  The Cancer Genome Atlas project was initiated by the National Cancer
Institute in order to characterize the genomes of hundreds of tumors of various
cancer types. While much effort has been put into detecting somatic genomic
variation in these data, somatic structural variation induced by the activity
of transposable element insertions has not been reported. Transposable elements
(TEs) are particularly relevant in cancer in part because of several known
cases in which a TE insertion is directly linked to cancer formation and
studies linking the epigenetic status of retrotransposons to carcinogenesis and
patient outcome. Additionally, evidence for somatic retrotransposition in
eukaryotic genomes suggests that some tissues and therefore some cancer types
may be disposed to increased retrotransposition. We built upon previous work to
develop a highly efficient computational pipeline for the detection of
non-reference mobile ele- ment insertions from high-throughput paired-end whole
genome sequencing data that is capable of detecting breakpoints through a local
assembly strategy. Using this, we analyzed 33 whole genome tumor datasets with
paired normal samples from TCGA across 3 different cancer types: glioblastoma
multiforme (GBM), ovarian serous cystoadenocarcinoma (OV) and colorectal ade-
nocarcinoma (COAD). We detected 72 insertions in colon samples, almost all of
them LINE-1 elements, and none in GBM or OV. The amount of somatic
retrotransposition varies widely between samples with 61 insertions present in
one case. The lack of somatic retrotransposon insertions in GBM and OV samples
suggests that TE activity in cancer is restricted to certain cancer types.
