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. Several candidate genes that have been associated with type 2 diabetes in other populations have been evaluated for association in Pima Indians. The majority of genes seen in other populations appear to have consistent effects in Pimas, though only a few show statistical significance. 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. Recently genome-wide association studies initially with 100,000 markers and later with 1,000,000 markers have identified several additional potential susceptibility genes for young-onset diabetes and for obesity. One of these, in DNER, has strong effects in Pima, but not in other populations. Replication studies in larger sample sizes are planned, as are functional studies. Variants in candidate genes, such as LPP, GCK and MC4R show nominally significant association with diabetes, obesity and related traits in Pimas;rare variants in MCR4 are also associated with obesity particularly in childhood. In addition, Studies of DNA methylation derived from peripheral blood in Pima Indians have shown patterns that are associated with exposure to a diabetic intrauterine environment, a strong risk factor for future development of diabetes. 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 from other populations are also being typed to determine their role susceptibilty to diabetes and obesity in the Pimas. Whole genome sequencing is also being conducted in a small number of participants. The data from these studies will initially be used to impute untyped variants from the genome-wide association data;data from these studies suggest that existing reference panels are not accurate for imputation in American Indians. The sequence data are also being used to design a custom genotyping platform that will capture common variation in Pima Indians, and this will allow for larger, more powerful, genome-wide association studies. 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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