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Cancer biomarkers and the role of NGS in advanced cancer testing
Cancer biomarkers are molecules that can be detected in tumor tissue or blood (sometimes called liquid biopsy) that provide information about a tumor’s biology. These tumor-specific molecules can involve changes in the DNA and RNA or even changes at the protein level that may indicate sensitivity to a particular treatment (i.e., targeted therapy or immunotherapy). Biomarkers may enable precision oncology research by elucidating the biological mechanisms that drive tumor development, progression, and resistance.
Next-generation sequencing (NGS) is a powerful technology that allows for the simultaneous analysis of multiple biomarkers from a single sample in a cost- and time-efficient manner. While tissue NGS is the gold standard for gaining insights into the biology of a tumor, liquid biopsy–based NGS is emerging as a highly sensitive method to understand resistance mechanisms as the tumor evolves. Liquid biopsies samples may be used as an alternative when tissue samples are not available. Moreover, liquid biopsy testing may complement tissue testing to better understand inter- and intra-tumor heterogeneity.
Figure 1. Relevant and emerging biomarkers in different cancer types detected by Oncomine CGP research assays.
Oncomine Solutions for biomarker testing in clinical research
Featured biomarkers
MTAP deficiency testing in solid tumors
MTAP deficiency is emerging as a critical biomarker shaping the future of targeted and immuno-oncology research. This concise guide breaks down the biology of MTAP loss, its relevance across solid tumors, and the testing strategies enabling its study.
Figure 2. Genetic map of chromosome 9 showing the 9p21.3 locus containing the MTAP, CDKN2A, CDKN2B, and IFN gene cluster. Figure from Brune et al.1, used with changes under terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0) (creativecommons.org/licenses/by/4.0).
HRR and HRD testing in ovarian cancer
BRCA1/2 proteins play critical roles in DNA repair by the homologous recombination repair (HRR) pathway, and loss of BRCA1/2 function has been well studied as a cause of homologous recombination deficiency (HRD). Learn how NGS can identify both causes and consequences of HRD.
Figure 3. HRR pathway. Non-gray genes are covered by the Oncomine Comprehensive Assay Plus. Teal genes were included in clinical trials of prostate cancer clinical research samples.
ESR1 mutation testing in metastatic breast cancer
Estrogen Receptor 1 (ESR1) encodes estrogen receptor α and plays a critical role in breast cancer by regulating the response to estrogen. Mutations in ESR1 are an active area of investigation, and NGS allows for comprehensive analysis, unveiling the intricate genomic alterations and complex mechanisms.
Figure 4. Schematic diagram of ERα mutations and their frequencies in metastatic breast cancer after treatment.2
Biomarker testing in advanced breast cancer
Recent advances in breast cancer research have uncovered many relevant and emerging biomarkers that go beyond immunohistochemical-based biomarkers. Find out why NGS technologies for broad molecular profiling are becoming necessary.
Figure 5. NGS uses a single assay to assess relevant and emerging biomarkers in breast cancer research.
For Research Use Only. Not for use in diagnostic procedures.
References
1. Brune MM, Savic Prince S, Vlajnic T et al. (2024) MTAP as an emerging biomarker in thoracic malignancies. Lung Cancer 197:107963.
2. Ma CX, Reinert T, Chmielewska I, Ellis MJ (2015) Mechanisms of aromatase inhibitor resistance. Nat Rev Cancer 15(5):261−275.
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