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The meta-analyzed GWAS summary statistics for 35 lab biomarkers described in 'Genetics of 35 blood and urine biomarkers in the UK Biobank'

dataset
posted on 19.06.2020 by Yosuke Tanigawa, Nasa Sinnott-Armstrong, Manuel Rivas

The dataset contains meta-analyzed GWAS summary statistics 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 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.

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:

  • CHROM: the chromosome
  • POS: the position
  • MarkerName: the variant identifier
  • REF: the reference allele
  • ALT: the alternate allele
  • Effect: the effect size (BETA) estimate
  • StdErr: the standard error of effect size estimate
  • P-value: the p-value of the association
  • Direction: the direction of effect size
  • HetISq, HetChiSq, HetDf, HetPVal: heterogeneity statistics from METAL

Note that we used GRCh37/hg19 genome reference in the analysis and the BETA is always reported for the alternate allele.

Please also check the METAL documentation (https://genome.sph.umich.edu/wiki/METAL_Documentation).

The summary statistic files are compressed with bgzip and indexed with tabix (the .tbi files). One should be able to read those files with the standard gzip/zcat.

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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