Polygenic type 2 diabetes prediction at the limit of common variant detection

Jason L. Vassy, Marie France Hivert, Bianca Porneala, Marco Dauriz, Jose C. Florez, Josée Dupuis, David S. Siscovick, Myriam Fornage, Laura J. Rasmussen-Torvik, Claude Bouchard, James B. Meigs*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

78 Scopus citations


Genome-wide association studies (GWAS) may have reached their limit of detecting common type 2 diabetes (T2D)-associated genetic variation.We evaluated the performance of current polygenic T2D prediction. Using data from the Framingham Offspring (FOS) and the Coronary Artery Risk Development in Young Adults (CARDIA) studies, we tested three hypotheses: 1) a 62-locus genotype risk score (GRSt ) improves T2D prediction compared with previous less inclusive GRSt; 2) separate GRS for b-cell (GRSb) and insulin resistance (GRSIR) independently predict T2D; and 3) the relationships between T2D and GRSt, GRSb, or GRSIR do not differ between blacks and whites. Among 1,650 young white adults in CARDIA, 820 young black adults in CARDIA, and 3,471 white middle-aged adults in FOS, cumulative T2D incidence was 5.9%, 14.4%, and 12.9%, respectively, over 25 years. The 62- locus GRSt was significantly associated with incident T2D in all three groups. In FOS but not CARDIA, the 62- locus GRSt improved the model C statistic (0.698 and 0.726 for models without and with GRSt, respectively; P < 0.001) but did not materially improve risk reclassification in either study. Results were similar among blacks compared with whites. The GRSb but not GRSIR predicted incident T2D among FOS and CARDIA whites. At the end of the era of common variant discovery for T2D, polygenic scores can predict T2D in whites and blacks but do not outperform clinicalmodels. Further optimization of polygenic prediction may require novel analytic methods, including less common as well as functional variants.

Original languageEnglish (US)
Pages (from-to)2172-2182
Number of pages11
Issue number6
StatePublished - Jun 2014

ASJC Scopus subject areas

  • Internal Medicine
  • Endocrinology, Diabetes and Metabolism


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