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Last Updated: 05/12/15

Molecular Characterization of the NCI-60

The cell lines within the NCI-60 panel of human tumor cell lines are perhaps some of the most extensively characterized cell lines in broad laboratory use. These data are publicly available on the DTP web site here.

Of particular interest to those concerned about cell line identity, the cell lines have been characterized using ~120,000 SNP arrays (1) and by oligonucleotide-base HLA typing (2). Mutations in a number of cancer-relevant genes have been analyzed in these cell lines (3). They have also been subjected to spectral karyotyping (data available at: http://www.ncbi.nlm.nih.gov/projects/sky/) (4). The lines have also been characterized for variations in short tandem repeats (STR) (5), although there are some technical issues in applying this technology, which was developed as a forensic tool, to cancer cell lines. In particular, polyploidy and/or increased mutation rates that are characteristics of some of the cell lines may require adjustments in interpretation of STR data. Additional characterization of the NCI-60 panel will be posted periodically.

Previous analyses (esp. the SNP arrays and HLA typing) have shown that several pairs of cell lines within the NCI60 panel are from the same individual. STR profiling also finds these cell lines to be “matched pairs.” The data point to events early in the derivation of these cell lines — it appears that the versions of these cell lines in use throughout the research community are the same as the versions in the DTP collection. For a further discussion of these cell lines, please see:

In addition to these methods of cell line characterization, data from numerous other studies are available for these cell lines through the DTP web site here.

  1. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML, Fisher DE, Sellers WR. Nature. 2005 Jul 7;436(7047):117-22.
  2. HLA class I and II genotype of the NCI-60 cell lines. Adams S, Robbins FM, Chen D, Wagage D, Holbeck SL, Morse HC 3rd, Stroncek D, Marincola FM. J Transl Med. 2005 Mar 4;3(1):11.
  3. http://www.sanger.ac.uk/genetics/CGP/NCI60/
  4. Karyotypic complexity of the NCI-60 drug-screening panel. Roschke AV, Tonon G, Gehlhaus KS, McTyre N, Bussey KJ, Lababidi S, Scudiero DA, Weinstein JN, Kirsch IR.Cancer Res. 2003 Dec 15;63(24):8634-47.
  5. DNA fingerprinting of the NCI-60 cell line panel. Lorenzi PL, Reinhold WC, Varma S, Hutchinson AA, Pommier Y, Chanock SJ, Weinstein JN. Mol Cancer Ther. 2009 Apr;8(4):713-24.