Human omni express exome bead chip kit

A total of 58 previously reported type 2 diabetes-associated single nucleotide polymorphisms were selected for genotyping in the MDCS (Additional file 1: Table S1) [24 (link), 28 (link)]. Genotyping was performed by MassARRAY iPLEX (Sequenom, San Diego, CA, USA) or Taqman 5′ nuclease (Applied Biosystems, Foster City, CA, USA) assays according to the manufacturers’ instructions. The concordance rate was >99 % in 5500 samples which were genotyped using Human Omni Express Exome Bead Chip Kit (Illumina, San Diego, CA, USA). Genotyping success rate ranged between 96 and 99 %. All genotypes were in the Hardy-Weinberg equilibrium (P > 0.0009).

Genotyping was performed at the Clinical Research Centre, Malmö, Sweden, using Sequenom MassARRAY iPLEX (Sequenom, San Diego, CA, USA) according to the manufacturers’ instructions. The concordance rate was >99% in a subset of 5500 samples which were additionally genotyped using Human Omni Express Exome Bead Chip Kit (Illumina, San Diego, CA, USA). Genotyping success rate was 97.3%. No deviation from the Hardy-Weinberg equilibrium was observed (P = 0.82). In total, 20,929 subjects in the current study population had genotype data for the SLC30A8 rs13266634 variant.

A MALDI-TOF mass spectrometer (Sequenom MassArray, Sequenom, San Diego, CA) was used to genotype DNA samples using Sequenom reagents and protocols. Proxy SNPs were identified using SNAP version 2.2.2 when commercial primers were not available. SNPs that failed Sequenom genotyping were genotyped individually using TaqMan or KASPar allelic discrimination on an ABI 7900HT (Applied Biosystems, Life Technologies, Carlsbad, CA). All included 48 SNPs had genotyping success rate above 93%, and 45 of the SNPs had a success rate above 95%. The concordance rate was > 99% for all 48 SNPs, including the three SNPs with success rates between 93 and 95%, in 5500 samples which were additionally re-genotyped using Human Omni Express Exome Bead Chip Kit (Illumina, San Diego, CA, USA).