Assessing mutations in cancer by second-generation genome sequencing.

摘要

Second-generation genome sequencing offers high resolution, high-throughput solutions for assessing mutations in human cancers. One of the most deadly and heavily mutated forms of human cancer is glioblastoma multiforme (GBM), grade IV astrocytoma. In a pilot experiment, we performed whole genome sequencing on the human glioma cell line U87MG using the Life Technologies SOLiD platform. We demonstrated unparalleled sensitivity for small insertions and deletions (indels), single nucleotide variants (SNVs) and structural variations. In the process of analyzing the U87MG sequence data, we developed Breakway, a program to assess structural variants with SOLID data. As a follow-up, a primary GBM bearing a common amplification at 12q13-15 was sequenced. We further assessed this amplification by sequencing three additional low-depth GBMs on the Illumina Genome Analyzer II. We found evidence for two subtypes of amplification events: single, equal copy number amplicons and sporadic, varied copy number amplicons. According to data from the Cancer Genome Atlas for 326 GBMs, amplifications of the CDK4 gene in 12q13-15 correlate with GBM subtype shifts. These data suggest reduced genomic stability in this region in some GBMs.