Somatic retrotransposition in the cancer genome

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, February 2014.Cataloged from PDF version of thesis.Includes bibliographical references (pages 128-144).Cancer is a complex disease of the genome exhibiting myriad somatic mutations, from single nucleotide changes to various chromosomal rearrangements. The technological advances of next-generation sequencing enable high-throughput identification and characterization of these events genome-wide using computational algorithms. Retrotransposons comprise 42% of the human genome and have the capacity to "jump" across the genome in a copy-and-paste manner. Recent studies have identified families of retrotransposable elements that are currently active. In fact, retrotransposons constitute a major source of human genetic variation, and somatic retrotransposon insertions have been implicated in several cancers, including an insertion into the APC tumor suppressor in a colorectal tumor. Because of the highly repetitive nature of these elements, however, the full extent of somatic retrotransposon movement across cancer remains largely unexplored. To this end, we developed TranspoSeq, a computational framework that identifies retrotransposon insertions from paired-end whole genome sequencing data, and TranspoSeq- Exome, a tool that localizes these insertions from whole-exome data. TranspoSeq identifies novel somatic retrotransposon insertions with high sensitivity and specificity in simulated data and with a 94% validation rate via site-specific PCR. Next, we applied these methods to wholegenomes from 200 tumor/normal pairs and whole-exomes from 767 tumor/normal pairs across 11 tumor types as part of The Cancer Genome Atlas (TCGA) Pan-Cancer Project. We discover more than 800 somatic retrotransposon insertions primarily in lung squamous, head and neck, colorectal and endometrial carcinomas, while glioblastoma multiforme and acute myeloid leukemia show no evidence of somatic retrotransposition. Moreover, many somatic retrotransposon insertions occur in known cancer genes. TranspoSeq-Exome uncovers 35 additional somatic retrotransposon insertions into exonic regions, including an insertion into an exon of the PTEN tumor suppressor in endometrial cancer. Finally, we integrate orthogonal genomic and clinical data to characterize features of retrotransposon insertion and samples that exhibit extensive somatic retrotransposition. We present a large-scale, comprehensive analysis of retrotransposon movement across tumor types using next-generation sequencing data. Our results suggest that somatic retrotransposon insertions may represent an important class of tumor-specific structural variation in cancer and future studies should incorporate this form of somatic genome aberration.by Elena Helman.Ph. D