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The snpnet polygenic risk score coefficients for 35 lab biomarkers described in 'Genetics of 35 blood and urine biomarkers in the UK Biobank'

dataset
posted on 19.06.2020, 17:43 by Yosuke Tanigawa, Nasa Sinnott-Armstrong, Manuel Rivas
The dataset contains the coefficients of the polygenic risk scores for 35 biomarker traits described in the following preprint:
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-deliminated 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

Funding

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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  • HG - National Human Genome Research Institute (NHGRI)

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