A prior genomic linkage scan in Pima Indians indicated an obesity susceptibility locus on chromosome 11q23-24 (LOD=3.6). There was also evidence that the same genomic region contained a susceptibility locus for type 2 diabetes mellitus (T2DM)(LOD=1.7). Bivariate linkage analysis for the combined phenotype diabesity gave the strongest evidence for a disease locus (LOD= 5.2). The region of linkage spans 24 Mb. To narrow this region, single nucleotide polymorphisms (SNPs) were genotyped in 1300 subjects at a 5 kb density, across the entire 24 Mb, for linkage disequilibrium (LD) mapping. Several years ago, many of our most interesting SNPs were additionally genotyped in the FUSION study of Finns, independent case/control samples for either T2DM or obesity from Botnia, Helsinki, and Malmo, a large collection of metabolically phenotyped Caucasians from Denmark, Caucasian children from the Leipziger School Children study, Caucasians from the UK (Oxford), Mexican Americans from the VAGES study, and Mexican Americans from Starr County. Results from these replication groups for genes in our region of linkage on chromosome 11q23-25 showed that variants near ETS-1 on chromosome 11 replicated in three out of five studies. A variant in TREH on chromosome 11 showed significant associations in 6 out of seven studies, but the risk allele was inconsistent among the various ethnic groups, so it remains debatable whether this variant replicated. My lab further followed up on significant associations identified by LD mapping by directly sequencing 74 positional candidate genes under the peak of linkage on chromosome 11q23-25. Variation within IGSF4 and ETS-1 were the most strongly associated with BMI and variation within TREH was the most strongly associated with T2DM. We completed functional analysis of variants within TREH, which encodes trehalase. We measured serum trehalase activity in 570 non-diabetic subjects and found that trehalase activity was highly associated with a non-synonymous Arg486Trp variant and a promoter variant at -100 b.p. (p=10-12 and p=10-15, respectively, adjusted for age, sex, heritage and family membership). Haplotype analysis showed that subjects who were homozygous for 3 variants (Trp486, Ala389, and C at -100 b.p.) had the lowest trehalase activity and had the lowest prevalence of T2DM. However, in a prospective study, we were unable to demonstrate that a low plasma trehalase activity (independent of genotype) predicted the development of T2DM. Therefore, we believe we have uncovered the genetic basis for the bimodal appearance of trehalase activity (14), and although these variants are associated with T2DM, they may not be causative for T2DM. We also performed funtional studies for variants in a highly conserved, intergenic region distal to ETS-1. These variants are associated with BMI in Pima Indians, where the association becomes significantly greater among the families with evidence for linkage on chrom. 11q23. We collaborated with the Mouse Metabolism lab of NIDDK to show that female ETS-1 hemizygous mice have significantly higher body fat as compared to their wild type littermates. Within the past year we assembled two large population-based samples of Pima Indians from the Gila River Indian Community. The first sample consisted of 3501 full heritage Pima Indians (median age = 39 years with a prevalence of diagnosed diabetes = 45%). The second sample consisted of 3723 subjects who were predominately of mixed heritage (median age = 23 years with a prevalnce of diagnosed diabetes = 20%). We recently genotyped variation within TREH, IGSF4 and ETS-1 in these large samples of DNA. Variation within TREH was significantly associated with diabetes in both of these independent samples, signifying that this effect is widespread and highly reproducible. In contrast, variation within IGSF4 was very strongly associated with BMI among full heritage Pima Indians, but the effect was not as pronounced among individuals who were not full heritage Pima Indians. Finally, Ets-1 which provided the most significant associations with BMI among families which contributed to the initial linkage signal on Chromosome 11, does not appear to be a major gene for BMI in the general Pima population.

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