forked from awslabs/open-data-registry
-
Notifications
You must be signed in to change notification settings - Fork 0
/
broad-gnomad.yaml
77 lines (77 loc) · 7.51 KB
/
broad-gnomad.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
Name: Genome Aggregation Database (gnomAD)
Description: |
The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators that aggregates and harmonizes both exome and genome data from a wide range of large-scale human sequencing projects. The summary data provided here are released for the benefit of the wider scientific community without restriction on use.
The v4.1 data set (GRCh38) spans 730,947 exome sequences and 76,215 whole-genome sequences from unrelated individuals, of [diverse ancestries](https://gnomad.broadinstitute.org/stats#diversity), sequenced sequenced as part of various disease-specific and population genetic studies.
The gnomAD Principal Investigators and team can be found [here](https://gnomad.broadinstitute.org/team), and the groups that have contributed data to the current release are listed [here](https://gnomad.broadinstitute.org/about).
Sign up for the gnomAD mailing list [here](http://broad.io/gnomad_list).
Documentation: https://gnomad.broadinstitute.org/about
Contact: gnomad@broadinstitute.org
ManagedBy: gnomAD Production Team at the Broad Institute
UpdateFrequency: Data from new releases are made public as soon as they are available. New releases, including both minor and major versions, have historically been issued on the order of once per year.
Tags:
- aws-pds
- population genetics
- population
- whole genome sequencing
- genomic
- genetic
- life sciences
- bioinformatics
- short read sequencing
License: "[MIT](https://github.com/broadinstitute/gnomad_methods/blob/master/LICENSE); [terms of use](https://gnomad.broadinstitute.org/terms)"
Resources:
- Description: gnomAD summary data aggregated from large-scale human genome and exome sequencing projects.
ARN: arn:aws:s3:::gnomad-public-us-east-1
Region: us-east-1
Type: S3 Bucket
DataAtWork:
Tools & Applications:
- Title: Hail utilities for gnomAD
URL: https://pypi.org/project/gnomad/
AuthorName: gnomAD Production Team
AuthorURL: https://github.com/orgs/broadinstitute/teams/gnomad/members
- Title: gnomAD quality control GitHub repository
URL: https://github.com/broadinstitute/gnomad_qc
AuthorName: gnomAD Production Team
AuthorURL: https://github.com/orgs/broadinstitute/teams/gnomad/members
- Title: Hail
URL: https://hail.is/
AuthorName: Hail Team
AuthorURL: https://hail.is/
Publications:
- Title: A genomic mutational constraint map using variation in 76,156 human genomes. Nature 625, 92–100 (2024)
URL: https://doi.org/10.1038/s41586-023-06045-0
AuthorName: Chen, S., Francioli, L. C., Goodrich, J. K., Collins, R. L., Wang, Q., Alföldi, J., Watts, N. A., Vittal, C., Gauthier, L. D., Poterba, T., Wilson, M. W., Tarasova, Y., Phu, W., Yohannes, M. T., Koenig, Z., Farjoun, Y., Banks, E., Donnelly, S., Gabriel, S., Gupta, N., Ferriera, S., Tolonen, C., Novod, S., Bergelson, L., Roazen, D., Ruano-Rubio, V., Covarrubias, M., Llanwarne, C., Petrillo, N., Wade, G., Jeandet, T., Munshi, R., Tibbetts, K., gnomAD Project Consortium, O’Donnell-Luria, A., Solomonson, M., Seed, C., Martin, A. R., Talkowski, M. E., Rehm, H. L., Daly, M. J., Tiao, G., Neale, B. M., MacArthur, D. G. & Karczewski, K. J.
- Title: The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020)
URL: https://doi.org/10.1038/s41586-020-2308-7
AuthorName: Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., Wang, Q., Collins, R. L., Laricchia, K. M., Ganna, A., Birnbaum, D. P., Gauthier, L. D., Brand, H., Solomonson, M., Watts, N. A., Rhodes, D., Singer-Berk, M., England, E. M., Seaby, E. G., Kosmicki, J. A., ... MacArthur, D. G.
- Title: A structural variation reference for medical and population genetics. Nature 581, 444–451 (2020)
URL: https://doi.org/10.1038/s41586-020-2287-8
AuthorName: Collins, R. L., Brand, H., Karczewski, K. J., Zhao, X., Alföldi, J., Francioli, L. C., Khera, A. V., Lowther, C., Gauthier, L. D., Wang, H., Watts, N. A., Solomonson, M., O’Donnell-Luria, A., Baumann, A., Munshi, R., Walker, M., Whelan, C., Huang, Y., Brookings, T., ... Talkowski, M. E.
- Title: Transcript expression-aware annotation improves rare variant interpretation. Nature 581, 452–458 (2020)
URL: https://doi.org/10.1038/s41586-020-2329-2
AuthorName: Cummings, B. B., Karczewski, K. J., Kosmicki, J. A., Seaby, E. G., Watts, N. A., Singer-Berk, M., Mudge, J. M., Karjalainen, J., Kyle Satterstrom, F., O’Donnell-Luria, A., Poterba, T., Seed, C., Solomonson, M., Alföldi, J., The Genome Aggregation Database Production Team, The Genome Aggregation Database Consortium, Daly, M. J., & MacArthur, D. G.
- Title: Evaluating potential drug targets through human loss-of-function genetic variation. Nature 581, 459–464 (2020)
URL: https://doi.org/10.1038/s41586-020-2267-z
AuthorName: Minikel, E. V., Karczewski, K. J., Martin, H. C., Cummings, B. B., Whiffin, N., Rhodes, D., Alföldi, J., Trembath, R. C., van Heel, D. A., Daly, M. J., Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Schreiber, S. L., & MacArthur, D. G.
- Title: Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes. Nature Communications 11, 2539 (2020)
URL: https://doi.org/10.1038/s41467-019-12438-5
AuthorName: Wang, Q., Pierce-Hoffman, E., Cummings, B. B., Karczewski, K. J., Alföldi, J., Francioli, L. C., Gauthier, L. D., Hill, A. J., O’Donnell-Luria, A. H., Genome Aggregation Database (gnomAD) Production Team, Genome Aggregation Database (gnomAD) Consortium, & MacArthur, D. G.
- Title: The effect of LRRK2 loss-of-function variants in humans. Nature Medicine (2020)
URL: https://doi.org/10.1038/s41591-020-0893-5
AuthorName: Whiffin, N., Armean, I. M., Kleinman, A., Marshall, J. L., Minikel, E. V., Goodrich, J. K., Quaife, N. M., Cole, J. B., Wang, Q., Karczewski, K. J., Cummings, B. B., Francioli, L., Laricchia, K., Guan, A., Alipanahi, B., Morrison, P., Baptista, M. A. S., Merchant, K. M., Genome Aggregation Database Production Team, ... MacArthur, D. G.
- Title: Characterising the loss-of-function impact of 5’ untranslated region variants in 15,708 individuals. Nature Communications 11, 2523 (2020)
URL: https://doi.org/10.1038/s41467-019-10717-9
AuthorName: Whiffin, N., Karczewski, K. J., Zhang, X., Chothani, S., Smith, M. J., Gareth Evans, D., Roberts, A. M., Quaife, N. M., Schafer, S., Rackham, O., Alföldi, J., O’Donnell-Luria, A. H., Francioli, L. C., Genome Aggregation Database (gnomAD) Production Team, Genome Aggregation Database (gnomAD) Consortium, Cook, S. A., Barton, P. J. R., MacArthur, D. G., & Ware, J. S.
- Title: Technical artifact drives apparent deviation from Hardy-Weinberg equilibrium at CCR5-∆32 and other variants in gnomAD. bioRxiv (p. 784157)
URL: https://doi.org/10.1101/784157
AuthorName: Karczewski, K. J., Gauthier, L. D., Daly, M. J.
- Title: Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016)
URL: https://doi.org/10.1038/nature19057
AuthorName: Lek, M., Karczewski, K., Minikel, E. et al.
- Title: gnomAD v2.1
URL: https://gnomad.broadinstitute.org/blog/2018-10-gnomad-v2-1/
AuthorName: Laurent Francioli, Grace Tiao, Konrad Karczewski, Matthew Solomonson, Nick Watts
- Title: gnomAD v3.0
URL: https://gnomad.broadinstitute.org/blog/2019-10-gnomad-v3-0/
AuthorName: Laurent Francioli, Daniel MacArthur