True Comprehensive
Genomic Profiling

Oncomine Comprehensive Assay Plus


Common Limitations of Comprehensive Genomic Profiling (CGP)

  • Complicated workflows requiring up to 5 different instruments and software from up to 5 different suppliers require expertise and extensive hands on time.
  • Some assays are not able to detect mutational signatures relevant for today's precision oncology research such as homologous recombination deficiency (HRD), tumor mutational burden (TMB) and microsatellite instability (MSI). Such assays are not comprehensive of increasingly complex and emerging biomarkers.
  • High sample input requirements of some hybrid capture-based NGS assays could result in >50% of samples not being eligible for testing1. With such assays, potentially more than half of the samples will not generate valid results.




On-Demand Webinar Series

Hear from experts using
the Oncomine Comprehensive Assay Plus





Dr. Nicola Normanno, Director, Translational Research, National Cancer Institute, Italy - Pascale Foundation


Future Clinical Perspective of HRD Testing in Ovarian Cancer Samples Using NGS CGP

In this webinar, Dr. Nicola Normanno presents a research study of the analytical validation for the in-house assessment of HRD with the Oncomine Comprehensive Assay Plus on a cohort of ovarian cancer samples, including how the genomic instability metric (GIM) compares to orthogonal methods, and a retrospective analysis of clinical outcomes from the same cohort.


From BRCA to HRD testing in ovarian cancer

In this webinar, Dr. Nicola Normanno provides an overview of methods for assessing HRD, and his experience evaluating the Oncomine Comprehensive Assay Plus, a targeted NGS approach that can help clinical research in identifying all relevant biomarkers, including HRD.



Oncomine Comprehensive Assay Plus

The Oncomine Comprehensive Assay Plus is a next-generation sequencing (NGS) solution that enables true comprehensive genomic profiling (CGP) without any compromises.



True End-to-End Workflow

Minimize the resources and expertise required to generate CGP results by combining a highly automated workflow with a complete bioinformatics pipeline all from a single supplier.

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All Relevant Biomarkers

All relevant single gene and complex biomarkers including homologous recombination deficiency (HRD) based on genomic instability metric (GIM), tumor mutational burden (TMB) and microsatellite instability (MSI).

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Minimal Sample Input

Low FFPE sample input of 20 ng DNA and RNA means more, and smaller, samples can be tested

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True end-to-end

Empower lab efficiency by reducing hands on time and possible errors due to handling. The highly automated workflow with Ion Torrent Chef and Ion Torrent GeneStudio S5 with dedicated bioinformatics pipelines including Oncomine Reporter means ~1 hour of hands-on time.

True Comprehensive Profiling

Single-gene biomarkers—Broad range of single-gene variants, such as single-nucleotide variants (SNVs), insertions and deletions (indels), novel and known fusions, splice variants, and copy number variants (CNVs), including both copy number gains and losses

Multiple-gene biomarkers—Tumor mutational burden (TMB), predisposition to genetic hypermutability by comparing microsatellite instability (MSI) regions, and analyze mutational signatures for insights into etiological factors in tumorigenesis

Homologous recombination deficiency— Assess causes and consequences HRD including mutations in 42 key genes in the homologous recombination repair (HRR) pathway as well as genomic scarring by the GIM.

Read Article: A Comprehensive Answer for Cancer: Is Comprehensive Genomic Profiling Always the Right Approach?

Tissue is NOT an issue for Oncomine Comprehensive Assay Plus

A multi-center study reported that more than half of all samples would not be suitable for hybrid capture-based NGS, while 93.8% of samples below 25mm2 were successfully tested by amplicon-based NGS methods.

  • Many clinical research samples are small biopsies core fine-needle aspirates
  • Some NGS methods require as high as 50 to 1,000 ng sample input, which cannot be obtained from small biopsies




HRD & HRR Clinical Research

Homologous recombination deficiency is becoming an important new biomarker in precision oncology clinical research.Under normal conditions, genes in the HRR pathway repair DNA damage. Errors in the HRR pathway, such as loss-of-function or deleterious mutations in the associated genes, can lead to higher levels of genomic instability - the HRD phenotype. HRD has been shown to be relevant in certain tumors, such as ovarian and prostate cancers, and is being extensively studied in clinical research.

HRD can be assessed using two main strategies:

  1. Detection of genetic causes, such as germline or somatic mutations of HRR genes.
  2. Measuring the consequence of HRD through presence of genomic scarring/instability.





Mutation Detection of HRR Pathway Genes

The significant role of HRR genes in maintaining genome stability and tumor suppression has been studied extensively,
especially in the BRCA1 and BRCA2 genes. In recent years, it has been demonstrated that alterations in other homologous recombination repair pathway genes may lead to genomic instability and cancer cell development. The status of HRR genes are now considered an important biomarkers for precision oncology research.




Genomic Instability Measurement

The Oncomine Comprehensive Assay Plus measures genomic scarring with the genomic instability metric (GIM). GIM is a numeric value between 0 and 100 that summarizes unbalanced copy number changes using genomic segmentation.

Figure B demonstrates  sample-level LOH compared with Applied Biosystems(TM) OncoScan(TM) CNV Assay and Figure C shows a comparison of GIM for BRCA-positive and BRCA-negative ovarian cancer samples (n = 46). No: no pathogenic BRCA1 or BRCA2 mutation present. Yes: pathogenic BRCA1 or BRCA2 mutation present. Source: internal R&D data.

Is comprehensive genomic profiling (CGP)
the answer to everything ?

No, one size does not fit all. For example, let’s take non-small cell lung cancer (NSCLC) samples. All biomarkers relevant for clinical research can be tested by one, 50 gene targeted panel. It’s cheaper, faster, and it requires less sample input, which is critical in NSCLC, where “tissue is still an issue”. There are four key scenarios in which comprehensive genomic profiling
would be most impactful.

Learn about them in The Pathologist Article “A Comprehensive Answer for Cancer”.

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If you are interested in learning more about our Oncomine NGS solutions for comprehensive genomic profiling of solid tumors, a local representation can contact you to set up a demo, or discuss pricing options.




For Research Use Only. Not for use in diagnostic procedures.