Cancer genome sequencing

Cancer genome sequencing is the whole genome sequencing of a single, homogeneous or heterogeneous group of cancer cells. It is a biochemical laboratory method for the characterization and identification of the DNA or RNA sequences of cancer cell(s).

Unlike whole genome (WG) sequencing which is typically from blood cells, such as J. Craig Venter's and James D. Watson’s WG sequencing projects, saliva, epithelial cells or bone - cancer genome sequencing involves direct sequencing of primary tumor tissue, adjacent or distal normal tissue, the tumor micro environment such as fibroblast/stromal cells, or metastatic tumor sites.

Similar to whole genome sequencing, the information generated from this technique include: identification of nucleotide bases (DNA or RNA), copy number and sequence variants, mutation status, and structural changes such as chromosomal translocations and fusion genes.

Cancer genome sequencing is not limited to WG sequencing and can also include exome, transcriptome, micronome sequencing, and end-sequence profiling. These methods can be used to quantify gene expression, miRNA expression, and identify alternative splicing events in addition to sequence data.

The first report of cancer genome sequencing appeared in 2006. In this study 13,023 genes were sequenced in 11 breast and 11 colorectal tumors. A subsequent follow up was published in 2007 where the same group added just over 5,000 more genes and almost 8,000 transcript species to complete the exomes of 11 breast and colorectal tumors. A cancer genome to be sequenced was from cytogenetically normal acute myeloid leukaemia by Ley et al. in November 2008. The first breast cancer tumor was sequenced by Shah et al. in October 2009, the first lung and skin tumors by Pleasance et al. in January 2010, and the first prostate tumors by Berger et al. in February 2011.

Historically, cancer genome sequencing efforts has been divided between transcriptome-based sequencing projects and DNA-centered efforts.

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