Summary statistics for kidney stone GWAS in UK Biobank

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