Abstract C10: Complete genome sequencing of complex tumors and matched normals results in sensitive detection of somatic events

For a comprehensive understanding of the tumor genome, it is important to identify all somatic event types: point mutations, small insertions and deletions, copy number aberrations, translocations, inversions, gene fusions, and more. Complete genome sequencing and analysis of paired tumor and normal samples yields a comprehensive view of the mutational landscape in the tumor. An integrated pipeline for the sequencing, computational analysis and annotation of complete human cancer genomes has been developed. Sequencing is performed on Complete Genomics DNA nanoarrays using a nonsequential, unchained read technology to generate 70base-pair paired end reads. Assembly, mapping, and variation calling are performed using methods that have recently been optimized for more sensitive detection of variants of low allelic fraction, as would occur in heterogeneous and/or aneuploid tumor genomes. Algorithmic enhancements designed to accommodate non-diploid genomes result in increased call rates and higher accuracy. Higher coverage levels also help to reduce error rates and improve the sensitivity of somatic variation detection. Approaches adopted to ensure a highly accurate and sensitive representation of tumor genomes will be presented. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr C10.