We used export_snpnet_BETA.R to export the PRS coefficients and released it on figshare.
The snpnet polygenic risk score coefficients for 35 lab biomarkers described in 'Genetics of 35 blood and urine biomarkers in the UK Biobank'
The dataset contains the coefficients of the polygenic risk scores for 35 biomarker traits described in the following pre-print:
N. Sinnott-Armstrong*, Y. Tanigawa*, et al, Genetics of 38 blood and urine biomarkers in the UK Biobank. bioRxiv, 660506 (2019). doi:10.1101/660506
Note that we are preparing a revised version of the manuscript and this dataset contains 35 (instead of 38) biomarker phenotypes.
We provide the list of 35 biomarkers in "list_of_35_biomarkers.tsv". We used the "Phenotype_name" column in this table for the file names.
For each phenotype, we provide a compressed tab-delimited table, named "snpnet.BETAs.[Phenotype_name].tsv.gz", which contains the coefficients (weights) of the polygenic risk score and have the following columns:
- CHROM: the chromosome
- 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