In the current project, genetic determinants of type 2 diabetes mellitus and obesity are being sought using techniques of genetic linkage and association analysis. Lymphoblast cell lines have been established from informative pedigrees. DNA is available from other families in nuclear pellets extracted from blood specimens obtained in the epidemiologic studies and is amplified by whole genome amplification when needed. Genome-wide mapping studies, initially using linkage methods and more recently using association methods, are being used to identify regions containing variants conferring susceptibility to diabetes and obesity in Pima Indians and other American Indian populations. Exhaustive association analyses are being conducted of regions identified by these approaches and of other candidate genes in an attempt to help identify causative variants. Whole genome sequencing studies are also being pursued, as are analyses of epigenetic factors (e.g. DNA methylation). Several candidate genes that have been associated with type 2 diabetes in other populations have been evaluated for association in Pima Indians. In general most established variants associated with type 2 diabetes in other populations are also associated in Pima Indians, albeit with small effects which are often not individually statistically significant. Some variants identified in other populations (e.g. TCF7L2) appear to have little effect. Variants in established type 2 diabetes genes, MOB2, KLF14 and KCNQ1, are subject to parent-of-origin effects and these parent-of-origin effects replicate in Pimas. The effect of the KCNQ1 variants is particularly strong; with consideration of the parent-of-origin effect these variants account for 4% of liability in susceptibility to diabetes. Genome-wide association studies have also been conducted- initially using standard commercial genotyping arrays and selected samples, and, more recently, in larger population samples (N=11,000) using Amerindian-specific arrays developed from whole genome sequence data in 296 Pima Indians, as have exome sequencing studies in 8,000 individuals. These studies have identified several additional potential susceptibility genes for diabetes and for obesity. Recent analyses have identified a variant at high frequency in Amerindian and (Mexican-Americans) that is protective for type 2 diabetes. In addition an Amerindian-specific variant in PTF1 with suggestive association with diabetes has been identified, as has a variant with sex-specific effects on diabetes and lower birth weight in IGF1R. Meta-analyses including multiple trans-ethnic populations have identified loci associated with lean body mass. Currently fine-mapping studies with additional variants are being conducted to extract more of the genetic information in regions identified as potentially involved in diabetes susceptibility. Through collaborations, studies are being conducted to determine if any of the signals identified in the present mapping studies replicate in other populations. Variants reproducibly associated with type 2 diabetes and obesity from other populations continue to be typed to determine their role susceptibility to diabetes and obesity in the Pimas. Whole genome sequencing is also being conducted in a small number of participants. Population-based linkage approaches are also being explored as a complementary mapping strategy. Additional American Indian participants are being recruited for replication studies.
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