Cancer genome sequencing
[3] 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.
[4] The first whole cancer genome to be sequenced was from cytogenetically normal acute myeloid leukaemia by Ley et al. in November 2008.
The Cancer Genome Anatomy Project (CGAP) was first funded in 1997[10] with the goal of documenting the sequences of RNA transcripts in tumor cells.
[11] As technology improved, the CGAP expanded its goals to include the determination of gene expression profiles of cancerous, precancerous and normal tissues.
[23][24] In a Nature study published in 2011, Ding et al. identified cellular fractions characterized by common mutational changes to illustrate the heterogeneity of a particular tumor pre- and post-treatment vs. normal blood in one individual.
To investigate these events, the discovery sample set will include DNA from primary tumor, normal tissue (from the same individuals) and cancer cell lines.
Currently the cancer tissue being collected include: central nervous system, breast, gastrointestinal, gynecologic, head and neck, hematologic, thoracic, and urologic.
The ICGC’s goal is “To obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe”.
[30] To facilitate further improvement in somatic mutation detection in cancer, the Sequencing Quality Control Phase 2 Consortium has established a pair of tumor-normal cell lines as community reference samples and data sets for the benchmarking of cancer mutation detections.
[33] A personal-genomics analysis requires further functional characterization of the detected mutant genes, and the development of a basic model of the origin and progression of the tumor.
[21][22] As of February 2012, this has only been done for patients clinical trials designed to assess the personal genomics approach to cancer treatment.
[33] If cell survival is determined by many mutations of small effect, it is unlikely that genome sequencing will uncover a single "Achilles heel" target for anti-cancer drugs.
However, somatic mutations tend to cluster in a limited number of signalling pathways,[29][33][34] which are potential treatment targets.
Clinically significant properties of tumors, including drug resistance, are sometimes caused by large-scale rearrangements of the genome, rather than single mutations.
[35] Cancer genome sequencing can be used to provide clinically relevant information in patients with rare or novel tumor types.
