729 research outputs found

    The power of numbers

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    The technical and methodological advancements, as well as the knowledge accrued over the past decade on the haplotype block structure of the human genome, have enabled investigators to tackle the complexity of the genetic architecture of type 2 diabetes in populations of European and non-European descent by performing large-scale genome-wide association studies (GWAS) for both common and rare genetic variants. Interestingly, while interpreting the GWAS results one may observe that as the number of identified type 2 diabetes risk variants has increased over time, and the loci uncovered by earlier GWAS have been further replicated in larger association studies, the individual (per-allele) effect estimate has become smaller than the one originally detected in the discovery GWAS. This may be due to the non-mutually exclusive occurrence of two statistical phenomena, usually dubbed as "winner's curse" and "spectrum bias" effects. The present commentary discusses the work of the China Kadoorie Biobank Collaborative Group, which sought to provide a demonstration of the calculation of (relatively) unbiased allelic effect sizes for a set of 56 established type 2 diabetes risk variants in a large population-based cohort study of Chinese adult individuals. In particular we critically discuss whether theGWAS approach should remain a matter of statistical constraints only, or whether its integration with functional maps may highlight some sub-threshold loci as informative as those that reach genome-wide significance. The complementary information that could arise from the full integration of the genetic and functional maps holds the promise of potentially uncovering clinically relevant mechanistic insights and might expand the regulatory framework in which to interpret the functional follow-up and fine-mapping currently ongoing at established type 2 diabetes risk loci

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

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    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 1%) 100K SNPs in LD (r2 > 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.National Heart, Lung, and Blood Institute's Framingham Heart Study (N01-HC-25195); National Institutes of Health National Center for Research Resources Shared Instrumentation grant (1S10RR163736-01A1); National Center for Research Resources General Clinical Research Center (M01-RR-01066); American Diabetes Association Career Developement Award; GlaxoSmithKline; Merck; Lilly; National Institutes of Health Research Career Award (K23 DK659678-03

    A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study

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    <p>Abstract</p> <p>Background</p> <p>Glomerular filtration rate (GFR) and urinary albumin excretion (UAE) are markers of kidney function that are known to be heritable. Many endocrine conditions have strong familial components. We tested for association between the Affymetrix GeneChip Human Mapping 100K single nucleotide polymorphism (SNP) set and measures of kidney function and endocrine traits.</p> <p>Methods</p> <p>Genotype information on the Affymetrix GeneChip Human Mapping 100K SNP set was available on 1345 participants. Serum creatinine and cystatin-C (cysC; n = 981) were measured at the seventh examination cycle (1998–2001); GFR (n = 1010) was estimated via the Modification of Diet in Renal Disease (MDRD) equation; UAE was measured on spot urine samples during the sixth examination cycle (1995–1998) and was indexed to urinary creatinine (n = 822). Thyroid stimulating hormone (TSH) was measured at the third and fourth examination cycles (1981–1984; 1984–1987) and mean value of the measurements were used (n = 810). Age-sex-adjusted and multivariable-adjusted residuals for these measurements were used in association with genotype data using generalized estimating equations (GEE) and family-based association tests (FBAT) models. We presented the results for association tests using additive allele model. We evaluated associations with 70,987 SNPs on autosomes with minor allele frequencies of at least 0.10, Hardy-Weinberg Equilibrium p-value ≥ 0.001, and call rates of at least 80%.</p> <p>Results</p> <p>The top SNPs associated with these traits using the GEE method were rs2839235 with GFR (p-value 1.6*10<sup>-05</sup>), rs1158167 with cysC (p-value 8.5*10<sup>-09</sup>), rs1712790 with UAE (p-value 1.9*10<sup>-06</sup>), and rs6977660 with TSH (p-value 3.7*10<sup>-06</sup>), respectively. The top SNPs associated with these traits using the FBAT method were rs6434804 with GFR(p-value 2.4*10<sup>-5</sup>), rs563754 with cysC (p-value 4.7*10<sup>-5</sup>), rs1243400 with UAE (p-value 4.8*10<sup>-6</sup>), and rs4128956 with TSH (p-value 3.6*10<sup>-5</sup>), respectively. Detailed association test results can be found at <url>http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007</url>. Four SNPs in or near the <it>CST</it>3 gene were highly associated with cysC levels (p-value 8.5*10<sup>-09 </sup>to 0.007).</p> <p>Conclusion</p> <p>Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.</p
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