Listen to Sandip Patel, MD, Medical Oncologist at Moores Cancer Center and others discuss the value CGP offers to patients and healthcare providers.
What Is Comprehensive Genomic Profiling?
Comprehensive genomic profiling (CGP) is a next-generation sequencing (NGS) approach that uses a single assay to assess relevant cancer biomarkers, as established in guidelines and clinical trials, for therapy guidance. CGP allows labs to:
- Achieve comprehensive coverage of pan-cancer content
- Save time and samples with a multiplex assay
- Reduce costs by avoiding iterative testing
- Perform tests on different sample types, such as tissue or liquid biopsies
- Address the needs of the oncology community both today and tomorrow
1. Detect Multiple Biomarkers in a Single Assay
NGS-based CGP assays provide nucleotide-level resolution of DNA or RNA across multiple genes, enabling identification of numerous types of genomic variants without a priori knowledge of specific mutations. Many of these variants include biomarkers associated with approved and developing therapies across multiple tumor types:
- Single-nucleotide variants (SNVs) and insertions or deletions (indels)
- Gene fusions and RNA splice variants
- Copy-number variants (CNVs)
- Tumor mutational burden (TMB)
- Microsatellite Instability (MSI)
2. Consolidate Testing to Save Time and Precious Samples
CGP consolidates biomarker detection into a single multiplex assay, eliminating the need for sequential testing. With a single test, you can assess the most prevalent as well as rare biomarkers. By assessing all biomarkers at once, you may increase chances of finding a positive biomarker. This potentially provides faster results, limits the input of precious biopsy samples, and may reduce the need for rebiopsy1-3.
3. Identify Actionable Alterations
CGP can offer actionable results to help identify more effective therapeutic paths for cancer patients. When tissue biopsies are unavailable, CGP from liquid biopsy may provide helpful information about a tumor's genomic make-up. CGP using tissue and liquid biopsy together may reveal more insights into a tumor's composition.
Modeling studies have shown that by acquiring critical information with higher efficiency, CGP has demonstrated potential cost savings and shorter time to test result 2.
"The key benefit of an NGS approach is that you can combine all of the tests into one single test. It gives you the same answers, quicker."
Professor Andrew Beggs Discusses CGP
Professor Andrew Beggs of the University of Birmingham shares his point of view on comprehensive genomic profiling as an approach for assessing biomarkers for therapy selection and clinical trial enrollment.
How CGP Compares to Other NGS Methods
CGP vs Single Gene Assays
Single gene assays are limited to a single biomarker. Many times these assays do not cover the entire gene sequence, with the risk of missing important gene alterations.
CGP vs Targeted Panels
Targeted panels typically offer hotspot coverage of genes instead of the entire coding sequence. As a result they can miss important alterations.
A comprehensive single assay that assesses a wide range of biomarkers increases the chances of obtaining relevant information vs. targeted panels.
CGP vs Exome Sequencing
CGP can yield TMB results comparable to whole-exome sequencing at a lower cost.
Because whole-exome sequencing may be cost-prohibitive when developing a personalized medicine approach, there is interest in obtaining accurate TMB assessment with less sequencing.
Reasons to Bring CGP In-House
Adding comprehensive genomic profiling to your lab’s in-house offerings can provide a number of added benefits. These include:
- Obtaining results faster vs relying on another lab’s bandwidth
- Building your own database for future reanalysis needs
- Using less slides than when you send out CGP samples
- Retaining access to the original data, not just the final report
Pan-Cancer Coverage
Comprehensive genomic profiling provides tumor-agnostic testing for hundreds of relevant biomarkers in a single assay, offering significant savings in sample, time, and cost.
Gene content is typically designed to be relevant across multiple tumor types, in contrast to older single-marker or hotspot assays that are often cancer-type specific.
Relevant Biomarkers for CGP Test Inclusion per Guidelines
| Pan-Cancer Biomarkers NTRK1 NTRK2 NTRK3 MSI TMB | ||||||||
|---|---|---|---|---|---|---|---|---|
| Lung | Melanoma | Colon | Ovarian | Breast | Gastric | Bladder | Sarcoma | |
| AKT1 | BRAF | AKT1 | BRAF | AKT1 | BRAF | MSH5 | ALK | |
| ALK | CTNNB1 | BRAF | BRCA1 | AR | KIT | PMS2 | APC | |
| BRAF | GNA11 | HRAS | BRCA2 | BRCA1 | KRAS | TSC1 | BRAF | |
| DDR2 | GNAQ | KRAS | KRAS | BRCA2 | MET | CDK4 | ||
| EGFR | KIT | MET | PDGFRA | ERBB2 | MLH1 | CTNNB1 | ||
| ERBB2 | MAP2K1 | MLH1 | FOXL2 | FGFR1 | PDGFRA | ETV6 | ||
| FGFR1 | NF1 | MSH2 | TP53 | FGFR2 | TP53 | EWSR1 | ||
| FGFR3 | NRAS | MSH6 | PIK3CA | FOXO1 | ||||
| KRAS | PDGFRA | NRAS | PTEN | GLI1 | ||||
| MAP2K1 | PIK3CA | PIK3CA | KJT | |||||
| MET | PTEN | PMS2 | MDM2 | |||||
| NRAS | TP53 | PTEN | MYOD1 | |||||
| PIK3CA | SMAD4 | NAB2 | ||||||
| PTEN | TP53 | NF1 | ||||||
| RET | PAX3 | |||||||
| TP53 | PAX7 | |||||||
| PDGFRA | ||||||||
| PDGFRB | ||||||||
| SDHB | ||||||||
| SDHC | ||||||||
| SMARCB1 | ||||||||
| TFE3 | ||||||||
| WT1 | ||||||||
The genes shown here are not an exhaustive list.
Consult with an expert to learn more about CGP
Hear from Cancer Experts
Carlo B. Bifulco, MD: Comprehensive Genomic Profiling
Carlo B. Bifulco, MD provides his point of view on CGP as an approach for assessing biomarkers for therapy selection and clinical trial enrollment.
Brain Cancer Genomic Profiling
Researchers discuss the value of comprehensive NGS panels for brain tumor studies.
Sandip Patel, MD: Comprehensive Genomic Profiling
Sandip Patel, MD, from UCSD Moores Cancer Center discusses why he believes CGP is poised to become standard of care in oncology.
Featured Webinars & Podcasts
Enabling CGP from Liquid Biopsy Samples
Learn about critical workflow and bioinformatics considerations when consolidating biomarker testing into a panel that enables CGP from liquid biopsy samples in clinical trials.
Comprehensive Genomic Profiling
In this podcast episode, Dr. Brian Piening of the Providence Cancer Institute explains how NGS is changing the standard of care in oncology.
Enabling Scalable CGP from FFPE Samples
Experts discuss why they decided to implement in-house CGP, share analytical performance data, and provide details about their end-to-end workflow.
Molecular profiling for precision cancer therapies
Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial
Feasibility and utility of a panel testing for 114 cancer-associated genes: A hospital-based study
Related Solutions
ctDNA Sequencing
NGS offers the sensitivity researchers need to analyze low levels of circulating tumor DNA (ctDNA) in the bloodstream.
Immuno-Oncology Research
See how NGS can provide insights into immunotherapy response factors and tumor immune evasion mechanisms.
Cancer Whole-Genome Sequencing
Get a base-by-base view of the unique mutations and genomic alterations present in cancer tissue.
Cancer Exome Sequencing
Focus on assessing coding regions, which frequently contain mutations that affect tumor progression.
References
- Pennel AP, Mutebi A, Zheng-Yi Z, et al. Economic Impact of Next-Generation Sequencing Versus Single-Gene Testing to Detect Genomic Alterations in Metastatic Non–Small-Cell Lung Cancer Using a Decision Analytic Model. JCO Precis Oncol. 2019. doi.org/10.1200/PO.18.00356.
- National Comprehensive Cancer Network. https://www.nccn.org/professionals/physician_gls/default.aspx. Accessed March 25, 2019.
- Lindeman NI, et al. Guideline from the college of American pathologists, the international association for the study of lung cancer, and the association of molecular pathology: updated molecular testing guideline for the selection of lung cancer patients for treatment with targeted tyrosine kinase inhibitors. J Thor Onc. 2017;13(3):323-358.