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Cancer Genetic Variations Database Generated for Therapies

DNA fragment (Wikimedia Commons)

(Wikimedia Commons)

Researchers at National Cancer Institute (NCI), part of National Institutes of Health, cataloged the genetic variations of nine leading types of cancers, and are making the data available to the cancer research community. The team led by pharmacologist Yves Pommier and geneticist Paul Meltzer posted its findings today online in the journal Cancer Research (paid subscription required), published by American Association for Cancer Research.

Pommier, Meltzer, and colleagues analyzed the NCI-60 cancer cell panel, a frequently studied collection of cells from nine types of cancer: breast, ovary, prostate, colon, lung, kidney, brain, leukemia, and melanoma. The analysis conducted a whole exome sequencing of each of the 60 cell lines in the collection. Whole exome sequencing analyzes the coding regions in the DNA, taking a representative subset of the whole genome that still covers the vast majority of disease causing mutations.

The researchers extracted DNA from each of the cell lines and identified the genetic coding variants for each type of cancer, both the variations corresponding to the normal population and those variations that are cancer-specific. Data on the cells with cancer-specific variants were then subjected to the Super Learner prediction algorithm to measure the sensitivity of the cells to 103 cancer drugs already approved by the FDA, and 207 new drugs still being tested or reviewed.

Preliminary returns from the analysis showed correlations between genes associated with cancer — e.g., TP53, BRAF, ERBBs, and ATAD5 — and a number of cancer drugs: nutlin, vemurafenib, erlotinib, and bleomycin. The NCI team expects the more than 6 billion connections between mutations in specific genes and drugs targeting those gene defects to generate many more useful correlations.

The data sets generated by the analysis are available in various formats in two genomic database portals: CellMiner offered by NCI and Ingenuity Systems.

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