Screening of 134 Single Nucleotide Polymorphisms (SNPs) Previously Associated With Type 2 Diabetes Replicates Association
With 12 SNPs in Nine Genes
Cristen J. Willer 1 ,
Lori L. Bonnycastle 2 ,
Karen N. Conneely 1 ,
William L. Duren 1 ,
Anne U. Jackson 1 ,
Laura J. Scott 1 ,
Narisu Narisu 2 ,
Peter S. Chines 2 ,
Andrew Skol 1 ,
Heather M. Stringham 1 ,
John Petrie 2 ,
Michael R. Erdos 2 ,
Amy J. Swift 2 ,
Sareena T. Enloe 2 ,
Andrew G. Sprau 2 ,
Eboni Smith 2 ,
Maurine Tong 2 ,
Kimberly F. Doheny 3 ,
Elizabeth W. Pugh 3 ,
Richard M. Watanabe 4 ,
Thomas A. Buchanan 5 ,
Timo T. Valle 6 ,
Richard N. Bergman 7 ,
Jaakko Tuomilehto 6 8 ,
Karen L. Mohlke 9 ,
Francis S. Collins 2 and
Michael Boehnke 1
1 Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
2 Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland
3 Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
4 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
5 Department of Medicine, Division of Endocrinology, Keck School of Medicine, University of Southern California, Los Angeles,
California
6 Diabetes and Genetic Epidemiology Unit, Department of Epidemiology and Health Promotion, National Public Health Institute,
Helsinki, Finland
7 Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California
8 Department of Public Health, University of Helsinki, Helsinki, Finland, and the South Ostrobothnia Central Hospital, Seinäjoki,
Finland
9 Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
Address correspondence and reprint requests to Michael Boehnke, PhD, Department of Biostatistics, School of Public Health,
University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109-2029. E-mail: boehnke{at}umich.edu
Abstract
More than 120 published reports have described associations between single nucleotide polymorphisms (SNPs) and type 2 diabetes.
However, multiple studies of the same variant have often been discordant. From a literature search, we identified previously
reported type 2 diabetes–associated SNPs. We initially genotyped 134 SNPs on 786 index case subjects from type 2 diabetes
families and 617 control subjects with normal glucose tolerance from Finland and excluded from analysis 20 SNPs in strong
linkage disequilibrium ( r 2 > 0.8) with another typed SNP. Of the 114 SNPs examined, we followed up the 20 most significant SNPs ( P < 0.10) on an additional 384 case subjects and 366 control subjects from a population-based study in Finland. In the combined
data, we replicated association ( P < 0.05) for 12 SNPs: PPARG Pro12Ala and His447, KCNJ11 Glu23Lys and rs5210, TNF −857, SLC2A2 Ile110Thr, HNF1A/TCF1 rs2701175 and GE117881_360, PCK1 −232, NEUROD1 Thr45Ala, IL6 −598, and ENPP1 Lys121Gln. The replication of 12 SNPs of 114 tested was significantly greater than expected by chance under the null hypothesis
of no association ( P = 0.012). We observed that SNPs from genes that had three or more previous reports of association were significantly more
likely to be replicated in our sample ( P = 0.03), although we also replicated 4 of 58 SNPs from genes that had only one previous report of association.
FUSION, Finland-United States Investigation of NIDDM Genetics
LD, linkage disequilibrium
MAF, minor allele frequency
MODY, maturity-onset diabetes of the young
NGT, normal glucose tolerance
SNP, single nucleotide polymorphism
WHR, waist-to-hip ratio
Footnotes
Additional information for this article can be found in an online appendix at http://diabetes.diabetesjournals.org .
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore
be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
Accepted September 18, 2006.
Received April 7, 2006.
DIABETES...

Screening of 134 Single Nucleotide Polymorphisms (SNPs) Previously Associated With Type 2 Diabetes Replicates Association With 12 SNPs in Nine Genes

10.2337/db06-0461