Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation

ObjectiveThere is significant interest in developing early passage cell lines with matched normal reference DNA to facilitate a precision medicine approach in assessing drug response. This study aimed to establish early passage cell lines, and perform whole exome sequencing and short tandem repeat profiling on matched normal reference DNA, primary tumour and corresponding cell lines. MethodsA cell culture based, in vitro study was conducted of patients with primary human papillomavirus positive and human papillomavirus negative tumours. ResultsFour early passage cell lines were established. Two cell lines were human papillomavirus positive, confirmed by sequencing and p16 immunoblotting. Short tandem repeat profiling confirmed that all cell lines were established from their index tumours. Whole exome sequencing revealed that the matched normal reference DNA was critical for accurate mutational analysis: a high rate of false positive mutation calls were excluded (87.6 per cent). ConclusionEarly passage cell lines were successfully established. Patient-matched reference DNA is important for accurate cell line mutational calls.

Automated summary

This study aimed to establish early passage cell lines with matched normal reference DNA for precision medicine in drug response evaluation. It successfully established early passage cell lines and confirmed their association with the primary tumor through short tandem repeat profiling. The study highlights the importance of matched normal reference DNA for accurate mutational analysis in cell lines.