Genome-Wide Association with Diabetes-Related Traits in the Framingham Heart Study

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Genome-Wide Association with Diabetes-Related Traits in the Framingham Heart Study

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Title: Genome-Wide Association with Diabetes-Related Traits in the Framingham Heart Study
Author: Manning, Alisa K; Liu, Chunyu; Cupples, L Adrienne; Dupuis, Josée; Meigs, James Benjamin; Fox, Caroline; Florez, Jose Carlos

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Citation: Meigs, James B., Alisa K. Manning, Caroline S. Fox, Jose C. Florez, Chunyu Liu, L. Adrienne Cupples, and Josée Dupuis. 2007. Genome-wide association with diabetes-related traits in the Framingham Heart Study. BMC Medical Genetics 8, Suppl 1: S16.
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Abstract: Background: Susceptibility to type 2 diabetes may be conferred by genetic variants having modest effects on risk. Genome-wide fixed marker arrays offer a novel approach to detect these variants. Methods: We used the Affymetrix 100K SNP array in 1,087 Framingham Offspring Study family members to examine genetic associations with three diabetes-related quantitative glucose traits (fasting plasma glucose (FPG), hemoglobin A1c, 28-yr time-averaged FPG (tFPG)), three insulin traits (fasting insulin, HOMA-insulin resistance, and 0–120 min insulin sensitivity index); and with risk for diabetes. We used additive generalized estimating equations (GEE) and family-based association test (FBAT) models to test associations of SNP genotypes with sex-age-age2-adjusted residual trait values, and Cox survival models to test incident diabetes. Results: We found 415 SNPs associated (at p < 0.001) with at least one of the six quantitative traits in GEE, 242 in FBAT (18 overlapped with GEE for 639 non-overlapping SNPs), and 128 associated with incident diabetes (31 overlapped with the 639) giving 736 non-overlapping SNPs. Of these 736 SNPs, 439 were within 60 kb of a known gene. Additionally, 53 SNPs (of which 42 had \(r^2 < 0.80\) with each other) had p < 0.01 for incident diabetes AND (all 3 glucose traits OR all 3 insulin traits, OR 2 glucose traits and 2 insulin traits); of these, 36 overlapped with the 736 other SNPs. Of 100K SNPs, one (rs7100927) was in moderate LD (\(r^2 = 0.50\)) with TCF7L2 (rs7903146), and was associated with risk of diabetes (Cox p-value 0.007, additive hazard ratio for diabetes = 1.56) and with tFPG (GEE p-value 0.03). There were no common (MAF > 1%) 100K SNPs in LD (\(r^2 > 0.05\)) with ABCC8 A1369S (rs757110), KCNJ11 E23K (rs5219), or SNPs in CAPN10 or HNFa. PPARG P12A (rs1801282) was not significantly associated with diabetes or related traits. Conclusion: Framingham 100K SNP data is a resource for association tests of known and novel genes with diabetes and related traits posted at Framingham 100K data replicate the TCF7L2 association with diabetes.
Published Version: doi://10.1186/1471-2350-8-S1-S16
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