Brain tumour cell line authentication, an efficient alternative to capillary electrophoresis by using a microfluidics-based system

Background. The current method for cell line authentication is short tandem repeat PCR (STR-PCR) -based genotyping involving co-amplification of a panel of STR loci by multiplex PCR and the downstream fragment length analysis (FLA), usually performed by capillary electrophoresis. FLA by capillary electrophoresis is time-consuming and can be expensive as the facilities are generally not accessible for many research laboratories. Methods. In the present study, a microfluidic electrophoresis system, the Agilent 2100 Bioanalyzer, was utilised to analyse the STR-PCR fragments from 10 human genomic loci of a number of human cell lines, including 6 gliomas, 1 astrocyte, 1 rhabdomyosarcoma, 1 primary lung cancer and 1 lung brain metastatic cancer; and this was compared to the standard method, i.e. capillary electrophoresis, using the Applied Biosystems 3130xl Genetic Analyzer. Results. The microfluidic electrophoresis method produced highly reproducible results with good sensitivity in sizing of multiple PCR fragments and each cell line demonstrated a unique DNA profile. Furthermore, DNA fingerprinting of samples from 5 different passage numbers of the same cell line showed excellent reproducibility when FLA was performed with the Bioanalyzer, indicating that no cross-contamination had occurred during the culture period. Conclusion. This novel application provides a straightforward and cost-effective alternative to STR-based cell line authentication. In addition, this application would be of great value for cell bank repositories to maintain and distribute precious cell lines.