Cancer Biomarker Detection

two women wearing white lab coats and blue gloves looking at a tablet

Identify actionable cancer biomarkers

The number of cancer biomarkers with associated targeted therapies continues to increase. We are at a place now with NGS-based comprehensive genomic profiling where one biopsy, one test, and one report can lead to improved outcomes for cancer patients, thereby advancing precision medicine and improving patient health and wellness.1-2

There are several key considerations when evaluating a cancer biomarker test to aid with therapy selection.

Biomarkers in US guidelines and drug labels for highly prevalent tumors 1,3
solid tumor pan cancer outlined

Maximize biomarker data from one biopsy

Conventional testing with techniques like FISH, PCR and IHC are insufficient to assess all relevant cancer biomarkers and preserve precious tissue samples. Individual sequential biomarker tests are common; however, they have some disadvantages. First, these tests require a significant amount of biopsy sample that’s not always accessible. Second, these single gene tests have limited content and may miss the opportunity to identify a positive biomarker.

A next-generation sequencing (NGS)-based biomarker test can analyze hundreds of clinically actionable cancer biomarkers simultaneously. This additional data provides more opportunity to match patients with appropriate molecular treatment regime. A single NGS-based biomarker test can replace multiple single-gene tests or small hotspot panels.4-7

If tissue biopsies are unavailable, comprehensive genomic profiling (CGP) from liquid biopsy may provide helpful information about a tumor's genomic make-up. This can decrease the need to rebiopsy and save precious time in the care continuum.8

Examples of key cancer biomarkers

Immunotherapy biomarkers

In addition to genes specifically involved in immune pathways, associated biomarkers have emerged that rely upon assessment of numerous genomic loci, such as tumor mutational burden (TMB) and microsatellite instability (MSI).

Gene fusions

Associated with the increasing number of discovered fusion events is the number of clinically actionable cancer biomarkers. Examples of clinically actionable gene fusions include NTRK and RET gene fusions.

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Homologous recombination deficiency (HRD)

HRD (homologous recombination deficiency) is a phenotype used to describe loss of function in the HRR (homologous recombination repair) pathway. When this occurs, cells are unable to repair double-stranded DNA breaks, leading to tumorigenesis.

HRD can be measured by "cause," such as a BRCA mutation or by "consequence" in the form of genomic scarring. NGS technology can assess both causal genes and genomic scarring.

Learn more about HRD

SNVs, CNVs, & indels

There are multiple types of mutations that are associated with cancer-related genes, such as single-nucleotide variants (SNVs), insertions and deletions (indels), and copy-number variants (CNVs).

Traditionally these specific biomarkers have been analyzed with single-gene tests, but as the number of biomarkers increases for each cancer type, more labs have turned to NGS methods that can analyze numerous genes and variant types in a single assay.

CGP for cancer biomarker detection

Comprehensive genomic profiling (CGP) consolidates hundreds of cancer-related biomarkers into a single assay, eliminating the need for sequential testing. CGP can detect biomarkers at nucleotide-level resolution and typically comprises all major genomic variant classes (SNVs, indels, CNVs, fusions, and splice variants), as well as large genomic signatures (TMB and MSI), maximizing the ability to find clinically actionable alterations.

Learn more about CGP
Improving patient outcomes with CGP

Maximize identification of molecularly matched therapies.

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Cancer biomarkers for CGP test inclusion

CGP provides tumor-agnostic testing for hundreds of relevant cancer biomarkers, per guidelines, in a single assay, potentially offering significant savings in sample, time, and cost.

Pan-Cancer Biomarkers      NTRK1        NTRK2        NTRK3        MSI        TMB        RET        BRAF
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.

Featured webinars

Weill Cornell pathology lab implements CGP

These walk-away automation methods for Illumina kits eliminate the need to develop your own method and can help you reduce hands-on time and minimize errors.

Emerging biomarkers in thyroid cancer and NSCLC

Dr. Sandip Patel of UCSD provides an overview of biomarker-guided therapies for thyroid cancer and non-small cell lung cancer (NSCLC) and discusses key emerging biomarkers for these indications along with their supporting evidence.

Broad oncology biomarker detection with CGP

Phil Febbo, MD discusses the benefits of CGP and how it’s becoming a new standard of care in oncology.

Scientists discuss cancer biomarker findings

Identifying biomarkers for response and resistance to anti-cancer immunotherapy

Dr Eliezer Van Allen highlights how NGS can identify biomarkers of response and resistance to immunotherapy, and can determine how cancers develop resistance to immune checkpoint blockade.

Accurate identification of cancer biomarkers

Scientists discuss the advantages of comprehensive NGS-based panels for biomarker discovery.

NGS proves invaluable for biomarker discovery

Phil Febbo, MD discusses the benefits of CGP and how it’s becoming a new standard of care in oncology.

Interested in receiving newsletters, case studies, and information on oncology?

Related content

Tumor mutational burden

NGS methods enable efficient assessment of tumor mutational burden and identification of neoantigens.

ctDNA as a noninvasive cancer biomarker

NGS methods enable efficient assessment of tumor mutational burden and identification of neoantigens.

Cancer epigenetics

NGS and microarray technologies can detect altered DNA methylation patterns and other epigenetic modifications that regulate cancer progression.

References
  1. US Food & Drug Administration. Hematology/Oncology (Cancer) Apporvals & Safety Notifications. US FDA website. Updated February 9, 2021. Accessed December 1, 2020.
  2. Singal G, Miller PG, Agarwala V, et al. Association of Patient Characteristics and Tumor Genomics With Clinical Outcomes Among Patients With Non-Small Cell Lung Cancer Using a Clinicogenomic Database. JAMA. 2019 Apr 9;321(14):1391-1399. doi: 10.1001/jama.2019.3241.
  3. PierianDx. Next Generation Knowledge. PierianDx - Genomic Knowledgebase for Clinical Next Generation Knowledge. Accessed March 1, 2020.
  4. Malone ER, Oliva M, Sabatini PJB, Stockley TL, Siu LL. Molecular profiling for precision cancer therapies. Genome Med. 2020 Jan 14;12(1):8. doi: 10.1186/s13073-019-0703-1.
  5. Reitsma M, Fox J, Borre PV, et al. Effect of a Collaboration Between a Health Plan, Oncology Practice, and Comprehensive Genomic Profiling Company from the Payer Perspective. J Manag Care Spec Pharm. 2019 May;25(5):601-611. doi: 10.18553/jmcp.2019.18309.
  6. Kopetz S, Mills Shaw KR, Lee JJ, et al. Use of a Targeted Exome Next-Generation Sequencing Panel Offers Therapeutic Opportunity and Clinical Benefit in a Subset of Patients With Advanced Cancers. JCO Precis Oncol. 2019 Mar 8;3:PO.18.00213. doi: 10.1200/PO.18.00213.
  7. Drilon A, Wang L, Arcila ME, et al. Broad, hybrid capture-based next-generation sequencing identifies actionable genomic alterations in lung adenocarcinomas otherwise negative for such alterations by other genomic testing approaches. Clin Cancer Res. 2015 Aug 15;21(16):3631-9. doi: 10.1158/1078-0432.CCR-14-2683.
  8. Rolfo C, Mack P, Scagliotti G, et al. Liquid biopsy for advanced NSCLC: a consensus statement from the international association for the study of lung cancer. J Thorac Oncol. 2021 Oct;16, (10):1647-62. doi: 10.1016.