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UKBiobank_KSD_GWAS_ICD_OPCS_withexclusions.txt (777.65 MB)

Summary statistics for kidney stone GWAS in UK Biobank

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posted on 2023-11-24, 11:44 authored by Catherine LovegroveCatherine Lovegrove, Jelena Bešević, Akira Wiberg, Ben Lacey, Thomas J. Littlejohns, Naomi Allen, Michelle Goldsworthy, Jihye Kim, Fadil Hannan, Gary C. Curhan, Benjamin W. Turney, Mark McCarthyMark McCarthy, Anubha Mahajan, Rajesh V. Thakker, Michael V Holmes, Dominic Furniss, Sarah Howles

Genome-wide association studies (GWAS) were performed in the UK Biobank, excluding participants with conditions predisposing to kidney stone disease (Supplementary Table 3). Genotyping was undertaken using UK-BiLEVE and UK-Biobank Axiom Arrays and called using array intensity data and a custom genotype-calling pipeline. PLINKv1.9 and Rv3.6.1 were used for quality control (QC). Sample-, individual-, and SNP-level QC exclusions are shown in Supplementary Methods.

UK Biobank phasing on autosomes was performed with SHAPEIT3 using the 1000 Genomes phase 3 dataset as a reference panel. The Haplotype Reference Consortium reference panel and a merged UK10K/1000 Genomes Phase 3 panel were used in imputation. The resultant dataset comprised 92,693,895 autosomal SNPs, short indels, and large structural variants.

A total of 547,011 genotyped and 8,397,548 imputed autosomal SNPs and 733,758 genotyped and 2,635,881 X-chromosome SNPs with MAF ≥0.01 and Info Score ≥0.9 were used at GWAS, using a linear mixed noninfinitesimal model implemented in BOLT-LMMv2.3


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