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Sanger Institute, ABI Collaborating on Cancer Genome Study

NEW YORK (GenomeWeb News) – Researchers from the Wellcome Trust Sanger Institute and Applied Biosystems are collaborating on a sequencing project aimed at garnering a detailed understanding of the genetic variation associated with cancer development, ABI announced today.
Under the collaboration, investigators from the UK and the US plan to sequence a cancer genome and normal DNA from cell lines derived from one individual with small cell lung cancer using five ABI SOLiD Systems and deep-shotgun resequencing. The project, which is an extension of the Sanger Institute’s Cancer Genome Project, builds on recently published research revealing structural variation within normal and cancerous cell lines at low coverage.
For this project, the team plans to survey both SNPs and structural variations to get deeper coverage and a more comprehensive view of genetic variation in cancer. The team hopes to achieve 20-fold genome coverage of both the cancer genome and normal genome using paired-end reads and inserts of various sizes — up to 10,000 base pairs. To aid sequence assembly, they reportedly plan to use the SOLiD System’s mate-pair analysis.
“We anticipate that the SOLiD System’s high-throughput capabilities will allow us to cost-effectively reduce the number of runs needed to achieve the 20-fold coverage we are seeking, and will enable us to identify and recognize single nucleotide polymorphisms and rearrangements more accurately,” Mike Stratton, co-head of the Sanger Institute’s Cancer Genome Project, said in a statement.
Preliminary results are expected to be presented at the Biology of Genomes meeting at Cold Spring Harbor Laboratory next week.

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