Abstract
It is well established that genomic alterations play an essential role in oncogenesis, disease progression, and response of tumors to therapeutic intervention. The advances of next-generation sequencing technologies (NGS) provide unprecedented capabilities to scan genomes for changes such as mutations, deletions, and alterations of chromosomal copy number. However, the cost of full-genome sequencing still prevents the routine application of NGS in many areas. Capturing and sequencing the coding exons of genes (the “exome”) can be a cost-effective approach for identifying changes that result in alteration of protein sequences. We applied an exome-sequencing technology (Roche Nimblegen capture paired with 454 sequencing) to identify sequence variation and mutations in eight commonly used cancer cell lines from a variety of tissue origins (A2780, A549, Colo205, GTL16, NCI-H661, MDA-MB468, PC3, and RD). We showed that this technology can accurately identify sequence variation, providing ∼95% concordance with Affymetrix SNP Array 6.0 performed on the same cell lines. Furthermore, we detected 19 of the 21 mutations reported in Sanger COSMIC database for these cell lines. We identified an average of 2,779 potential novel sequence variations/mutations per cell line, of which 1,904 were non-synonymous. Many non-synonymous changes were identified in kinases and known cancer-related genes. In addition we confirmed that the read-depth of exome sequence data can be used to estimate high-level gene amplifications and identify homologous deletions. In summary, we demonstrate that exome sequencing can be a reliable and cost-effective way for identifying alterations in cancer genomes, and we have generated a comprehensive catalogue of genomic alterations in coding regions of eight cancer cell lines. These findings could provide important insights into cancer pathways and mechanisms of resistance to anti-cancer therapies.
Highlights
All cancer cells have somatic mutations in their genomes, such as single nucleotide mutations, insertions, deletions, and copy-number gain or loss
We demonstrate that exome sequencing can be a reliable and cost effective way for identifying genomic alterations in cancer genome, and generated a comprehensive catalogue of genomic alterations in coding regions of eight cancer cell lines
Exome capture and sequencing results Exome capture and 454 sequencing technologies were applied to DNA samples from eight cancer cell lines
Summary
All cancer cells have somatic mutations in their genomes, such as single nucleotide mutations, insertions, deletions, and copy-number gain or loss. Genomic lesions in cancer cells disrupt normal functions and pathways such as proliferation and apoptosis, and are essential for tumor genesis, growth, and metastasis. Each tumor carries a unique combination of mutations in its genome, leading to heterogeneity in cancer prognosis and responses to therapeutic intervention. Treatment with small molecule inhibitors of the epidermal growth factor receptor (EGFR) has been shown to primarily benefit lung cancer patients that carry certain somatic mutations in their EGFR gene [1,2]. Deep systematic characterization of somatic mutations in cancer genomes promises to be a powerful tool for both understanding cancer pathways and developing targeted therapeutics
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