Tanigawa, Yosuke Sinnott-Armstrong, Nasa Rivas, Manuel The snpnet polygenic risk score coefficients for 35 lab biomarkers described in 'Genetics of 35 blood and urine biomarkers in the UK Biobank' <div>The dataset contains the coefficients of the polygenic risk scores for 35 biomarker traits described in the following preprint:</div><div>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<br><br>Note that we are preparing a revised version of the manuscript and this dataset contains 35 (instead of 38) biomarker phenotypes.<br><br>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.<br><br>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:</div><div>- CHROM: the chromosome</div><div>- POS: the position</div><div>- ID: the variant identifier</div><div>- REF: the reference allele</div><div>- ALT: the alternate allele</div><div>- BETA: the coefficients (weights) of the PRS<br><br>Note that we used GRCh37/hg19 genome reference in the analysis and the BETA is always reported for the alternate allele.<br><br>We used the BASIL algorithm implemented in R snpnet package, which is described in another preprint:<br>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</div> polygenic risk score effect sizes;polygenic risk score;Polygenic risk score (PRS);Polygenic risk score;LASSO regression models;L1 penalized regression model 2020-06-19
    https://nih.figshare.com/articles/dataset/The_snpnet_polygenic_risk_score_coefficients_for_35_lab_biomarkers_described_in_Genetics_of_35_blood_and_urine_biomarkers_in_the_UK_Biobank_/12298838
10.35092/yhjc.12298838.v1