Graduation Date

Spring 5-7-2016

Document Type


Degree Name

Doctor of Philosophy (PhD)


Genetics, Cell Biology & Anatomy

First Advisor

San Ming Wang


Next-generation sequencing (NGS) is a high throughput technique used to sequence large amounts of DNA in a short amount of time. However, a limitation to NGS is that the generated data is in a single consensus sequence without distinguishing between variants on homologous chromosomes. Separating or phasing the variants from the maternal and paternal chromosomes can provide information about the genetic origin of disease and information about how DNA nucleotide alterations interact in cis. This dissertation explores a new technical method of using restriction enzymes during NGS library preparation and its ability to increase the amount of phasing information that can be derived from NGS data. This study provides evidence that increasing the fragment size of NGS libraries can increase the amount of variant phasing information derived from NGS data.

BRCA1 is a well-known tumor suppressor that, when mutated, predisposes the mutation carrier to breast cancer. BRCA1 mutation carriers have a 44-75% risk of developing breast cancer by age 70. In this study, we used next-generation sequencing data to identify germline genetic variants that modify the risk of breast cancer in BRCA1 mutation carriers. With the use of both biological and statistical filters, five variants were identified that changed breast cancer risk in BRCA1 mutation carriers. Furthermore, it was shown that two of the affected genes alter the growth of BRCA1 mutation breast cell lines. Perhaps, more importantly, the two variants were shown to alter the function of the affected genes. This is the first study to provide functional evidence on how common genetic variants can modify the risk of breast cancer in BRCA1 mutation carriers.