2454 Nucleic Acids Research, 2008, Vol. 36, No. 7 Figure 5. Pair-wise distances of 93 cell lines genotyped on Sequenom platform. With the goal of exporting the SPIA assay to other platforms, we tested a 34 SNP panel using the Sequenom platform on a set of 93 cell lines. The statistical test was applied to get individual score for each distance. The pair made of MCF7 and BT20 was scored as ‘match’ (green dot), accordingly with expectations. One pair out of 4277 was scored as ‘uncertain’ (blue dot). All others 4276 pairs were correctly scored as ‘diﬀerent’. The list of the 93 cell lines is reported in the Supplementary Material. meaning that up to 20% of the genotype calls on chromosome 11 diﬀer between the two passages. Indeed, these human papillomavirus (HPV) transfected cell lines are known to be aﬀected by the introduction of E7, a HPV gene (26,27), resulting in instability on chromosome 11. This experiment demonstrated that SPIA correctly iden- tiﬁes a cell line regardless of the passage number and that using a dedicated panel of SNPs provides a useful quantitative approach to monitor genetic drift of cell lines, important for characterization of mammalian embryonic cell lines, which may exhibit genetic instability over time. A genotyping-based assay for tumor sample fingerprinting One goal of the SPIA panel was to make it small enough to allow it to be exported for routine use in the research laboratory settings. Limited panels of small numbers of microsatellite markers or SNPs are commonly used for identiﬁcation; however, given concerns regarding error rates and non-informative SNP calls, these panels have only limited value, especially when working with a variety of samples. Therefore with the goal of exporting the SPIA panel to other platforms, we tested the panel using Sequenom mass spectrometric genotyping technology. This MALDI-TOF mass spectrometer system can diﬀer- entiate SNP alleles given the diﬀerent molecular weights of the allele-speciﬁc products. This system also has the advantage of being fully automated and regularly used in genome centers throughout the world. We evaluated the pair-wise distances on a set of 34 SNPs for a set of 93 cell lines. The 34 SNPs were picked from the ranked list of SNPs. Figure 5 shows the pair-wise distances. The mean and the median distances are 0.656 and 0.594, respectively, and the minimum and maximum distances are 0.059 and 0.941. As expected, the cell lines MCF7 and BT20 were scored as ‘similar’. DISCUSSION Accurate tracking and labeling of samples is critical to experimental integrity in the genomic era. This is particularly true for cell lines, which are often cultured over a period of years and are handed from one labora- tory to another. Recent reports of inadvertent cross- contamination or labeling mistakes can stay hidden from researchers for years (2,28). Given the large number of published reports that use functional cell line data to make signiﬁcant claims with respect to cellular mechanisms of tumor biology and that this data may even serve as the basis for pre-clinical therapeutic trials, establishment of the proper identity is critical. While experimentally possible, extensive genome-wide genotyping of cell lines as part of standard operating procedures (SOPs) in a laboratory is not practical or cost-eﬀective. Therefore, we developed the SPIA assay that allows investigators to accurately identify cell lines taking into account both issues of cost and feasibility. SPIA is based on the selection of highly informative SNPs for the creation of a DNA sample-speciﬁc barcode that can be used for a likelihood evaluation of the DNA identity. This assay was demonstrated to be suitable for the identity check of a broad range of cell lines by using 40 SNPs. The more SNPs in the panel, the more conﬁdent the ﬁnal DNA identity determination. To select an optimized SNP panel we developed an in silico approach by mining 50 K genotype data from more than 150 cancer cell lines, derived from 11 diﬀerent