gdc/README.md | 11 +++++++---- crdc/gdc/aml_target_gdc/meta_study.txt | 2 +- crdc/gdc/bll_target_gdc/README.md | 11 +++++++---- crdc/gdc/bll_target_gdc/meta_study.txt | 2 +- crdc/gdc/nbl_target_gdc/README.md | 11 +++++++---- crdc/gdc/nbl_target_gdc/meta_study.txt | 2 +- crdc/gdc/os_target_gdc/README.md | 11 +++++++---- crdc/gdc/os_target_gdc/meta_study.txt | 2 +- crdc/gdc/wt_target_gdc/README.md | 11 +++++++---- crdc/gdc/wt_target_gdc/meta_study.txt | 2 +- 12 files changed, 48 insertions(+), 30 deletions(-) diff --git a/crdc/gdc/alal_target_gdc/README.md b/crdc/gdc/alal_target_gdc/README.md index 4815d45474..db33e32ea1 100644 --- a/crdc/gdc/alal_target_gdc/README.md +++ b/crdc/gdc/alal_target_gdc/README.md @@ -27,7 +27,9 @@ Survival fields are calculated from the clinical data and added as new columns i ### Timeline data -- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. +- Timeline data is extracted from the clinical data and stored in separate data files. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +#### Patient status data - For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. @@ -35,9 +37,9 @@ Survival fields are calculated from the clinical data and added as new columns i The following status values are supported in `data_timeline_status.txt`: -- `__time0__` -- `demo__days_to_death` -- `diag__days_to_last_follow_up` +- (time 0) → `Initial Diagnosis` +- `demo__days_to_death` → `DECEASED` +- `diag__days_to_last_follow_up` → `Last Follow Up` ### Other transformations - `"not reported"` values are replaced with blanks. @@ -92,6 +94,7 @@ Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on t - Samples that lack any genomic data are removed from the clinical sample file. - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - TMB scores are calculated and added to the clinical sample file using a curation-provided script. - Case lists are generated under `case_lists/` using a curation-provided script. - The validator script is run and the HTML report is saved under `validation_reports/`. diff --git a/crdc/gdc/alal_target_gdc/meta_study.txt b/crdc/gdc/alal_target_gdc/meta_study.txt index 2f73e20fa4..cc0b2b601a 100644 --- a/crdc/gdc/alal_target_gdc/meta_study.txt +++ b/crdc/gdc/alal_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: alal cancer_study_identifier: alal_target_gdc name: Acute Leukemias of Ambiguous Lineage - Phase III (TARGET, GDC) short_name: ALAL -description: TARGET Acute Leukemias of Ambiguous Lineage - Phase III. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info +description: TARGET Acute Leukemias of Ambiguous Lineage - Phase III. Source data from NCI GDC and generated in Dec 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/aml_target_gdc/README.md b/crdc/gdc/aml_target_gdc/README.md index ac86cf6396..6925c6895d 100644 --- a/crdc/gdc/aml_target_gdc/README.md +++ b/crdc/gdc/aml_target_gdc/README.md @@ -27,7 +27,9 @@ Survival fields are calculated from the clinical data and added as new columns i ### Timeline data -- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. +- Timeline data is extracted from the clinical data and stored in separate data files. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +#### Patient status data - For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. @@ -35,9 +37,9 @@ Survival fields are calculated from the clinical data and added as new columns i The following status values are supported in `data_timeline_status.txt`: -- `__time0__` -- `demo__days_to_death` -- `diag__days_to_last_follow_up` +- (time 0) → `Initial Diagnosis` +- `demo__days_to_death` → `DECEASED` +- `diag__days_to_last_follow_up` → `Last Follow Up` ### Other transformations - `"not reported"` values are replaced with blanks. @@ -92,6 +94,7 @@ Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on t - Samples that lack any genomic data are removed from the clinical sample file. - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - TMB scores are calculated and added to the clinical sample file using a curation-provided script. - Case lists are generated under `case_lists/` using a curation-provided script. - The validator script is run and the HTML report is saved under `validation_reports/`. diff --git a/crdc/gdc/aml_target_gdc/meta_study.txt b/crdc/gdc/aml_target_gdc/meta_study.txt index 05c30e1aa2..ccce1996de 100644 --- a/crdc/gdc/aml_target_gdc/meta_study.txt +++ b/crdc/gdc/aml_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: aml cancer_study_identifier: aml_target_gdc name: Acute Myeloid Leukemia (TARGET, GDC) short_name: AML -description: TARGET Acute Myeloid Leukemia. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info +description: TARGET Acute Myeloid Leukemia. Source data from NCI GDC and generated in Dec 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/bll_target_gdc/README.md b/crdc/gdc/bll_target_gdc/README.md index 62aad53666..110e694a07 100644 --- a/crdc/gdc/bll_target_gdc/README.md +++ b/crdc/gdc/bll_target_gdc/README.md @@ -27,7 +27,9 @@ Survival fields are calculated from the clinical data and added as new columns i ### Timeline data -- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. +- Timeline data is extracted from the clinical data and stored in separate data files. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +#### Patient status data - For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. @@ -35,9 +37,9 @@ Survival fields are calculated from the clinical data and added as new columns i The following status values are supported in `data_timeline_status.txt`: -- `__time0__` -- `demo__days_to_death` -- `diag__days_to_last_follow_up` +- (time 0) → `Initial Diagnosis` +- `demo__days_to_death` → `DECEASED` +- `diag__days_to_last_follow_up` → `Last Follow Up` ### Other transformations - `"not reported"` values are replaced with blanks. @@ -92,6 +94,7 @@ Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on t - Samples that lack any genomic data are removed from the clinical sample file. - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - TMB scores are calculated and added to the clinical sample file using a curation-provided script. - Case lists are generated under `case_lists/` using a curation-provided script. - The validator script is run and the HTML report is saved under `validation_reports/`. diff --git a/crdc/gdc/bll_target_gdc/meta_study.txt b/crdc/gdc/bll_target_gdc/meta_study.txt index 1778bf774b..bcf124e6e7 100644 --- a/crdc/gdc/bll_target_gdc/meta_study.txt +++ b/crdc/gdc/bll_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: bll cancer_study_identifier: bll_target_gdc name: B-Lymphoblastic Leukemia/Lymphoma - Phase II (TARGET, GDC) short_name: BLL -description: TARGET B-Lymphoblastic Leukemia/Lymphoma - Phase II. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info +description: TARGET B-Lymphoblastic Leukemia/Lymphoma - Phase II. Source data from NCI GDC and generated in Dec 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/nbl_target_gdc/README.md b/crdc/gdc/nbl_target_gdc/README.md index e4eca551d5..73c17a150d 100644 --- a/crdc/gdc/nbl_target_gdc/README.md +++ b/crdc/gdc/nbl_target_gdc/README.md @@ -27,7 +27,9 @@ Survival fields are calculated from the clinical data and added as new columns i ### Timeline data -- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. +- Timeline data is extracted from the clinical data and stored in separate data files. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +#### Patient status data - For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. @@ -35,9 +37,9 @@ Survival fields are calculated from the clinical data and added as new columns i The following status values are supported in `data_timeline_status.txt`: -- `__time0__` -- `demo__days_to_death` -- `diag__days_to_last_follow_up` +- (time 0) → `Initial Diagnosis` +- `demo__days_to_death` → `DECEASED` +- `diag__days_to_last_follow_up` → `Last Follow Up` ### Other transformations - `"not reported"` values are replaced with blanks. @@ -92,6 +94,7 @@ Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on t - Samples that lack any genomic data are removed from the clinical sample file. - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - TMB scores are calculated and added to the clinical sample file using a curation-provided script. - Case lists are generated under `case_lists/` using a curation-provided script. - The validator script is run and the HTML report is saved under `validation_reports/`. diff --git a/crdc/gdc/nbl_target_gdc/meta_study.txt b/crdc/gdc/nbl_target_gdc/meta_study.txt index 7ee68c073b..fa7282dcec 100644 --- a/crdc/gdc/nbl_target_gdc/meta_study.txt +++ b/crdc/gdc/nbl_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: nbl cancer_study_identifier: nbl_target_gdc name: Neuroblastoma (TARGET, GDC) short_name: NBL -description: TARGET Neuroblastoma. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info +description: TARGET Neuroblastoma. Source data from NCI GDC and generated in Dec 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/os_target_gdc/README.md b/crdc/gdc/os_target_gdc/README.md index f3f0557abd..2a8eb44bcc 100644 --- a/crdc/gdc/os_target_gdc/README.md +++ b/crdc/gdc/os_target_gdc/README.md @@ -27,7 +27,9 @@ Survival fields are calculated from the clinical data and added as new columns i ### Timeline data -- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. +- Timeline data is extracted from the clinical data and stored in separate data files. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +#### Patient status data - For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. @@ -35,9 +37,9 @@ Survival fields are calculated from the clinical data and added as new columns i The following status values are supported in `data_timeline_status.txt`: -- `__time0__` -- `demo__days_to_death` -- `diag__days_to_last_follow_up` +- (time 0) → `Initial Diagnosis` +- `demo__days_to_death` → `DECEASED` +- `diag__days_to_last_follow_up` → `Last Follow Up` ### Other transformations - `"not reported"` values are replaced with blanks. @@ -92,6 +94,7 @@ Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on t - Samples that lack any genomic data are removed from the clinical sample file. - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - TMB scores are calculated and added to the clinical sample file using a curation-provided script. - Case lists are generated under `case_lists/` using a curation-provided script. - The validator script is run and the HTML report is saved under `validation_reports/`. diff --git a/crdc/gdc/os_target_gdc/meta_study.txt b/crdc/gdc/os_target_gdc/meta_study.txt index bd3f529855..b426629ccd 100644 --- a/crdc/gdc/os_target_gdc/meta_study.txt +++ b/crdc/gdc/os_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: os cancer_study_identifier: os_target_gdc name: Osteosarcoma (TARGET, GDC) short_name: OS -description: TARGET Osteosarcoma. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info +description: TARGET Osteosarcoma. Source data from NCI GDC and generated in Dec 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file diff --git a/crdc/gdc/wt_target_gdc/README.md b/crdc/gdc/wt_target_gdc/README.md index dd89847203..1b13cc5341 100644 --- a/crdc/gdc/wt_target_gdc/README.md +++ b/crdc/gdc/wt_target_gdc/README.md @@ -27,7 +27,9 @@ Survival fields are calculated from the clinical data and added as new columns i ### Timeline data -- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. +- Timeline data is extracted from the clinical data and stored in separate data files. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`. + +#### Patient status data - For TARGET, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field. @@ -35,9 +37,9 @@ Survival fields are calculated from the clinical data and added as new columns i The following status values are supported in `data_timeline_status.txt`: -- `__time0__` -- `demo__days_to_death` -- `diag__days_to_last_follow_up` +- (time 0) → `Initial Diagnosis` +- `demo__days_to_death` → `DECEASED` +- `diag__days_to_last_follow_up` → `Last Follow Up` ### Other transformations - `"not reported"` values are replaced with blanks. @@ -92,6 +94,7 @@ Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on t - Samples that lack any genomic data are removed from the clinical sample file. - Metadata headers are added to the clinical patient and sample files using a curation-provided script. + - TMB scores are calculated and added to the clinical sample file using a curation-provided script. - Case lists are generated under `case_lists/` using a curation-provided script. - The validator script is run and the HTML report is saved under `validation_reports/`. diff --git a/crdc/gdc/wt_target_gdc/meta_study.txt b/crdc/gdc/wt_target_gdc/meta_study.txt index 1fd5f8e8f7..be8d027e1b 100644 --- a/crdc/gdc/wt_target_gdc/meta_study.txt +++ b/crdc/gdc/wt_target_gdc/meta_study.txt @@ -2,6 +2,6 @@ type_of_cancer: wt cancer_study_identifier: wt_target_gdc name: Wilms' Tumor (TARGET, GDC) short_name: WT -description: TARGET Wilms' Tumor. Source data from NCI GDC and generated in Nov 2024 using ISB-CGC BigQuery tables. More info +description: TARGET Wilms' Tumor. Source data from NCI GDC and generated in Dec 2024 using ISB-CGC BigQuery tables. More info reference_genome: hg38 groups: PUBLIC \ No newline at end of file