overgrowth of a contaminating cell line with a shorter doubling time after extended cultivation. In many cases, scientists are unaware that such errors have occurred. Contamination remains a persistent concern among biomedical researchers. Therefore, in an eﬀort to identify latent cross-contamination or other errors in mislabeling, cell lines included in the NCI60 panel were systematically genotyped at the Sanger Institute using the Aﬀymetrix single nucleotide polymorphism (SNP) array (10K SNP array) (Cancer Genome Project, http://www.sanger.ac.uk/ genetics/CGP/Genotyping/synlinestable.shtml). In this study, the presumed breast adenocarcinoma cell line, NCI-ADR-RES (2), and human ovarian carcinoma cell line, OVCAR-8, were determined to share 99% of genotype calls (out of 10 000 SNPs). The Sanger Institute also reported that two glioblastoma cell lines, SNB19 and U-251, exhibited a near-identical genotype. The MDA- MB435 cell line, another presumed breast adenocarci- noma cell line, was determined to be genotypically identical to the M14 melanoma cell line (3). These errors due to inadvertent cross-contamination or processing remain largely unrecognized by investigators and may have profound adverse eﬀects on experimental results and their interpretation. MDA-MB435 alone is cited in over 400 publications as a breast cancer cell line. Cross-contamination and mislabeling may represent a signiﬁcant confounder to experimental interpretation (4–6) and cases of cell line mistaken identity leading to spurious results are a major concern (7). Occasionally researchers adopt techniques to control for this problem, such as short tandem repeats (STR) DNA ﬁngerprinting (8). It has been shown that random dinucleotide markers, the most informative class of microsatellites, are 5–8 times more informative than random SNPs, but 2–12% of SNPs are more informative than the median dinucleotides (9). Indeed, SNPs as DNA markers have been shown to be well suited for diﬀerent purposes such as animal identi- ﬁcation (10), identiﬁcation of population ancestry (11) and for forensic purposes (12). The advent of high-throughput genotyping both high- lights the challenges of sample identity veriﬁcation and provides a mechanism for its resolution. The ability of high-density oligonucleotide arrays to accurately genotype hundreds of thousands of SNP loci in parallel provides an unequivocal molecular ﬁngerprint of each sample. Genotypic diﬀerences between two individuals along the entire genome would score less than 0.1%. However, when genotyping SNPs the percentage of genotype diﬀerences will signiﬁcantly increase. Our analysis of several hundred tumor samples, cell lines and xenografts using SNP arrays has uncovered several instances in which samples thought to be distinct were actually genetically identical. This stimulated our interest in genetic-based methods to precisely identify DNA samples a priori. To this end, we have developed an assay that employs 30–50 single loci across the genome and is capable of distinguishing any two DNA samples based on genotype calls. Concomitantly, this assay can correctly identify a given DNA sample by comparing the genotype call set (‘barcode’) within a reference database Nucleic Acids Research, 2008, Vol. 36, No. 7 2447 that contains bar codes of the most commonly used cell lines. Widespread application of this approach may reduce erroneous experimentation and data interpretation asso- ciated with inaccurate tumor sample identity, thereby providing a signiﬁcant beneﬁt to cancer scientists. MATERIALS AND METHODS Oligonucleotide SNP Array Analysis SNP detection on the 50K Xba array was performed as described previously (3,13–15). Arrays were scanned with a GeneChip Scanner 3000. Genotyping calls and signal quantiﬁcation were obtained with GeneChip Operating System 1.1.1 and Aﬀymetrix Genotyping Tools 2.0 software. Cell lines The initial dataset included genotype data of 155 cell lines derived from diﬀerent organs including: breast (50), colorectal (12), endometrial (4), glioma (11), leukemia (6), lung (27), melanoma (12), ovarian (6), pancreas (3), prostate (4), and renal (18) cell lines. All these were neoplastic cell lines, except for two non-malignant breast cell lines. Seven additional cell lines were used only for the validation step of the study (analysis on Sequenom platform): prostate (5), and lung (2). The NCI60 cancer cell line collection (16–18) is included in the study dataset. A complete annotated list of the cell lines used in this study is included in the Supplementary Material ‘List of Cell Lines used in the SPIA study’. Establishment of N15C6 and N33B2 cell lines. The N15C6 and N33B2 epithelial cell lines were established from normal prostate tissues explanted from two diﬀerent patients and immortalized through transduction with the recombinant LXSNE6E7 retrovirus harboring the human papilloma virus E6 and E7 genes as described previously (19). Transduced cells were selected by use of 400 mg/ml geneticin. After an initial round of cell death and crisis, cells resistant to geneticin grew out and were considered immortal after 10 passages. Spectral karyotype analysis demonstrated both cell lines to be pseudo-diploid. The N15C6 (at passage 45, 10 cells analyzed) karyo- type was determined as: 44, X, dupinv(Y)(q11q12), i(5)(p10), der(8;19)(q10;p10), der(11;15)(q10;q10), der (13;20)(q10;q10), 16, +20, del(22)(q13) (20). The N33B2 karyotype (at passage 21, 9 cells analyzed) was determined as: 40–44, X,Y, -19 (4/7 cells), -22 (5/7 cells), der(1)t(1;13)(p36;q32) (6/7 cells), i(8q) (5/7 cells), der(13)t(11;13)(p10;q10) (2/7 cells), der(15)t(15;19) (q10;p10) (3/7 cells) (21). In this study we used eight passages of N15C6 (passages: 48, 50, 52, 54, 56, 58, 60, 63) and six passages of N33B2 (passages: 21, 27, 33, 35, 37, 39). Genotype distance To quantitatively evaluate how similar two DNA samples are, we introduce a similarity measure D. D is propor- tional to the number of genotype mismatches between the