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National Cancer Institute Opens Genetic Variation Database of of Cancer

A comprehensive analysis of coding variants in the NCI-60 panel of cell lines identified by whole exome sequencing, providing a list of possible cancer specific variants for the community.

Abstract

The NCI-60 cell lines are the most frequently studied human tumor cell lines in cancer research. This panel has generated the most extensive cancer pharmacology database worldwide. In addition, these cell lines have been intensely investigated, providing a unique platform for hypothesis-driven research focused on enhancing our understanding of tumor biology. Here, we report a comprehensive analysis of coding variants in the NCI-60 panel of cell lines identified by whole exome sequencing, providing a list of possible cancer specific variants for the community. Furthermore, we identify pharmacogenomic correlations between specific variants in genes such as TP53BRAFERBBs, andATAD5 and anticancer agents such as nutlin, vemurafenib, erlotinib, and bleomycin showing one of many ways the data could be used to validate and generate novel hypotheses for further investigation. As new cancer genes are identified through large-scale sequencing studies, the data presented here for the NCI-60 will be an invaluable resource for identifying cell lines with mutations in such genes for hypothesis-driven research. To enhance the utility of the data for the greater research community, the genomic variants are freely available in different formats and from multiple sources including the CellMiner and Ingenuity websites. Cancer Res; 73(14); 4372–82. ©2013 AACR.

 

NCI60 WES data Available from:

Cellminer:http://discover.nci.nih.gov/cellminer/

Ingenuity:http://www.ingenuity.com/NCI60_WES

BAM_files:http://watson.nci.nih.gov/projects/nci60/wes/BAMS/

DTP_drug_screen:http://dtp.nci.nih.gov/branches/btb/ivclsp.html

DTP_molecular_targets_screen:http://dtp.nci.nih.gov/mtargets/mt_index.html (Last accessed 5/28/13).