├── .gitattributes ├── NHL.meta.gz ├── lung.meta.gz ├── bladder.meta.gz ├── breast.meta.gz ├── cervix.meta.gz ├── colon.meta.gz ├── endom.meta.gz ├── kidney.meta.gz ├── leukemia.meta.gz ├── melanoma.meta.gz ├── ovary.meta.gz ├── pancreas.meta.gz ├── prostate.meta.gz ├── rectum.meta.gz ├── thyroid.meta.gz ├── gastricesoph.meta.gz ├── oralpharynx.meta.gz ├── README.txt └── README.md /.gitattributes: -------------------------------------------------------------------------------- 1 | *.meta.gz filter=lfs diff=lfs merge=lfs -text 2 | -------------------------------------------------------------------------------- /NHL.meta.gz: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:344f40053bf89ad77b47f1fbc944cb40948ccb4566b55cc065eda8f2a82e72d5 3 | size 256235128 4 | -------------------------------------------------------------------------------- /lung.meta.gz: 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-------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:802936b58aad605f806825d1ee99d24472edd9cc1f2de764e97ef4e59d2a4231 3 | size 256812934 4 | -------------------------------------------------------------------------------- /README.txt: -------------------------------------------------------------------------------- 1 | #### Prepared on 07/14/2020 ### 2 | 3 | This README file accompanies the following 17 files that contain GWAS summary statistics for 17 cancers based on a meta-analysis of the UK Biobank and GERA cohorts, as reported in Rashkin et al. (2020) bioRxiv 635367; doi: https://doi.org/10.1101/635367 4 | 5 | Columns for each of the files listed above are as follows: 6 | 7 | CHR: chromosome 8 | BP: basepair position in hg19/build 37 9 | uniqID: variant name 10 | A1: effect allele 11 | A2: other allele 12 | N: number of studies (N=1 for variants in UKB or GERA only) 13 | P: p-value (fixed effects meta-analysis) 14 | P_random: p-value (random effects meta-analysis) 15 | OR: odds ratio (fixed effects) 16 | OR_random: odds ratio (random effects) 17 | Q: p-value for Cochran’s Q heterogeneity test 18 | I: I^2 heterogeneity index (0-100) 19 | ID: variant name (rsID) 20 | totN: sample size 21 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # pancancer_pleiotropy 2 | This README file accompanies the following 17 files that contain GWAS summary statistics for 17 cancers based on a meta-analysis of the UK Biobank and GERA cohorts. 3 | 4 | **A description of how these summary statistics were generated and applied to investigate heritability and pan-cancer pleiotropy can be found [here](https://www.biorxiv.org/content/10.1101/635367v2.full):** 5 | 6 | Rashkin et al., *Pan-Cancer Study Detects Novel Genetic Risk Variants and Shared Genetic Basis in Two Large Cohorts*, bioRxiv 2019 7 | 8 | Files are stored with Git Large File Storage (Git-LFS). 9 | 10 | Columns for each of the files listed above are as follows: 11 | | Column Name | Description | 12 | | --- | ---------- | 13 | | CHR | chromosome | 14 | | BP | basepair position in hg19/build 37 | 15 | | uniqID | variant name | 16 | | A1 | effect allele | 17 | | A2 | other allele | 18 | | N | number of studies (N=1 for variants in UKB or GERA only) | 19 | | P | p-value (fixed effects meta-analysis) | 20 | | P_random | p-value (random effects meta-analysis) | 21 | | OR | odds ratio (fixed effects) | 22 | | OR_random | odds ratio (random effects) | 23 | | Q | p-value for Cochran’s Q heterogeneity test | 24 | | I | I^2 heterogeneity index (0-100) | 25 | | ID | variant name (rsID) | 26 | | totN | sample size | 27 | --------------------------------------------------------------------------------