SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy

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• 作者：John P Didion (6) (7) (8)
  Ryan J Buus (6) (7) (8)
  Zohreh Naghashfar (9)
  David W Threadgill (10) (11)
  Herbert C Morse III (9)
  Fernando Pardo-Manuel de Villena (6) (7) (8)
  
  6. Department of Genetics ; University of North Carolina at Chapel Hill ; CB 7295 ; Chapel Hill ; NC ; 27599-7264 ; USA
  7. Lineberger Comprehensive Cancer Center ; University of North Carolina at Chapel Hill ; CB 7295 ; Chapel Hill ; NC ; 27599-7264 ; USA
  8. Carolina Center for Genome Science ; University of North Carolina at Chapel Hill ; CB 7295 ; Chapel Hill ; NC ; 27599-7264 ; USA
  9. Laboratory of Immunogenetics ; National Institute of Allergy and Infectious Diseases ; National Institutes of Health ; Twinbrook I ; Room 1421 ; 5640 Fishers Lane ; Rockville ; MD ; 20852 ; USA
  10. Department of Veterinary Pathobiology ; College of Veterinary Medicine and Biomedical Sciences ; Texas A&M University ; College Station ; TX ; 77843 ; USA
  11. Department of Molecular and Cellular Medicine ; College of Medicine ; Texas A&M University ; College Station ; TX ; 77843 ; USA
  
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：2,861 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background The crisis of Misidentified and contaminated cell lines have plagued the biological research community for decades. Some repositories and journals have heeded calls for mandatory authentication of human cell lines, yet misidentification of mouse cell lines has received little publicity despite their importance in sponsored research. Short tandem repeat (STR) profiling is the standard authentication method, but it may fail to distinguish cell lines derived from the same inbred strain of mice. Additionally, STR profiling does not reveal karyotypic changes that occur in some high-passage lines and may have functional consequences. Single nucleotide polymorphism (SNP) profiling has been suggested as a more accurate and versatile alternative to STR profiling; however, a high-throughput method for SNP-based authentication of mouse cell lines has not been described. Results We have developed computational methods (Cell Line Authentication by SNP Profiling, CLASP) for cell line authentication and copy number analysis based on a cost-efficient SNP array, and we provide a reference database of commonly used mouse strains and cell lines. We show that CLASP readily discriminates among cell lines of diverse taxonomic origins, including multiple cell lines derived from a single inbred strain, intercross or wild caught mouse. CLASP is also capable of detecting contaminants present at concentrations as low as 5%. Of the 99 cell lines we tested, 15 exhibited substantial divergence from the reported genetic background. In all cases, we were able to distinguish whether the authentication failure was due to misidentification (one cell line, Ba/F3), the presence of multiple strain backgrounds (five cell lines), contamination by other cells and/or the presence of aneuploid chromosomes (nine cell lines). Conclusions Misidentification and contamination of mouse cell lines is potentially as widespread as it is in human cell culture. This may have substantial implications for studies that are dependent on the expected background of their cell cultures. Laboratories can mitigate these risks by regular authentication of their cell cultures. Our results demonstrate that SNP array profiling is an effective method to combat cell line misidentification.