Nucleic Acids Research Advance Access published online on February 27, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn089
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Computational Biology |
SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines
1Department of Pathology, Brigham and Women's Hospital, 2Harvard Medical School, 3Department of Medical Oncology and Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, MA, 4Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA and 5Department of Urology and Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI USA
*To whom correspondence should be addressed. Tel: +1 646 962 5616; Fax: +1 212 746 8816; Email: frd2004{at}med.cornell.edu
Received December 26, 2007. Revised February 10, 2008. Accepted February 11, 2008.
Translational research hinges on the ability to make observations in model systems and to implement those findings into clinical applications, such as the development of diagnostic tools or targeted therapeutics. Tumor cell lines are commonly used to model carcinogenesis. The same tumor cell line can be simultaneously studied in multiple research laboratories throughout the world, theoretically generating results that are directly comparable. One important assumption in this paradigm is that researchers are working with the same cells. However, recent work using high throughput genomic analyses questions the accuracy of this assumption. Observations by our group and others suggest that experiments reported in the scientific literature may contain pre-analytic errors due to inaccurate identities of the cell lines employed. To address this problem, we developed a simple approach that enables an accurate determination of cell line identity by genotyping 34 single nucleotide polymorphisms (SNPs). Here, we describe the empirical development of a SNP panel identification assay (SPIA) compatible with routine use in the laboratory setting to ensure the identity of tumor cell lines and human tumor samples throughout the course of long term research use.