Understanding the Patterns and Consequences of Single-Nucleotide Mutations in the Human Genome Using High-Throughput Sequencing.

Recent advances in high-throughput genome sequencing technology have paved the way for the field to gain a better understanding of single-nucleotide mutations in the human genome. Until recently, analysis of rare single-nucleotide variants in humans was restricted by technology that limited the expansion to larger sample sizes and greater numbers of loci. The three projects presented here overcome these limitations, using data and results from high-throughput studies to understand the innate features of the genome that influence how frequently different types of mutations occur and identify those mutations that lead to human genetic disease. First, I studied a rare Mendelian disorder, Martin-Probst Syndrome, which is characterized by sensorineural hearing loss and mental retardation. I used whole genome, whole exome, and X-specific exome sequencing across two affected male individuals from one family to identify mutations occurring in a previously identified X-chromosome haplotype block. After stringent filtering and validation steps, I identified two adjacent single-nucleotide mutations in the gene RAB40AL, likely leading to Martin-Probst Syndrome in this family. The second project was aimed at understanding the degree to which innate features of the genome influence the spontaneous single-nucleotide mutation rate in humans and evolutionary processes that alter fixation rates of single-nucleotide variants. I used rare variants (derived allele frequency < 0.0001) to analyze mutation patterns, and common variants and substitutions to study fixation processes. I found that GC content influences the mutation rate and fixation processes differently, especially with regard to distinct variant subtypes. Recombination rate, on the other hand, more strongly influences fixation, as evidenced by the stronger effect on common variants and substitutions than rare variants, consistent with biased gene conversion influencing variant patterns in humans. Finally, I developed a forward genetic simulation program, SubSim, that models subtype-specific selection and mutation, along with base composition, recombination rate and biased gene conversion. Subtype-specific selection and altering the base compositions are two features unique to SubSim. These advances in the available simulation software will help the field gain a better understanding of the evolutionary forces that lead to patterns of single-nucleotide mutation events and fixation of variants in the human genome.PhDHuman GeneticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/97888/1/vschaibl_1.pd