To identify genes that can lead to obesity of Pima Native American heritage, an array of experiments can be conducted to determine possible candidate genes that can increase the likelihood of being obese in a set population. The studies available to identify these genes were (1) inspect follow-up genes identified by a previous genome wide associations studies, GWAS, previously conducted for the 1120 American Indian subjects data available, (2) to directly sequence candidate genes in literature, (3) to analyze whole sequence data from Native American subjects, and lastly (4) to perform functional studies on most promising variants associated with BMI. Analyzing the results presented from my work required the use of biological techniques such as: DNA sequencing, DNA large scale genotyping, PCR amplification, DNA transfections, DNA ligations, in vitro Luciferase assay and Cell culture. Inspecting the follow-up genes identified by the conducted GWAS showed the potential for the MAP2K3 gene to be a candidate to increase obesity in the set population, involve two single nucleotide polymorphisms (SNPs, rs12882548, rs11652094), to affect body weight through complex mechanisms involving food intake and hypothalamic inflammation. The follow-up genes identified in the GWAS that had an effect on obesity showed to affect it through the mechanism of reducing energy expenditure. Through the analysis of SNPs two variants (rs10507100 and rs17087518) were identified to test their roles in the reduction of energy expenditure. Rs17087518 showed to have a role in a relatively reduced EE resulting in weight gain. Directly sequencing a candidate gene known as MRAP2 showed that the SNP rs1928281 did not have a significant difference on obesity in the Native American subjects (p =.09). Analyzing whole genome sequencing SNPs gave rise to novel variants by association analyses with energy expenditure and BMI in 235 whole genomes, the most significant SNP, rs4984683, was examined to determine the variability in energy expenditures. With set quality control assessment a list of variants were received and were then later assessed with other data available to make a connection to EE. Performing functional studies showed the possibility for rs2001651 and rs1466314 to have an effect on MAP2K3 expression level. The initial functional studies gave way to a more in-depth study of this gene to predict BMI in Caucasians and Native Americans, which in turn showed an association with BMI. The use of these techniques have been an indicator for current research in the determination of candidate genes across many diseases. The works presented is an example of the current works in genetics and an exploration of new mechanism to detect, and possibly treat, disease through personalized sequencing.
- Identification of Obesity Genes in Pima Native Americans