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The snpnet polygenic risk score coefficients for Testosterone levels described in 'Sex-specific genetic effects across biomarkers'

dataset
posted on 28.08.2020, 23:06 by Yosuke TanigawaYosuke Tanigawa, Emily FlynnEmily Flynn, Manuel Rivas
This dataset contains the coefficients of the polygenic risk scores for Testosterone levels described in the following publication:

E. Flynn, Y. Tanigawa, F. Rodriguez, R. B. Altman, N. Sinnott-Armstrong, M. A. Rivas, Sex-specific genetic effects across biomarkers. European Journal of Human Genetics, 1-10 (2020). https://doi.org/10.1038/s41431-020-00712-w

We provide 3 files corresponding to the polygenic risk score models training on the following set of individuals:

- "snpnet.BETAs.Testosterone.combined.tsv.gz": A PRS model trained on both male and female individuals
- "snpnet.BETAs.Testosterone.female-specific.tsv.gz": A PRS model trained on female individuals
- "snpnet.BETAs.Testosterone.male-specific.tsv.gz": A PRS model trained on male individuals

Those files are compressed tab-delimited table files, each of which contains the coefficients (weights) of the polygenic risk score and have the following columns:

- CHROM: the chromosome. The pseudoautosomal region in X chromosome is coded as XY.
- POS: the position
- ID: the variant identifier
- REF: the reference allele
- ALT: the alternate allele
- BETA: the coefficients (weights) of the PRS

Note that we used GRCh37/hg19 genome reference in the analysis and the BETA is always reported for the alternate allele.

We used the BASIL algorithm implemented in R snpnet package, which is described in another preprint:

J. Qian, et al, A Fast and Flexible Algorithm for Solving the Lasso in Large-scale and Ultrahigh-dimensional Problems. bioRxiv, 630079 (2019). doi:10.1101/630079

Funding

Toward improved understanding of sex differences in drug response: developing gene and pathway-based informatics methods to examine sex-differential genetic effects

United States National Library of Medicine

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SOFTWARE FOR LARGE-SCALE INFERENCE OF THE GENETICS OF LIFESTYLE MEASURES, BIOMARKERS, AND COMMON AND RARE DISEASES

National Human Genome Research Institute

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