The meta-analyzed GWAS summary statistics for 35 lab biomarkers described in 'Genetics of 35 blood and urine biomarkers in the UK Biobank' Yosuke Tanigawa Nasa Sinnott-Armstrong Manuel Rivas 10.35092/yhjc.12355382.v1 https://nih.figshare.com/articles/dataset/The_meta-analyzed_GWAS_summary_statistics_for_35_lab_biomarkers_described_in_Genetics_of_35_blood_and_urine_biomarkers_in_the_UK_Biobank_/12355382 <p>The dataset contains meta-analyzed GWAS summary statistics for 35 biomarker traits described in the following preprint:<br>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.</p> <p>For each phenotype, we provide two compressed tab-delimited files, named "[Phenotype_name].array.gz" and "[Phenotype_name].imp.gz", which contain the summary statistics for genetic variants on the genotyping array and the imputed dataset, respectively.<br><br>We used METAL for the meta-analysis for 4 populations (White British, non-British White, African, and South Asian) within UK Biobank. The files have the following columns:</p> <ul><li>CHROM: the chromosome</li><li>POS: the position</li><li>MarkerName: the variant identifier</li><li>REF: the reference allele</li><li>ALT: the alternate allele</li><li>Effect: the effect size (BETA) estimate</li><li>StdErr: the standard error of effect size estimate</li><li>P-value: the p-value of the association</li><li>Direction: the direction of effect size</li><li>HetISq, HetChiSq, HetDf, HetPVal: heterogeneity statistics from METAL</li></ul> <p>Note that we used GRCh37/hg19 genome reference in the analysis and the BETA is always reported for the alternate allele.<br><br>Please also check the METAL documentation (<a href="https://genome.sph.umich.edu/wiki/METAL_Documentation" rel="nofollow">https://genome.sph.umich.edu/wiki/METAL_Documentation</a>).<br><br>The summary statistic files are compressed with <code>bgzip</code> and indexed with <code>tabix</code> (the <code>.tbi</code> files). One should be able to read those files with the standard <code>gzip</code>/<code>zcat</code>.</p> 2020-06-19 17:39:11 biomarker genome-wide GWAS GWAS studies Meta-Analysis UK Biobank study