diff --git a/README.md b/README.md index f570376..ad40b3c 100755 --- a/README.md +++ b/README.md @@ -6,21 +6,21 @@ The CPSR workflow is integrated with the framework that underlies the [Personal *CPSR* accepts a query file from a single case/patient, containing raw germline variant calls encoded in the [VCF](https://samtools.github.io/hts-specs/VCFv4.2.pdf) format (i.e. SNVs/InDels). A comprehensive set of **virtual cancer predisposition gene panels** harvested from the [Genomics England PanelApp](https://panelapp.genomicsengland.co.uk/) allows the user to flexibly put a restriction on which genes and findings are displayed in the cancer predisposition report. -Snapshots of sections in the cancer predisposition genome report (artificial sample, with more findings than usual) are shown below: +Snapshots of sections in the [quarto](https://quarto.org)-based cancer predisposition genome report (artificial sample, with more findings than usual) are shown below: ![CPSR views](pkgdown/assets/img/cpsr_sc.png) ## News -- *May 2024*: **2.x.x release** +- *June 2024*: **2.x.x release** - New HTML report generation and layout with [quarto](https://quarto.org/) - Excel output supported - Updated virtual gene panels (Genomics England PanelApp, Cancer Gene Census) - Reference data updates, most importantly including - - ClinVar - May 2024 - - CIViC - May 2024 - - GENCODE - v45 - - Software updates - VEP 111 + - ClinVar - June 2024 + - CIViC - June 2024 + - GENCODE - v46 + - Software updates - VEP 112 - Extensive code clean-up and re-structuring - *November 2022*: **1.0.1 release** diff --git a/pkgdown/index.md b/pkgdown/index.md index 435b0e2..99d1c6a 100755 --- a/pkgdown/index.md +++ b/pkgdown/index.md @@ -8,7 +8,7 @@ The *Cancer Predisposition Sequencing Reporter (CPSR)* is a computational workfl *CPSR* accepts a query file with raw germline variant calls (SNVs/InDels) from a single sample (cancer patient), encoded in the [VCF format ](https://samtools.github.io/hts-specs/VCFv4.2.pdf). CPSR conducts comprehensive gene and variant annotation on the input calls, and generates a dedicated _variant HTML report_, that provides the following main functionality: -1) Flexible **selection of cancer predisposition genes** subject to analysis +1) Flexible **selection of cancer predisposition genes** subject to analysis and reporting 2) **Variant classification** (*Pathogenic* to _Benign_) through implementation of ACMG guidelines 3) **Biomarker matching** of sample variants (prognosis, diagnosis, drug sensitivity/resistance) 4) Reporting of **secondary/incidental findings** (ACMG recommendations) @@ -16,7 +16,7 @@ The *Cancer Predisposition Sequencing Reporter (CPSR)* is a computational workfl The workflow is integrated with the framework that underlies [Personal Cancer Genome Reporter - PCGR ](https://github.com/sigven/pcgr). While *PCGR* is intended for reporting and analysis of somatic variants detected in a tumor, *CPSR* is intended for reporting and ranking of germline variants in protein-coding genes that are implicated in cancer predisposition and inherited cancer syndromes. -Snapshots of sections in the cancer predisposition genome report: +Snapshots of sections in the [quarto](https://quarto.org)-based cancer predisposition genome report ((artificial sample, with more findings than usual): ![](img/cpsr_sc.png) @@ -29,10 +29,10 @@ Snapshots of sections in the cancer predisposition genome report: - Excel output supported - Updated virtual gene panels (Genomics England PanelApp, Cancer Gene Census) - Reference data updates, most importantly including - - ClinVar - May 2024 - - CIViC - May 2024 - - GENCODE - v45 - - Software updates - VEP 111 + - ClinVar - June 2024 + - CIViC - June 2024 + - GENCODE - v46 + - Software updates - VEP 112 - Extensive code clean-up and re-structuring * *November 2022*: **1.0.1 release** diff --git a/vignettes/output.Rmd b/vignettes/output.Rmd index 39d1c60..5a2ab36 100644 --- a/vignettes/output.Rmd +++ b/vignettes/output.Rmd @@ -127,6 +127,7 @@ sequence (picked by VEP's `--flag_pick_allele` option) | | `LOSS_OF_FUNCTION` | Loss-of-function variant | | `LOF_FILTER` | Loss-of-function filter | | `SPLICE_DONOR_RELEVANT` | Logical indicating if variant is located at a particular location near the splice donor site (`+3A/G`, `+4A` or `+5G`) | +| `BIOMARKER_MATCH` | Variant matches with germline biomarker evidence in CIViC/CGI. Format: \|\|::::\|. Multiple evidence items are separated by '&'. Example: civic|174|EID445:Colon/Rectum:Sensitivity/Response:D:Predictive:Germline&EID446:Colon/Rectum:Sensitivity/Response:D:Predictive:Germline|by_gene_mut. Matching type can be any of `by_genomic_coord`, `by_hgvsp_principal`, `by_hgvsc_principal`, `by_hgvsp_nonprincipal`, `by_hgvsc_nonprincipal`, `by_codon_principal`, `by_exon_mut_principal`, `by_gene_mut_lof`, `by_gene_mut` | | `REGULATORY_ANNOTATION` | Comma-separated list of all variant annotations of `Feature_type`, `RegulatoryFeature`, and `MotifFeature`. Format (separated by a `|`): ``, ``, ``, ``, ``, ``, ``, ``, `` |