Genome wide association study and identification of a protective missense variant on lipoprotein(a) concentration - GWAS summary statistics data files

Published: 02-03-2021| Version 1 | DOI: 10.17632/r5snpvg5ty.1
Contributor:
Abdullah Said

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GWAS summary statistics data files related to the article "Genome wide association study and identification of a protective missense variant on lipoprotein(a) concentration" by Said et al.

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Lp(a) (in nmol/L) was measured using an immuno-turbidimetric assay (Randox Bioscience, UK) on a Beckman Coulter AU5800 (Beckman Coulter (UK), Ltd). Genotyping and imputation Genomic quality control and imputation was performed by the Wellcome Trust Centre for Human Genetics. Participants with a mismatch between genetic and reported sex, high missingness, or excess heterozygosity were exlcuded. Genome Wide Association Study We performed GWAS for inverse rank normalized serum Lp(a) concentrations. GWAS using the genotyped and imputed data were performed using BOLT-LMM v2.3.1, which uses a linear mixed model that corrects for population structure and cryptic relatedness. In total, 19,400,838 SNPs were included per GWAS. The GWAS was adjusted for age at inclusion, squared age at inclusion, genotyping array (UK Biobank Axiom or UK BiLEVE Axiom), the first 30 principal components to adjust for population stratification (provided by UK Biobank), and lipid-lowering drug usage at inclusion. To obtain a set of independent SNPs per phenotype, SNPs with P<5×10-8 were clumped together based on linkage disequilibrium R2>0.005 and 2.5-Mb distance using the clumping procedure integrated in PLINK version 1.9. SNPs were excluded if the minor allele frequency was <0.005 or the INFO score was <0.3. A locus was defined as a 1-Mb region at either side of the sentinel SNP. Positions are based on GRCh37/hg19. A total of 371,212 individuals were included in the GWAS.