MAY 14, 2020 2:40 PM SGT

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

Speaker
  • Group Leader for Cancer Neoantigen Vaccine Development Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research (JFCR)
    Biography
      2008-2011: Doctor of Philosophy (Ph.D) in Medical Genomics, The University of Tokyo, Japan.
      2011-2012: JSPS Postdoctoral fellows at Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo and visiting researcher for the Division of Genetics, National Cancer Center Research Institute, Japan.
      2012-2014: Research Scientist at Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, The Institute of Physical and Chemical Research (RIKEN), Japan.
      2015-2016: Lecturer at Faculty of Pharmacy, University of Sydney, Australia.
      2017-Current: Group leader for Cancer Neoantigen Vaccine Development Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research (JFCR).

      Siew-Kee (Amanda) Low has been working extensively in genomic research that expands from cancer genomics, pharmacogenomics and various genomic studies for complex diseases. During her Ph.D. and postdoctoral fellows, she has performed comprehensive genomic analysis by utilizing large-scale genome-wide association studies (GWAS) and whole genome/exome studies to identify genetic variations associated with various complex diseases and pharmacogenomics studies. She is also the lead biostatistician representing Biobank Japan participating various international consortium. She has published in top-notch journals such as Nature Genetics, PNAS, Human Molecular genetics and etc.

      Currently, she is establishing the liquid biopsy system for cancer suivellance and monitoring in JFCR. As part of the Japan national project "Innovative AI hospital system", she is one of the leaders to standardize and implement liquid biopsy in the medical system in Japan.

    Abstract

    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


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