Bioinformatics detection and analysis of single nucleotide polymorphisms in the coding regions of the human genome

The majority of my graduate work has focused on detecting and analyzing single nucleotide polymorphisms in the human genome. Initially I tried to determine what observable data feature in EST alignments, or Unigene associated files, could be used to increase the accuracy of our evolving SNP detection method. I have evaluated the effects of various changes in our calculation to the SNP detection process and subsequently have helped to expand the number of SNPs available for use as genetic markers by contributing to efforts leading to the submission of thousands of SNPs to the dbSNP database. A secondary goal of my research was to assess the distribution of both SNP location (UTR vs. coding) and SNP protein impact (synonymous, conservative, or non-conservative) within gene sequences. Additionally, I compared the set of EST predicted SNPs we identified to an independent set of SNPs from the dbSNP database derived from genomic sequencing methods. The results of this work indicated that our SNPs were significantly enriched for cSN-Ps as compared to SNPs obtained from genomic sequencing methods: 50% of our SNPs were cSNPs versus 11% of genomic based sequenced SNPs. During this work I produced a comprehensive SNP map for 68 candidate obesity genes which provided a substantial asset to obesity researchers. Additionally, I generated a set of 906 neuropsychiatric genes and identified 1917 SNPs within functional protein regions in this gene set.; My graduate work has led to identification of thousands of SNPs in both obesity and neuronal candidate gene sets. These SNPs in these genes represent substantial resources for both obesity and neuroscience researchers. Additionally, my work has directly contributed to the understanding of cSNPs on proteins and is now shedding light on the role of non-conservative polymorphisms within the context of susceptibility to complex genetic diseases. In addition, each of the three major resources I worked on and/or produced (EST derived SNPs, obesity SNP map, neuropsychiatric gene set and SNP map) for the research community has been the largest addition of such a resource at the time I made it available.