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

在英国生物样本库（UK Biobank）中开展了全基因组关联研究（GWAS），排除了患有易患肾结石疾病的参与者（详见补充表3）。采用UK-BiLEVE和UK-Biobank Axiom Arrays进行基因分型，并利用阵列强度数据和自定义基因分型调用流程进行分型。使用PLINKv1.9和Rv3.6.1进行质量控制（QC）。样本、个体和单核苷酸多态性（SNP）水平的QC排除方法在补充方法中展示。利用SHAPEIT3在常染色体上进行了UK Biobank的连锁分析，以1000 Genomes第3阶段数据集作为参考面板。在推断中使用了haplotype参考联盟参考面板和合并的UK10K/1000 Genomes第3阶段面板。所得数据集包含92693895个常染色体SNP、短插入缺失和大型结构变异。在GWAS中使用了共计547011个已分型且8397548个推断的常染色体SNP以及733758个已分型和2635881个X染色体的SNP，这些SNP的Minor Allele Frequency（MAF）≥0.01且信息分数（Info Score）≥0.9，采用了在BOLT-LMMv2.3中实现的线性混合非无穷小模型。