AbstractObjectiveThere 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.