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

This dataset contains the coefficients of the polygenic risk scores for Testosterone levels described in the following publication:


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