SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy
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John P Didion, Ryan J Buus, Zohreh Naghashfar
1Department of Genetics, University of North Carolina at Chapel Hill, CB 7295, Chapel Hill, NC 27599-7264, USA. hmorse@niaid.nih.gov.
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.
Insights
Mouse cell line authentication is crucial. Single nucleotide polymorphism (SNP) profiling offers a robust method to detect misidentified or contaminated cell lines, ensuring research integrity.
Area of Science:
- Genomics
- Cell Biology
- Bioinformatics
Background:
- Misidentified and contaminated cell lines pose a significant challenge in biological research.
- While human cell line authentication is increasingly mandated, mouse cell line issues remain underpublicized.
- Short tandem repeat (STR) profiling, the standard method, has limitations in distinguishing closely related mouse strains and detecting karyotypic changes.
Purpose of the Study:
- To develop and validate a high-throughput method for authenticating mouse cell lines using single nucleotide polymorphism (SNP) profiling.
- To establish a reference database for common mouse strains and cell lines.
- To address the limitations of existing authentication methods like STR profiling.
Main Methods:
- Development of computational methods (Cell Line Authentication by SNP Profiling, CLASP) utilizing cost-efficient SNP arrays.
- Creation of a reference database for commonly used mouse strains and cell lines.
- Application of CLASP for authentication, copy number analysis, and contaminant detection.
Main Results:
- CLASP effectively discriminates between cell lines of diverse origins, including those from the same inbred strain.
- The method can detect contaminants at concentrations as low as 5%.
- Out of 99 tested cell lines, 15 showed significant genetic divergence, indicating misidentification, mixed strain backgrounds, contamination, or aneuploidy.
Conclusions:
- Misidentification and contamination of mouse cell lines may be as prevalent as in human cell cultures, impacting research reliability.
- Regular authentication of cell cultures is essential for mitigating risks associated with cell line integrity.
- SNP array profiling, as implemented by CLASP, provides an effective solution for combating mouse cell line misidentification and contamination.
