NCI Researchers Generate Largest Database of Cancer-specific Genetic Variations


National Cancer InstituteLast month, the American Association for Cancer Research (AACR) announced that researchers at the National Cancer Institute (NCI) had generated a data set of cancer-specific genetic variations, which the researchers were making freely available to the research community.  The data set of coding variants in the NCI-60 panel of cell lines was described in the July 15 issue of the AACR journal Cancer Research (Abaan et al., "The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology").  The NCI-60 human cancer cell line panel, which consists of 60 different cell lines representing cancers of the lung, colon, brain, ovary, breast, prostate, and kidney, as well as leukemia and melanoma, is used extensively by cancer researchers to discover anti-cancer drugs.  According to the article, the genomic variants identified in the NCI-60 panel are being made available at the NCI DTP, CellMiner, and Ingenuity websites.

Co-author Dr. Yves Pommier, chief of the NCI's Laboratory of Molecular Pharmacology, noted that the data set of coding variants constitutes "the largest database worldwide, containing 6 billion data points that connect drugs with genomic variants for the whole human genome across cell lines from nine tissues of origin, including breast, ovary, prostate, colon, lung, kidney, brain, blood, and skin."  He added that "[o]pening this extensive data set to researchers will expand our knowledge and understanding of tumorigenesis, as more and more cancer-related gene aberrations are discovered."

The comprehensive list of cancer-specific genetic variations was generated by conducting whole-exome sequencing of the NCI-60 human cancer cell line panel.  The genetic variations that were identified consisted of two types:  type I variants corresponding to variants found in the normal population, and type II variants, which are cancer-specific.

Preliminary studies conducted by the researchers indicate that the data set has the potential to enhance our understanding of the relationships between specific cancer-related genetic variations and drug response.  In particular, the researchers were able to predict the sensitivity of cells harboring type II variants to 103 anti-cancer drugs approved by the FDA and an additional 207 investigational new drugs.

One month prior to the release of the NCI-60 panel database, the Genetic Alliance, a network of more than 1,200 disease-specific advocacy organizations, thousands of universities, private companies, government agencies, and public policy organizations, announced the launch of an initiative to fill the public information gap caused by the lack of available genetic information for the BRCA1 and BRCA2 genes (see "Consortium Launches Public Database of BRCA Data").  The Genetic Alliance announcement came on the same day that the Supreme Court issued its decision in Association for Molecular Pathology v. Myriad Genetics, Inc.


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