Analysis of genomic rearrangements in cancer from high throughput sequencing data

• Main Author: Ballinger, Tracy J.
• Language: EN
• Published: University of California, Santa Cruz 2015
• Subjects: Bioinformatics
• Online Access: http://pqdtopen.proquest.com/#viewpdf?dispub=3729995

<p> In the last century cancer has become increasingly prevalent and is the second largest killer in the United States, estimated to afflict 1 in 4 people during their life. Despite our long history with cancer and our herculean efforts to thwart the disease, in many cases we still do not understand the underlying causes or have successful treatments. In my graduate work, I&rsquo;ve developed two approaches to the study of cancer genomics and applied them to the whole genome sequencing data of cancer patients from The Cancer Genome Atlas (TCGA). In collaboration with Dr. Ewing, I built a pipeline to detect retrotransposon insertions from paired-end high-throughput sequencing data and found somatic retrotransposon insertions in a fifth of cancer patients. </p><p> My second novel contribution to the study of cancer genomics is the development of the CN-AVG pipeline, a method for reconstructing the evolutionary history of a single tumor by predicting the order of structural mutations such as deletions, duplications, and inversions. The CN-AVG theory was developed by Drs. Haussler, Zerbino, and Paten and samples potential evolutionary histories for a tumor using Markov Chain Monte Carlo sampling. I contributed to the development of this method by testing its accuracy and limitations on simulated evolutionary histories. I found that the ability to reconstruct a history decays exponentially with increased breakpoint reuse, but that we can estimate how accurately we reconstruct a mutation event using the likelihood scores of the events. I further designed novel techniques for the application of CN-AVG to whole genome sequencing data from actual patients and applied these techniques to search for evolutionary patterns in glioblastoma multiforme using sequencing data from TCGA. My results show patterns of two-hit deletions, as we would expect, and amplifications occurring over several mutational events. I also find that the CN-AVG method frequently makes use of whole chromosome copy number changes following by localized deletions, a bias that could be mitigated through modifying the cost function for an evolutionary history. </p>