Iscan genotyping system

Genomic DNA was extracted from the buffy coats with a salting out method. Genomic and amplified DNA samples were quality-checked, quantified and normalized to approximately 100 ng/ml and 2.0 mg before genotyping. High throughput SNP genotyping was carried out using the Illumina iScan Genotyping System (Illumina, San Diego, CA, USA). 748 individuals were genotyped using the Illumina 660W-Quad SNP chip. SNP genotyping was done in accordance with manufacturer’s protocols. The Integrated mapping information is based on NCBI’s build 37. Pre-processing of the genotype data was performed with plink (v1.07), which is a free, open-source whole genome association analysis toolset, developed by Shaun Purcell at the Center for Human Genetic Research, Massachusetts General Hospital and Broad Institute of Harvard and MIT [22 (link),23 ]. The parameters used were mind = 0.01 and geno = 0.01. Furthermore SNPs with MAF < 0.05 and SNPs not in hardy Weinberg equilibrium (p < 10–4) were excluded leading to a set of 456,382 informative SNPs. Pair-wise linkage disequilibrium [24 (link)] was calculated with the LDlink web-based application using 1000 Genome phase 3 data (for the CEU population).

Before genotyping, a quality check of genomic and amplified DNA samples was conducted. Samples were then quantified and normalized to approximately 100 ng/ml and 2.0 mg. Genotyping of 748 DIOGenes participants was performed using an Illumina 660W-Quad SNP chip on the Illumina iScan Genotyping System (Illumina, San Diego, CA, USA) in accordance with manufacturer’s protocols. The integrated mapping information is based on NCBI’s build 37. 498,233 SNPs were genotyped with call rate > 98% and Hardy–Weinberg equilibrium p > 1.0 × 10⁻⁶. Imputation was performed on the Michigan Imputation Server^{58 (link)} using a European 1000 Genomes set reference panel. Imputation data was converted to best-guess genotypes (genotype probability threshold 0.8). Imputed genotypes with an imputation quality score <0.8 and a minor allele frequency < 5% were discarded. A total of 4,020,654 SNPs were available for analysis in 494 participants with proteomics data and a subset of 151 subjects with gene expression data before and after intervention. A description of the two cohorts is provided in Supplementary Table 2.