Linkage disequilibrium mapping of the replicated type 2 diabetes linkage signal on chromosome 1q

Inga Prokopenko, Eleftheria Zeggini, Robert L. Hanson, Braxton D. Mitchell, N. William Rayner, Pelin Akan, Leslie Baier, Swapan K. Das, Katherine S. Elliott, Mao Fu, Timothy M. Frayling, Christopher J. Groves, Rhian Gwilliam, Laura J. Scott, Benjamin F. Voight, Andrew T. Hattersley, Cheng Hu, Andrew D. Morris, Maggie Ng, Colin N A PalmerMarcela Tello-Ruiz, Martine Vaxillaire, Cong Rong Wang, Lincoln Stein, Juliana Chan, Weiping Jia, Philippe Froguel, Steven C. Elbein, Panos Deloukas, Clifton Bogardus, Alan R. Shuldiner, Mark I. McCarthy

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

OBJECTIVE-Linkage of the chromosome 1q21-25 region to type 2 diabetes has been demonstrated in multiple ethnic groups. We performed common variant fine-mapping across a 23-Mb interval in a multiethnic sample to search for variants responsible for this linkage signal. RESEARCH DESIGN AND METHODS-In all, 5,290 single nucleotide polymorphisms (SNPs) were successfully genotyped in 3,179 type 2 diabetes case and control subjects from eight populations with evidence of 1q linkage. Samples were ascertained using strategies designed to enhance power to detect variants causal for 1q linkage. After imputation, we estimate ∼80% coverage of common variation across the region (r2 > 0.8, Europeans). Association signals of interest were evaluated through in silico replication and de novo genotyping in ∼8,500 case subjects and 12,400 control subjects. RESULTS-Association mapping of the 23-Mb region identified two strong signals, both of which were restricted to the subset of European-descent samples. The first mapped to the NOS1AP (CAPON) gene region (lead SNP: rs7538490, odds ratio 1.38 [95% CI 1.21-1.57], P = 1.4 × 10-6, in 999 case subjects and 1,190 control subjects); the second mapped within an extensive region of linkage disequilibrium that includes the ASH1L and PKLR genes (lead SNP: rs11264371, odds ratio 1.48 [1.18 -1.76], P = 1.0 × 10-5, under a dominant model). However, there was no evidence for association at either signal on replication, and, across all data (>24,000 subjects), there was no indication that these variants were causally related to type 2 diabetes status. CONCLUSIONS-Detailed fine-mapping of the 23-Mb region of replicated linkage has failed to identify common variant signals contributing to the observed signal. Future studies should focus on identification of causal alleles of lower frequency and higher penetrance.

Original languageEnglish
Pages (from-to)1704-1709
Number of pages6
Issue number7
Publication statusPublished - 1 Jul 2009


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