OCT 22, 2020 4:40 PM CEST

First Experiences with Oncomine™ Comprehensive Assay Plus for comprehensive genomic profiling

C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Staff Pathologist, Institute for Pathology medica AG
    Biography

      After receiving her MD degree from the University of Zurich, Switzerland, Ines Raineri attended a postgraduate course for basic science at the same university. She then worked as postdoctoral fellow at the Institute for Medical Microbiology of the University of Basel, Switzerland, investigating HIV-promoter-insertions in the human genome. She received fellowships from the Swiss National Foundation, Ciba-Geigy Jubiläumsstiftung, Roche Research Foundation and Holderbank Stiftung to work as postdoctoral fellow at the University of California San Francisco, where she was later hired to work as research assistant geneticist. During her nearly 8 years at UCSF she was involved in generating transgenic cell lines and mice to study oxygen free radical metabolism. After returning to Switzerland, she worked again at the Institute for Medical Microbiology of the University of Basel, establishing knockdown systems to rapidly evaluate gene functions in embryonic stem cells. She then moved on to train as a board-certified pathologist and currently works as a staff pathologist at the Institute for Pathology medica AG in Zurich in molecular pathology, histology and cytology.


    Abstract

    IIdentification of relevant mutations, determination of tumor mutational burden (TMB) and microsatellite (MS) status are paramount to precision oncology research and the Oncomine Comprehensive Assay Plus (OCAP) measures the three markers in one assay. To establish OCAP in our laboratory, we analyzed 21 formalin-fixed paraffin-embedded cancer specimens which we previously had subjected to Oncomine Focus (OFA), Comprehensive (OCA) and/or Tumor Mutation Load (TML) assays, respectively. In addition, we had assessed microsatellite status (MSI) by MSI-PCR and/or immunohistochemistry for mismatch repair proteins in 16 of these samples. MSI-scores determined by OCAP consistently matched immunohistochemistry and/or PCR results, showing the accuracy of MSI calling by OCAP. TMB was assessed by TML assay and OCAP in 8 samples and in all cases comparable results were obtained. Two cases displayed high TMB scores (mutations/megabase) of 54.27/69.71 and 44.64/76.78 (OCA/P/TML), respectively. Intermediate TMB scores were obtained in two samples (6.66/6.7; 12.69/9.22; OCAP/TML) and four samples showed matching low TMB scores. A total of 56 single nucleotide variants and small INDELS were called by OFA, OCA and/or TML, in the 21 samples analyzed. In 54/57 cases variants were called by OCAP at a similar allele frequency. In three cases variants were not called due to quality issues. Copy number variations (CNV) were called in 17/21 OCAP performed, in 4 samples high MAPD values (>0.5) prevented CNV calling. A total of 16 copy number gains had been called by OCAv3 or OFA. 13/16 gains were confirmed by OCAP at similar copy numbers. In three cases of low level amplifications no significant increase in copy numbers was detected by OCAP compared to OCAv3. In conclusion, we show that OCAP with its subsequent analyses can be established and carried out in a molecular pathology laboratory, thus avoiding sending out of tissues with its negative effects on turnaround times and costs.

    Learning Objectives:
    1. Identify biomarkers relevant for clinical research
    2. Identify advantages/disadvantages of large panel genomic profiling


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