We recently received whole genome sequence reads on one Pima Indian. The sequencing work was done by Bejing Genomics Institute. In the past few months we wrote programs and successfully annotated all of the variants identified in this single sample. All of the variants predicting amino acid substitutions were also catalogued. Using NCBI reference genome build 36 and dbsnp129 as our reference, this Pima Indian had a total of 3.64 million SNPs, where 1.57 million SNPs were homozygous and the remaining 2.07 million SNPs were heterozygous. Of these SNPs, 3.17 million were known SNPs (already reported in dbSNP) and the remaining 0.47 million SNPs were novel (not reported in dbSNP). The novel SNP rate was 87.1%, which is close to the 90% standard line. We anticipate receiving 20 additional genomes for analysis within the next year. We have also recently received whole exome raw sequence data on 180 Pima Indians. All of these individuals have previously been studied as inpatients in our Clinical Research Center where they were characterized for metabolic traits related to diabetes and obesity. Sequencing of their exomes was done by Shanghai Bio. We have completed alignment of the raw reads and calculated that the average per-base coverage was 42x. All of these exomes have been annotated for SNP variation, small insertions and deletions (indels) and large mobile elements. Variants are undergoing bioinformatic analyses to predict which are likely to be damaging. Selected variants are either being validated by re-sequencing or are being directly genotyped in large samples for association analyses.

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Nair, Anup K; Baier, Leslie J (2018) Using Luciferase Reporter Assays to Identify Functional Variants at Disease-Associated Loci. Methods Mol Biol 1706:303-319
Muller, Yunhua L; Skelton, Graham; Piaggi, Paolo et al. (2018) Identification and functional analysis of a novel G310D variant in the insulin-like growth factor 1 receptor (IGF1R) gene associated with type 2 diabetes in American Indians. Diabetes Metab Res Rev 34:e2994
Nair, Anup K; Sutherland, Jeff R; Traurig, Michael et al. (2018) Functional and association analysis of an Amerindian-derived population-specific p.(Thr280Met) variant in RBPJL, a component of the PTF1 complex. Eur J Hum Genet 26:238-246
Piaggi, Paolo; Masindova, Ivica; Muller, Yunhua L et al. (2017) A Genome-Wide Association Study Using a Custom Genotyping Array Identifies Variants in GPR158 Associated With Reduced Energy Expenditure in American Indians. Diabetes 66:2284-2295
Hohenadel, M G; Baier, L J; Piaggi, P et al. (2016) The impact of genetic variants on BMI increase during childhood versus adulthood. Int J Obes (Lond) 40:1301-9
Traurig, Michael; Hanson, Robert L; Marinelarena, Alejandra et al. (2016) Analysis of SLC16A11 Variants in 12,811 American Indians: Genotype-Obesity Interaction for Type 2 Diabetes and an Association With RNASEK Expression. Diabetes 65:510-9
Baier, Leslie J; Muller, Yunhua Li; Remedi, Maria Sara et al. (2015) ABCC8 R1420H loss-of-function variant in a Southwest American Indian community: association with increased birth weight and doubled risk of type 2 diabetes. Diabetes :
Nair, Anup K; Baier, Leslie J (2015) Complex Genetics of Type 2 Diabetes and Effect Size: What have We Learned from Isolated Populations? Rev Diabet Stud 12:299-319
Muller, Yunhua L; Hanson, Robert L; Wiessner, Gregory et al. (2015) Assessing FOXO1A as a potential susceptibility locus for type 2 diabetes and obesity in American Indians. Obesity (Silver Spring) 23:1960-5
Nair, Anup K; Muller, Yunhua Li; McLean, Nellie A et al. (2014) Variants associated with type 2 diabetes identified by the transethnic meta-analysis study: assessment in American Indians and evidence for a new signal in LPP. Diabetologia 57:2334-8

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