Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.

ABSTRACT: Genomic structural variations (SVs) are pervasive in many types of cancers. Characterizing their underlying mechanisms and potential molecular consequences is crucial for understanding the basic biology of tumorigenesis. Here, we engineered a local assembly-based algorithm (laSV) that detects SVs with high accuracy from paired-end high-throughput genomic sequencing data and pinpoints their breakpoints at single base-pair resolution. By applying laSV to 97 tumor-normal paired genomic sequencing datasets across six cancer types produced by The Cancer Genome Atlas Research Network, we discovered that non-allelic homologous recombination is the primary mechanism for generating somatic SVs in acute myeloid leukemia. This finding contrasts with results for the other five types of solid tumors, i

SUBMITTER: Zhuang J 

PROVIDER: S-EPMC4787836 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature