Optimisation and validation of a nanopore-based sequencing method for potential molecular testing of CNS tumours

Abstract

Research shows the MinION sequencing device by Oxford Nanopore Technologies has the potential to overcome challenges posed by current NGS technologies used in isocitrate dehydrogenase (IDH) mutational testing for glioma diagnosis. However, MinION has not been validated for clinical practice using FFPE tissue. Thus, we developed and analytically tested a PCR amplicon-based assay in a CLIA setting to detect IDH SNVs on FFPE DNA using MinION. The assay revealed concordance, sensitivity, and specificity of 100%. Limit of blank was 1.5% and limit of detection was 3.3% at 500x depth. Total assay cost was $50–$134/sample with total turnaround time of less than two days.

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