title: Human biosample authentication using the high-throughput, cost-effective SNPtrace(TM) system.
abstract: Cell lines are the foundation for much of the fundamental research into the mechanisms underlying normal biologic processes and disease mechanisms. It is estimated that 15%-35% of human cell lines are misidentified or contaminated, resulting in a huge waste of resources and publication of false or misleading data. Here we evaluate a panel of 96 single-nucleotide polymorphism (SNP) assays utilizing Fluidigm microfluidics technology for authentication and sex determination of human cell lines. The SNPtrace Panel was tested on 907 human cell lines. Pairwise comparison of these data show the SNPtrace Panel discriminated among identical, related and unrelated pairs of samples with a high degree of confidence, equivalent to short tandem repeat (STR) profiling. We also compared annotated sex calls with those determined by the SNPtrace Panel, STR and Illumina SNP arrays, revealing a high number of male samples are identified as female due to loss of the Y chromosome. Finally we assessed the sensitivity of the SNPtrace Panel to detect intra-human cross-contamination, resulting in detection of as little as 2% contaminating cell population. In conclusion, this study has generated a database of SNP fingerprints for 907 cell lines used in biomedical research and provides a reliable, fast, and economic alternative to STR profiling which can be applied to any human cell line or tissue sample.
authors.affiliation: Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America.
authors.forename: May M Y
authors.initials: MM
authors.lastname: Liang-Chu
authors.affiliation: Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America.
authors.forename: Mamie
authors.initials: M
authors.lastname: Yu
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Haverty
authors.affiliation: Van Andel Research Institute, Cytogenetics, Grand Rapids, MI 49503, United States of America.
authors.forename: Julie
authors.initials: J
authors.lastname: Koeman
authors.affiliation: Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, United States of America.
authors.forename: Janet
authors.initials: J
authors.lastname: Ziegle
authors.affiliation: Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, United States of America.
authors.forename: Marie
authors.initials: M
authors.lastname: Lee
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America.
authors.forename: Richard
authors.initials: R
authors.lastname: Bourgon
authors.affiliation: Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Neve
mesh_terms: D018070:Biological Specimen Banks / Q000592:standards*; D002460:Cell Line; D058893:DNA Barcoding, Taxonomic / Q000379:methods* / Q000592:standards*; D005260:Female; D005838:Genotype; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D012732:Sex Determination Analysis; D032681:Spectral Karyotyping