Oncomine Precision Assay on Ion Torrent Genexus System for liquid biopsy sample

Molecular profiling is key in precision oncology research and whilst the tissue testing has become a routine, liquid biopsy might provide a non-invasive alternative when tissue biopsy is inaccessible. In future, detection of ctDNA could also provide a ‘real-time’ overview of disease burden owing to its short half-life and hence, useful in disease monitoring purposes.

To overcome the current obstacles of NGS systems, the Genexus Integrated Sequencer automates all steps of the targeted NGS workflow starting from nucleic acid of formalin-fixed paraffin-embedded tissues or plasma that significantly reduce laborious procedures. Importantly, the whole specimen-to-report workflow delivers results in a single day.

In this presentation, I will demonstrate the detection rate of alteration using Oncomine Precision Assay (OPA) on Genexus system using positive control samples, tissue and cell-free DNA. Nucleic acid was subjected to automated Genexus Integrated Sequencer for library construction using OPA panel, templating and sequencing. OPA covers key hotspot mutations, copy number gains or loss, fusion drivers. Particularly, among 44 of 48 (92%) cfDNA samples from non-small cell lung cancer were detected to carry at least one somatic mutation. Sensitizing EGFR mutations detected from 25 of 33 cfDNA of EGFR-positive plasma samples  were in complete concordance with tissue samples. Known resistance mutations of targeted therapies were also detected.

Learning Objectives:

1. Understand importance of NGS in molecular profiling of cancer

2. Define various NGS parameters and interpretation