Abstract 90: Mining for cancer causing mutations in whole genome sequence data

The Cancer Genome Project at the Wellcome Trust Sanger Institute, UK is using massively parallel sequencing technologies to systematically screen exome and genome sequence for diverse categories of mutations. The rapid developments in new sequencing technologies have allowed many new approaches for the detection and characterisation of a wide range of mutation types. We employ a variety of automated and semi-automated techniques to identify and classify copy number variation, chromosomal rearrangements, small insertion/deletion and substitution mutations in both cell lines and primary tumours. Large scale, genome wide changes are detected by mapping read-pairs to a reference genome. Copy number is assessed by taking correctly mapping read-pairs, applying a circular binary segmentation algorithm and correcting for regional mapping bias throughout the genome. Using the high quality read mappings where the paired reads are an unexpected distance apart, putative rearrangements can be identified and confirmed either by local de novo sequence assembly where high sequencing coverage is available or by capillary sequencing for low coverage data. Smaller scale mutations are detected using local read coverage to provide detailed information on the genotype and allelic content of samples. The detection techniques can be used on both whole genome and exome pull-down sequence data. Substitutions are detected using a novel algorithm based on expectation maximisation (Calculate Variants with Expectation Maximisation using New sequencing technology, or CaVEMaN) written in-house and confirmed using capillary sequencing. Putative mutations of all types are compared to external resources (eg Ensembl, dbSNP) to infer genomic context and possible deleterious consequences. In-house tools have been developed to help automate the curation and annotation of mutations and once confirmed they are submitted to COSMIC as gene associated mutations, small scale intragenic mutations, chromosomal rearrangements or fusion gene products. Reference URL9s Wellcome Trust Sanger Institute - http://www.sanger.ac.uk COSMIC - http://www.sanger.ac.uk/genetics/CGP/cosmic CGP - http://www.sanger.ac.uk/genetics/CGP/ Ensembl - http://www.ensembl.org dbSNP - http://www.ncbi.nlm.nih.gov/projects/SNP Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 90.