Comprehensive and simultaneous genomic profiling across 500+ genes, TMB, and MSI from 10ng FFPE sample

Comprehensive and simultaneous genomic profiling across 500+ genes, TMB, and MSI from 10 ng/pool FFPE sample

The Oncomine Comprehensive Assay Plus is a broad, pan-cancer multi-biomarker NGS solution that enables comprehensive genomic profiling of key targeted therapy and immunotherapy biomarkers such as TMB and MSI. This assay covers more than 500 unique genes and supports simultaneous analysis of both DNA and RNA in one workflow. Gene content is carefully selected to provide the most relevant insights and is based on extensive curation from the Oncomine Knowledgebase. Low sample input reccomendations of 10 ng/pool formalin-fixed, paraffin-embedded (FFPE) sample enables successful analysis of even small and challenging FFPE samples like fine needle aspirates or cytology samples.

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Key highlights of the Oncomine Comprehensive Assay Plus:

  • Profile 500+ unique genes across all classes of variants, including solid tumor driver genes
  • Detect relevant SNVs, indels, CNVs, gene fusions, splice variants in addition to TMB and MSI simultaneously
  • Achieve up to 99% sequencing success rate with 10 ng/pool FFPE input
  • Streamlined sample-to-report workflow generates insights in days

Oncomine Comprehensive Assay Plus gene content

The Oncomine Comprehensive Assay Plus includes hotspot SNVs and indels, CNVs, gene fusions, and splice variants.

500 Plus Genes Chart

Streamlined in-house NGS workflow

Even when faced with a broad, 500+ gene assay, the Oncomine workflow can take you from 10 ng/pool FFPE samples to variant data in just four days. After sample preparation, which includes extraction, library preparation, and templating, up to four samples can be multiplexed on the Ion 550 Chip and subsequently sequenced on the Ion GeneStudio S5 Plus or Ion GeneStudio S5 Prime systems. The Oncomine informatics workflow is an integrated, internally developed sample-to-report solution for data analysis, from initial sequence analysis from many variants to annotation of relevant cancer drivers to a final report from Oncomine Reporter. This simple, streamlined solution does not require any specialized bioinformatics expertise to get your variant data.

Prep Sequence Analyze Chart

Oncomine Reporter—understanding your variant data

Once your NGS data has been analyzed and annotated, the informatics workflow will generate an easy-to-use report that enables contextual investigation of sample-specific variants to understand their use with respect to labels, guidelines, and clinical trials.

OCA Plus Sample Report

Oncomine Comprehensive Assay Plus coverage

Assay performance on reference control

Variant type TP FP FN Sensitivity PH
SNV 2181 4 33 98.51% 99.82%
INDEL 62 2 1 98.41% 96.88%

Assay performance on CNV

  TP FP FN Sensitivity Specificity
CNV gain 34 1 12 97.1% 100%
CNV loss 17 2 12 89.4% 100%

Figure 1. To assess small-variant calling performance we performed sequencing experiments using the AcroMetrix Oncology Hotspot Control4 (AOHC) that contains hundreds of SNVs and tens of indels covered, containing tens of SNV/INDELs by Oncomine Comprehensive Assay Plus. Nine replicates of AOHC were sequenced. Performance was calculated as %sensitivity and %PPV (positive predictive value) in detection and measured. SNV performance was assessed at variant allele frequency of >= 5%, INDEL at variant allele frequency of >=20%.

Copy number detection performance was assessed against known copy-number status from characterized solid tumor FFPE samples (n=5) and commercially available ATCC (n=3) and Coriell Institute for Medical Research (n=14) cell lines. For the FFPE samples, known truth was determined using an orthogonal Oncomine NGS assay; for ATCCTM cell-lines, known truth was derived from the literature and publicly available genotyping expression arrays. For Coriell cell-lines, positive calls were inferred using the reported cytogenetic abnormalities and aneuploidy status. Gene-level copy-gain is called when the lower confidence interval (CI) of the copy number estimate is >4; copy-loss is called when the CI upper bound <2. For specificity calculations, wild-type copy-number estimates (autosomal copy number within (1.8, 2.2)) were considered as negative, while CN estimates outside that range were called positive.

Oncomine Comprehensive Assay Plus—tumor mutational burden (TMB) performance

in-silico OCA Plus target regions with whole exome sequencing (WES)


Comparison of OCA Plus with Assay F


Figure 2. TMB performance of Oncomine Comprehensive Assay Plus. Whole exome sequencing has traditionally been the method of choice for TMB quantitation. In-silico analysis against WES was performed to characterize TMB performance of OCA Plus. High correlation was demonstrated (Fig. 2A) via scatter plots show correlation between the targeted assay (y-axis) and WES (x-axis) mutation counts which was downloaded from TCGA MC33. A second comparison was conducted against a commercially available assay with real world samples. OCA Plus also shows high correlation to TMB determined using assay F (Fig. 2B).