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

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