Data Descriptor: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls
Flannick J., Fuchsberger C., Mahajan A., Teslovich TM., Agarwala V., Gaulton KJ., Caulkins L., Koesterer R., Ma C., Moutsianas L., McCarthy DJ., Rivas MA., Perry JRB., Sim X., Blackwell TW., Robertson NR., Rayner NW., Cingolani P., Locke AE., Tajes JF., Highland HM., Dupuis J., Chines PS., Lindgren CM., Hartl C., Jackson AU., Chen H., Huyghe JR., Van De Bunt M., Pearson RD., Kumar A., Müller-Nurasyid M., Grarup N., Stringham HM., Gamazon ER., Lee J., Chen Y., Scott RA., Below JE., Chen P., Huang J., Go MJ., Stitzel ML., Pasko D., Parker SCJ., Varga TV., Green T., Beer NL., Day-Williams AG., Ferreira T., Fingerlin T., Horikoshi M., Hu C., Huh I., Ikram MK., Kim BJ., Kim Y., Kim YJ., Kwon MS., Lee J., Lee S., Lin KH., Maxwell TJ., Nagai Y., Wang X., Welch RP., Yoon J., Zhang W., Barzilai N., Voight BF., Han BG., Jenkinson CP., Kuulasmaa T., Kuusisto J.
© The Author(s) 2017. To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ∼82 K Europeans via the exome chip, and ∼90% of low-frequency non-coding variants in ∼44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.