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. An autosomal genome-wide linkage study identified strong evidence for a locus influencing diabetes and diabetes/obesity on chromosomes 1q and 11q. Efforts to identify the causative polymorphism or polymorphisms in both of these regions are currently underway using both a systematic analysis of linkage disequilibrium and analyses of candidate genes. Genome-wide association mapping methods are also being used and exhaustive association analyses are being conducted of regions identified by the genome-wide association studies and of other candidate genes. Genetic variants in the trehalase gene, which is in the linked region on chromosome 11q, have shown consistent associations with diabetes and further replication studies are currently underway. In collaboration with the Sanger Centre a dense linkage disequilibrium map of chromosome 1q was generated for Pimas and for several other populations that have shown linkage to this region (the International 1q Type 2 Diabetes Consortium). There are several regions that appear to be associated with risk of type 2 diabetes in Pimas or other populations, but none show consistent associations across populations. Candidate genes in the region are currently being resequenced. Several candidate genes that have been associated in other populations have been evaluated. 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. 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. These include potential diabetes-susceptibility variants in a number of genes and potential obesity-susceptiblity variants in A2BP1 and MAP2K3. Replication studies in larger sample sizes are planned, as are functional studies. Variants in candidate genes, such as LEPR, LPGAT1 and SIRT1 show nominally significant association with diabetes, obesity and related traits in Pimas;rare variants in MCR4 are also associated with obesity particularly in childhood. 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. Additional American Indian participants are being recruited for replication studies.
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