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Sci Rep. 2016 Jul 26;6:28994. doi: 10.1038/srep28994.

Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication affecting cell function.

Author information

Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA.
Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
The Hamner Institutes for Health Sciences, Research Triangle Park, NC, USA.
Department of Biochemistry and Molecular &Cellular Biology, and Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
Agilent Technologies, Inc., Santa Clara, CA, USA.
Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
University of Konstanz, CAAT-Europe, Germany.


Common recommendations for cell line authentication, annotation and quality control fall short addressing genetic heterogeneity. Within the Human Toxome Project, we demonstrate that there can be marked cellular and phenotypic heterogeneity in a single batch of the human breast adenocarcinoma cell line MCF-7 obtained directly from a cell bank that are invisible with the usual cell authentication by short tandem repeat (STR) markers. STR profiling just fulfills the purpose of authentication testing, which is to detect significant cross-contamination and cell line misidentification. Heterogeneity needs to be examined using additional methods. This heterogeneity can have serious consequences for reproducibility of experiments as shown by morphology, estrogenic growth dose-response, whole genome gene expression and untargeted mass-spectroscopy metabolomics for MCF-7 cells. Using Comparative Genomic Hybridization (CGH), differences were traced back to genetic heterogeneity already in the cells from the original frozen vials from the same ATCC lot, however, STR markers did not differ from ATCC reference for any sample. These findings underscore the need for additional quality assurance in Good Cell Culture Practice and cell characterization, especially using other methods such as CGH to reveal possible genomic heterogeneity and genetic drifts within cell lines.

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