Cancer Biomarkers Explained: PD-L1, TMB, MSI, HER2, EGFR, KRAS, BRCA, ctDNA and How to Read Your Report (2026)
How biomarkers reveal cancer biology, guide diagnosis and prognosis, influence treatment selection, identify immunotherapy and targeted-therapy opportunities, track disease, reveal resistance, connect patients to precision clinical trials — and how to actually read the genomic or biomarker report that contains them.
Modern oncology is increasingly moving from treating cancer according to where it started to understanding what is driving the cancer biologically. That makes biomarkers one of the central building blocks of precision oncology — and makes the ability to read a biomarker report a genuinely practical skill for patients, families and healthcare providers.
Quick Answer
A cancer biomarker is a measurable biological characteristic — a DNA mutation, protein level, immune signal or other molecular feature — that helps classify a cancer, estimate its likely behavior, or predict whether a specific treatment is likely to help. A biomarker or genomic report lists which of these were tested and what was found, but a finding is only useful in context: the cancer type, stage, treatment history and strength of evidence all shape what a result actually means. No biomarker guarantees a treatment will work, and no negative result guarantees an alteration is absent.
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STAGE
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MOLECULAR PROFILE
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BIOMARKERS
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TREATMENT MATCH
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RESPONSE
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RESISTANCE
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NEW BIOMARKER
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NEXT TREATMENT / CLINICAL TRIAL
The goal is not simply to find a biomarker. The goal is to understand which biomarkers are clinically meaningful for the specific cancer and treatment decision — and to be able to read the report that delivers that information without being overwhelmed by it.
Table of Contents
- What Is a Cancer Biomarker?
- Biomarker vs Tumor Marker
- Why Biomarkers Matter in Cancer
- Major Categories of Cancer Biomarkers
- Genomic Biomarkers & Types of Genetic Alterations
- Protein and Expression Biomarkers
- Immune Biomarkers
- Epigenetic and Molecular Biomarkers
- Liquid Biopsy Biomarkers and ctDNA
- Major Cancer Biomarkers Explained (Table)
- Biomarkers by Cancer Type
- Biomarkers and Immunotherapy
- Biomarkers and Targeted Therapy
- Biomarkers and Treatment Resistance
- How Biomarker Testing Is Done
- How to Read a Genomic or Biomarker Report
- What Does a Negative Biomarker Test Mean?
- Limitations of Biomarker Testing
- Companion Diagnostics
- Biomarkers and Clinical Trials
- How Biomarkers Connect to Treatment: 5 Questions
- How SmartCancer Grades Evidence
- SmartCancer Biomarker Knowledge Graph
- The Future of Cancer Biomarkers
- Frequently Asked Questions
- Conclusion
What Is a Cancer Biomarker?
A biomarker is a measurable biological characteristic that can provide information about a disease or a biological process. In oncology, biomarkers can include:
- DNA mutations
- Gene fusions
- Gene amplifications
- Gene deletions
- Gene-expression patterns
- Proteins and protein-expression levels
- Chromosomal changes
- Microsatellite instability
- DNA mismatch-repair status
- Tumor mutational burden
- Epigenetic changes
- Circulating tumor DNA and circulating tumor cells
- Other molecules or biological characteristics
The National Cancer Institute (NCI) describes biomarker testing as laboratory testing of tissue, blood or other body fluids for genes, proteins or other molecules that may help with diagnosis, treatment planning, prognosis or monitoring.
Biomarker vs Tumor Marker: What’s the Difference?
The terms are sometimes used interchangeably, but they are not identical. A tumor marker traditionally refers to a substance produced by cancer cells, or by the body in response to cancer, that can be detected in tissue, blood, urine or other body fluids. Modern oncology has expanded this concept to include genomic and molecular characteristics of tumors.
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For SmartCancer, the preferred hierarchy is: Biomarker (genomic, protein, immune, epigenetic, cellular, molecular) → Tumor Markers (traditional circulating or tissue markers) as one subset within it. NCI notes that tumor markers increasingly include genomic markers such as gene mutations, gene-expression patterns and other changes in tumor DNA (NCI, last updated Dec 2021).
Why Biomarkers Matter in Cancer
Cancer is not one disease. Even two patients with the same anatomical diagnosis may have substantially different molecular characteristics, and biomarkers can help identify these differences.
Diagnosis
Help classify or identify particular cancers and subtypes.
Prognosis
Provide information about likely disease behavior or outcome.
Treatment Selection
Identify biomarkers associated with potential benefit from specific treatments.
Immunotherapy
Help identify patients who may be candidates for certain immune-based treatments.
Monitoring
Track disease-associated signals during or after treatment.
Resistance
Identify molecular changes associated with treatment failure or acquired resistance.
Clinical Trials
Help identify eligibility for biomarker-driven research, including hereditary risks relevant to family members.
Minimal Residual Disease
Support research and clinical monitoring approaches that detect very small amounts of residual disease in selected settings.
Biomarker testing is an important component of precision medicine because it can help clinicians select treatments more likely to benefit particular patients and avoid some treatments less likely to work.
Major Categories of Cancer Biomarkers
| Category | Main Question | Examples |
|---|---|---|
| Diagnostic | What cancer or subtype is present? | Pathology markers, gene rearrangements, immunophenotyping |
| Prognostic | What does the biomarker tell us about disease behavior? | Selected genomic alterations, expression signatures |
| Predictive | Is a particular treatment more or less likely to work? | EGFR, HER2, BRAF, MSI-H/dMMR, selected fusions |
| Pharmacodynamic | Is the biological target responding to treatment? | Pathway inhibition or target modulation |
| Monitoring | Is disease changing over time? | Selected tumor markers, ctDNA, circulating tumor cells |
| Resistance | Why did treatment stop working? | Acquired mutations, bypass alterations, lineage changes |
Diagnostic Biomarkers
Diagnostic biomarkers help identify, classify or characterize disease, using molecular alterations and protein-expression patterns alongside pathology, imaging and clinical information. NCI notes that tumor-marker measurements are usually combined with other diagnostic information because elevated markers can occur in noncancerous conditions, and some cancers do not produce elevated levels of a particular marker.
Prognostic Biomarkers
A prognostic biomarker provides information about the likely course or behavior of a disease independent of whether a particular treatment is used. This information can contribute to decisions about disease risk, recurrence risk, treatment intensity, monitoring strategy and clinical-trial selection. Prognostic does not mean predictive — a biomarker can be associated with a better or worse outcome without telling us that a particular drug will work.
Predictive Biomarkers
A predictive biomarker is associated with the likelihood of response or resistance to a particular treatment. A biomarker linked to a biological target can point toward a matching therapy with a higher expected probability of benefit — this distinction between prognostic and predictive is fundamental to precision oncology. NCI gives EGFR alterations in non-small cell lung cancer as an example of biomarker testing that can help identify patients who may benefit from EGFR-targeted treatment.
Pharmacodynamic Biomarkers
Pharmacodynamic biomarkers provide information about whether a treatment is producing the intended biological effect. For example, an investigational drug may be designed to inhibit a signaling pathway, and researchers may measure a downstream biological signal to determine whether the pathway is actually being affected. These biomarkers are particularly important in early drug development because they can help answer: Did the drug reach its intended target? Was the target sufficiently inhibited? Did the expected biological change occur? Could lack of clinical response be explained by inadequate target engagement?
Monitoring Biomarkers
Some biomarkers can be measured repeatedly to provide information about disease over time, including PSA, CA-125, CEA, CA 19-9, thyroglobulin, circulating tumor DNA, circulating tumor cells and other disease-specific markers. NCI lists tumor markers as potentially useful for assessing treatment response or recurrence in selected cancers. A biomarker trend should not automatically be interpreted as equivalent to tumor shrinkage or progression on imaging — the meaning of a marker depends on the specific cancer, treatment and clinical context.
Genomic Biomarkers & Types of Genetic Alterations
Genomic biomarkers are among the most important components of modern precision oncology. Reports commonly describe alterations using the following terms:
| Alteration Type | What It Means |
|---|---|
| Single-nucleotide variant (point mutation) | A single DNA base is changed. |
| Insertion | One or more DNA bases are added. |
| Deletion | DNA bases are removed. |
| Indel | A combined term for small insertions and deletions. |
| Amplification | A gene or genomic region is present in unusually high copy number. |
| Copy-number loss | A gene or genomic region has reduced or absent copy number. |
| Gene fusion | Two previously separate genes become joined through a genomic rearrangement; some cancers contain highly important oncogenic fusions. |
| Splice alteration | A variant affects how RNA is processed from DNA. |
| Structural variant | A larger genomic rearrangement alters the structure of chromosomes or genes. |
Microsatellite instability (MSI) and tumor mutational burden (TMB) are also genomic measures, but because both are primarily used as immune/immunotherapy biomarkers, they are covered in detail in the Immune Biomarkers section below.
Protein and Expression Biomarkers
Not all clinically relevant biomarkers are DNA mutations. Protein expression and other molecular measurements can be critical, including HER2 protein expression, PD-L1 expression, hormone receptors such as estrogen receptor and progesterone receptor, CD markers used in hematologic malignancies, and other immunohistochemical markers. The method used to measure a biomarker matters — a gene amplification, a mutation and a protein-expression measurement are not interchangeable concepts even when they concern the same biological pathway.
Immune Biomarkers
Immuno-oncology has created a major new category of biomarkers. Biomarker-guided immunotherapy is not based on one universal marker — the clinically useful biomarker depends on the cancer, treatment, assay and regulatory indication.
PD-L1 Explained
PD-L1 is a protein that can be expressed by tumor cells and/or cells within the tumor microenvironment. PD-L1 testing is often used to help inform decisions about immune checkpoint inhibitors in certain cancers. A report may use scoring systems such as TPS (Tumor Proportion Score) or CPS (Combined Positive Score) — these are not interchangeable. A result such as “PD-L1 TPS 60%” therefore cannot be interpreted without knowing the cancer type, assay, scoring method and clinical context. See the dedicated PD-L1 Explained guide for a deeper dive.
Tumor Mutational Burden Explained
Tumor mutational burden (TMB) estimates the number of mutations identified per amount of DNA analyzed, commonly reported as mutations per megabase (for example, “TMB: 12 mutations/Mb”). Higher TMB can be associated with increased production of abnormal tumor-derived antigens in some settings, and TMB has been investigated as a biomarker for immunotherapy. However, TMB is not a universal “immunotherapy score.” Interpretation depends on the assay, cancer type, threshold used, other biomarkers and the clinical setting. See Tumor Mutational Burden Explained for more detail.
MSI and MMR Explained
Microsatellite instability (MSI) reflects abnormalities involving repetitive DNA sequences. Mismatch repair (MMR) is a DNA-repair system involving proteins such as MLH1, MSH2, MSH6 and PMS2. Reports may use terms such as MSI-high, MSI-low, microsatellite stable (MSS), dMMR (deficient mismatch repair) or pMMR (proficient mismatch repair). MSI/MMR status can have important implications for treatment and, in some circumstances, hereditary cancer evaluation.
HER2 Explained
HER2 is a protein encoded by the ERBB2 gene. HER2 status can be assessed using different methods, including immunohistochemistry (IHC) and in situ hybridization techniques. Depending on the cancer and treatment context, reports may describe HER2-positive, HER2-negative, HER2-low, HER2-ultralow, HER2 amplification or HER2 overexpression. These terms are not necessarily interchangeable, and the clinical significance depends on the cancer type and testing methodology.
ER and PR Explained
Estrogen receptor (ER) and progesterone receptor (PR) testing are particularly important in breast cancer and can help determine whether hormone-directed treatment may have a role. The report may provide the percentage of cells expressing the receptor and the intensity of staining, depending on the testing system. As with other biomarkers, the result should be interpreted together with tumor type, stage, HER2 status and the overall clinical picture.
Tumor-Infiltrating Immune Cells
Research biomarkers reflecting the immune environment surrounding tumors, currently used mainly in investigational settings.
Epigenetic and Molecular Biomarkers
Cancer biology is influenced not only by DNA sequence changes but also by changes in gene regulation. Potential biomarker classes include DNA methylation, chromatin modifications, microRNA profiles, RNA expression patterns, alternative splicing and other epigenetic signatures. Many of these remain primarily research tools or emerging biomarkers rather than established clinical tests.
SmartCancer evidence rule: A biologically interesting biomarker is not automatically a clinically validated biomarker.
Liquid Biopsy Biomarkers and ctDNA
A liquid biopsy analyzes cancer-associated material found in blood or another body fluid, including circulating tumor DNA (ctDNA), cell-free DNA, circulating tumor cells (CTCs), RNA, extracellular vesicles and other tumor-derived molecules. NCI describes liquid biopsy as a way to analyze biomarkers from cancer cells or tumor-derived material in body fluids such as blood.
Potential applications of ctDNA specifically include identifying targetable alterations, monitoring molecular response, detecting emerging resistance alterations, evaluating minimal residual disease in selected settings, and helping guide repeat molecular testing. However, a negative liquid biopsy does not necessarily prove that a mutation is absent from the tumor — some tumors shed very little DNA into the bloodstream, and assay sensitivity varies. When clinically important information is not detected in blood, tissue testing may still be necessary depending on the circumstances.
Major Cancer Biomarkers Explained
The following biomarkers are among the most important nodes in the SmartCancer Oncology Knowledge Graph.
| Biomarker | Biological Category | Major Clinical Relevance |
|---|---|---|
| EGFR | Mutation / alteration | Targeted therapy selection in selected cancers, especially NSCLC |
| ALK | Gene rearrangement | Targeted therapy selection in selected cancers |
| ROS1 | Gene fusion | Targeted therapy selection in selected NSCLC |
| KRAS | Mutation | Important for treatment selection in selected cancers and specific variants |
| BRAF | Mutation | Targeted treatment decisions in selected cancers |
| HER2 / ERBB2 | Amplification / overexpression / mutation | Targeted therapy and antibody-drug conjugate selection in selected cancers |
| BRCA1 / BRCA2 | DNA-repair gene alteration | Risk assessment and treatment selection in selected cancers |
| MSI-H | Genomic instability | Important immunotherapy biomarker in selected cancers |
| dMMR | DNA mismatch-repair deficiency | Diagnosis, hereditary-risk assessment and treatment selection |
| PD-L1 | Protein expression | Immunotherapy selection in selected cancers |
| TMB | Genomic measure | Immunotherapy decision-making in selected contexts |
| NTRK fusion | Gene fusion | Potential tissue-agnostic targeted therapy opportunity in selected settings |
| RET fusion | Gene fusion | Targeted therapy selection in selected cancers |
| MET alteration | Mutation / amplification / exon skipping | Targeted treatment decisions in selected cancers |
| PIK3CA | Mutation | Selected targeted/endocrine treatment decisions |
| IDH1 / IDH2 | Mutation | Diagnosis, classification and targeted treatment in selected cancers |
| PSMA | Cell-surface protein | Imaging and targeted radioligand strategies in prostate cancer |
NCI’s tumor-marker resources (last reviewed December 2023) include many of these markers, among them ALK, BRCA1/2, BCR-ABL, HER2, IDH1/2, KRAS, MSI/dMMR, NTRK, PD-L1, PIK3CA and TMB.
Biomarkers by Cancer Type
Lung Cancer Biomarkers
Non-small cell lung cancer is one of the clearest examples of biomarker-driven oncology. Important molecular biomarkers can include EGFR, ALK, ROS1, KRAS, BRAF, MET, RET, NTRK, ERBB2/HER2 and PD-L1. The appropriate testing strategy depends on histology, stage, treatment setting and the specific clinical question.
Breast Cancer Biomarkers
Breast cancer treatment is strongly influenced by biological subtype. Important biomarkers include estrogen receptor (ER), progesterone receptor (PR), HER2, BRCA1/2, PIK3CA, and other molecular alterations and genomic signatures in selected settings. Some genomic assays can also provide information about recurrence risk and help inform treatment decisions in selected breast cancers — NCI lists the 21-gene Oncotype DX signature among commonly used tumor-marker tests.
Colorectal Cancer Biomarkers
Important colorectal cancer biomarkers include KRAS, NRAS, BRAF, MSI, MMR/dMMR, HER2 in selected settings, and NTRK and other rare actionable alterations. RAS status can be particularly important when considering certain targeted therapies, while MSI/MMR status can have implications for immunotherapy and hereditary cancer assessment.
Prostate Cancer Biomarkers
Important prostate-cancer biomarkers and molecular targets include PSA, PSMA, BRCA1/2, other homologous-recombination repair genes, androgen receptor biology, and selected genomic signatures. Biomarkers may be relevant to diagnosis, prognosis, treatment selection, imaging, monitoring and clinical-trial eligibility.
Melanoma Biomarkers
Melanoma is another important biomarker-driven cancer. Important molecular categories include BRAF, NRAS, NF1, other genomic alterations, and immune-related biomarkers used in selected treatment contexts. Biomarker information can influence whether targeted therapy or immunotherapy is considered.
Ovarian and Gynecologic Cancer Biomarkers
Important biomarkers can include BRCA1/2, homologous recombination deficiency (HRD) and related genomic features, folate receptor alpha in selected ovarian cancers, MSI/MMR in selected tumors, and HER2 in selected settings.
Pancreatic Cancer Biomarkers
Pancreatic cancer can contain actionable molecular alterations in a subset of patients. Testing may identify alterations involving BRCA1/2, PALB2, KRAS, BRAF, HER2, MSI/MMR, NTRK and other rare actionable alterations. The prevalence of actionable alterations varies considerably, which is one reason molecular profiling can be particularly relevant in advanced disease.
Blood Cancer Biomarkers
Biomarkers are fundamental to the diagnosis and management of many hematologic malignancies. Examples include BCR-ABL, JAK2, PML-RARA, MYD88, TP53, IGH rearrangements, immunophenotyping markers and cytogenetic abnormalities. These biomarkers can contribute to diagnosis, classification, prognosis, treatment selection and monitoring.
Biomarkers and Immunotherapy
Immunotherapy has made biomarker selection increasingly important. Major concepts include PD-L1 protein expression, MSI-H (high microsatellite instability) and dMMR (deficient mismatch repair), and tumor mutational burden (TMB), each of which can provide predictive information in selected contexts.
Important: A biomarker associated with immunotherapy response does not mean every patient with that biomarker will respond. Biomarker status changes probability; it rarely guarantees an outcome.
Biomarkers and Targeted Therapy
Targeted therapy attempts to exploit specific biological characteristics of cancer cells: a molecular alteration produces an abnormal protein or pathway, which becomes a therapeutic target for a matched drug, leading to tumor response or eventual resistance. Examples include EGFR alterations → EGFR-directed therapies; ALK rearrangements → ALK-directed therapies; BRAF alterations → BRAF/MEK-directed strategies in selected cancers; HER2 alterations → HER2-directed therapies; NTRK fusions → TRK-directed therapies; RET alterations → RET-directed therapies; and selected KRAS alterations → mutation-specific targeted strategies. The specific treatment depends on the exact alteration, cancer type, treatment line and regulatory indication.
Biomarkers and Treatment Resistance
One of the most important concepts in precision oncology is that biomarkers can change — a tumor is not static.
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BIOMARKER PROFILE
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TARGETED TREATMENT
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SELECTIVE PRESSURE
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CLONAL EVOLUTION
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RESISTANT CLONE
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NEW BIOMARKER PROFILE
NCI notes that cancer biomarkers can change over time, meaning an older biomarker test may not fully represent the biology of a tumor at recurrence or progression. A patient may initially have Biomarker A → Treatment A → Response, and later develop Resistance Biomarker B, at which point Treatment A no longer works and a new treatment strategy is needed. This creates a dynamic biomarker-treatment loop.
Resistance may arise through several mechanisms: new mutations in the original drug target, activation of alternative signaling pathways, gene amplification, gene fusion, histologic or lineage transformation, loss of the treatment target itself, immune escape, or changes in the tumor microenvironment. A repeat biopsy or liquid biopsy may therefore reveal a molecular profile that differs from the original diagnosis, following the sequence: Diagnosis → Treatment → Response → Resistance → Reprofiling → Next Strategy.
How Biomarker Testing Is Done
Biomarker testing can use different biological samples and technologies:
- Tumor tissue – obtained through biopsy or surgery.
- Blood – used for circulating biomarkers and liquid biopsy approaches.
- Bone marrow – particularly important for many blood cancers.
- Urine and other fluids – used for selected biomarkers and research applications.
- Immunohistochemistry (IHC) – uses antibodies to detect proteins in tumor cells; HER2, ER, PR and PD-L1 are common examples, though exact testing and scoring vary by cancer.
- Fluorescence in situ hybridization (FISH) – can detect particular gene rearrangements or copy-number changes.
- Next-generation sequencing (NGS) – can simultaneously examine many genes; depending on the assay, testing may include DNA, RNA or both.
- Germline genetic testing – looks for inherited genetic variants present throughout the body rather than only within the tumor.
These tests are complementary. One test does not necessarily answer every clinically relevant question. NCI notes that solid-tumor biomarker testing commonly uses biopsy or surgical tissue, while blood-based testing may be used for liquid biopsy or blood cancers.
Tissue Biopsy vs Liquid Biopsy
| Feature | Tissue Testing | Liquid Biopsy |
|---|---|---|
| Sample | Tumor tissue | Usually blood |
| Advantages | Direct analysis of tumor tissue and pathology | Less invasive and potentially repeatable |
| Potential limitations | Requires adequate accessible tissue | May have insufficient tumor-derived material |
| Spatial information | Can provide information from sampled tumor site | May represent DNA shed from multiple tumor sites |
| Monitoring | Repeat biopsy can be difficult | Potentially useful for serial molecular monitoring in selected settings |
Liquid biopsy does not automatically replace tissue biopsy. The best approach depends on the cancer, clinical question, available tissue and validated test.
Single-Gene Testing vs Comprehensive Biomarker Panels
Testing can range from a single biomarker assay to broad genomic profiling: single-biomarker testing (useful when one specific biomarker is clearly relevant to a treatment decision), focused panels (a selected group of genes or biomarkers associated with a particular cancer), comprehensive genomic profiling (evaluating a much larger number of genomic alterations simultaneously), whole-exome sequencing (the protein-coding regions of genes), and whole-genome sequencing (the broader DNA sequence of the genome).
How to Read a Genomic or Biomarker Report
A typical report may contain unfamiliar terms such as EGFR L858R, KRAS G12C, HER2 amplification, PD-L1 TPS 60%, TMB 12 mutations/Mb, MSI-high, variant allele frequency, or variant of uncertain significance. These results are not simply a list of mutations — they are pieces of a larger clinical picture that can help oncologists understand how a particular cancer is behaving, which treatments may be relevant, whether resistance may be developing, and whether a clinical trial may be appropriate.
This section is designed to help patients and families understand the terminology and ask better questions — not to replace an oncologist, pathologist, genetic counselor, or molecular tumor board.
Anatomy of a Genomic Report
Although reports vary between laboratories, many contain several recurring sections:
- Patient and specimen information – cancer diagnosis, specimen type, collection date, accession number and other identifying information.
- Test methodology – whether DNA sequencing, RNA sequencing, IHC, FISH, PCR, liquid biopsy or another technology was used.
- Detected alterations – usually the section patients focus on first; lists genes and specific molecular alterations.
- Biomarker results – some reports separately display results such as PD-L1, TMB, MSI/MMR or HER2.
- Clinical interpretation – the laboratory’s categorization of findings by potential clinical significance.
- Therapy associations – drugs associated with a particular alteration; these lists should be interpreted carefully, since the presence of a biomarker does not necessarily mean a particular therapy is appropriate for every patient.
- Clinical trials – some commercial reports identify potentially relevant trials.
- Limitations – an extremely important section explaining what the assay could and could not detect.
Genes, Variants and Mutations
A gene is a segment of DNA containing biological information. A variant is a difference in DNA sequence. A mutation is commonly used in cancer medicine to describe an acquired genetic alteration, although “variant” is often the more precise technical term. For example, KRAS G12C means the KRAS protein has a specific alteration involving amino-acid position 12; EGFR L858R describes a particular EGFR protein alteration. The biological and clinical importance of a variant depends on the gene, exact alteration, cancer type and available evidence.
Pathogenic, Likely Pathogenic and VUS
Reports often classify variants according to their significance:
- Pathogenic – evidence supports that the variant has a disease-related biological effect.
- Likely pathogenic – the available evidence strongly suggests biological significance, although uncertainty remains.
- Variant of uncertain significance (VUS) – there is insufficient evidence to determine the clinical significance of the variant confidently.
- Benign / likely benign – generally indicates the variant is not believed to have meaningful disease-causing significance.
Important: A VUS should generally not be treated as though it were a confirmed pathogenic mutation. Its classification can change as scientific evidence accumulates. NCI specifically cautions that variants of unknown significance and benign changes generally should not be used to make treatment decisions.
This pathogenicity classification is a separate question from actionability (below): a variant can be confidently pathogenic without any matched therapy existing, and a variant with strong therapeutic implications can still carry residual uncertainty about its exact biological effect.
What Does “Actionable” Mean?
Actionable is one of the most important — and most misunderstood — words in genomic medicine. An actionable alteration generally means there is some clinically relevant intervention, management implication, approved therapy, diagnostic implication, or clinical-trial opportunity associated with the finding. But “actionable” does not automatically mean there is a cure, that the treatment will work, that the treatment is approved for every cancer containing the alteration, or that the patient should receive the drug immediately. Context matters. A biomarker may be:
- FDA-approved / guideline-supported – strong clinical evidence and an established use in a particular setting.
- Potentially actionable – evidence exists, but the clinical role may be less established.
- Clinical-trial relevant – the finding may help identify an investigational treatment.
- Biologically interesting – evidence exists mainly at the laboratory or mechanistic level.
What Is Variant Allele Frequency (VAF)?
Variant allele frequency (VAF) describes the proportion of sequencing reads containing a particular variant — for example, “VAF: 32%.” VAF can provide useful information, but it is not the same thing as “32% of the cancer cells have this mutation.” VAF can be influenced by tumor purity, copy-number changes, loss of heterozygosity, subclonal architecture, normal-cell DNA contamination, and technical characteristics of the assay. VAF therefore needs to be interpreted in context.
Somatic vs Germline Mutations
Somatic alterations arise during a person’s lifetime and may be present only in cancer cells or a subset of them. Germline alterations are inherited and are generally present throughout the body’s cells. This distinction matters because a tumor sequencing test can sometimes identify a finding that may warrant separate germline confirmation. Genes that can have hereditary cancer implications include BRCA1, BRCA2, PALB2, TP53, MLH1, MSH2, MSH6, PMS2, APC and other hereditary cancer-associated genes. Not every alteration in these genes is inherited — a genetic counselor or qualified clinician may be needed to determine whether germline testing is appropriate.
Example of a Fictional Genomic Report
The following is a simplified fictional example designed only to demonstrate how to read terminology — it does not describe a real patient.
Fictional example: Metastatic non-small cell lung cancer
EGFR: L858R detected
TP53: pathogenic variant detected
ALK: no alteration detected
ROS1: no alteration detected
KRAS: no clinically significant alteration detected
PD-L1: TPS 60%
TMB: 8 mutations/Mb
MSI: stable
How should this be approached? EGFR L858R is the first finding that deserves attention because it is a well-established oncogenic alteration in NSCLC with important treatment implications in appropriate clinical settings. TP53 may be biologically important, but detecting a TP53 alteration does not automatically mean there is an approved TP53-targeted treatment. PD-L1 TPS 60% provides information about PD-L1 expression, but should not be interpreted in isolation from the EGFR result and the overall clinical context. TMB 8 is a numerical biomarker result whose meaning depends on the assay, threshold and clinical setting. MSI stable indicates the tumor was not classified as MSI-high by that test. The important lesson: the report is not a menu of drugs. The oncologist integrates the molecular findings with pathology, stage, symptoms, imaging, treatment history and current guidelines.
Questions to Ask Your Oncologist
Patients can take the following checklist to an oncology appointment:
- What are the most clinically important findings in my report?
- Which findings are actionable today?
- Which findings are potentially actionable but experimental?
- Is there an FDA-approved or guideline-supported treatment associated with my biomarker?
- Does the biomarker apply to my specific cancer type?
- Could any finding indicate an inherited cancer risk?
- Do I need germline genetic testing or genetic counseling?
- Is my tumor suitable for comprehensive genomic profiling?
- Would RNA sequencing add useful information?
- Should the tumor be tested for PD-L1?
- What is my TMB?
- What is my MSI/MMR status?
- Should ctDNA or liquid biopsy be considered?
- If my cancer progresses, should molecular testing be repeated?
- Could a resistance mutation explain treatment failure?
- Are there biomarker-matched clinical trials?
- What does a “negative” result mean for this particular test?
- What limitations does my assay have?
What a Genomic Report Cannot Tell You
A genomic report is powerful, but it is not a crystal ball. It generally cannot tell you with certainty exactly how long you will live; whether a treatment will definitely work; whether a cancer will definitely recur; whether every cancer cell contains the same mutation; that a detected alteration is automatically treatable; that a negative result means the alteration is absolutely absent; or that an experimental therapy will work because it worked in a laboratory. Cancer outcomes are influenced by many variables, including tumor biology, stage, treatment response, resistance, overall health, metastatic sites and the characteristics of individual patients and tumors.
What Does a Negative Biomarker Test Mean?
One of the most important lessons in genomic medicine is: “not detected” does not always mean “not present.” A test can only detect what its technology is designed and sensitive enough to detect. A negative result can reflect the alteration genuinely being absent; low tumor content; low levels of ctDNA; technical limitations; an alteration outside the genes or regions tested; or an alteration type not captured by the assay. This is why a report’s limitations section deserves careful attention. NCI notes that biomarker testing may fail to identify a useful treatment match for several reasons, including insufficient tissue, absence of a matched therapy, and limitations of available treatment options.
Limitations of Biomarker Testing
Biomarker testing is powerful, but it is not a crystal ball.
- Tumor heterogeneity – different cancer cells within the same patient may carry different biomarkers.
- Evolution – tumor biology can change after treatment.
- Sampling – a biopsy represents the sampled tissue, not necessarily every tumor site.
- Detection limits – low-level alterations may not be detected.
- Unknown biology – many detected alterations have no established treatment implication.
- Drug availability – a matched biomarker does not guarantee access to a corresponding therapy.
- Drug response – a biomarker match does not guarantee that the treatment will work.
- Assay differences – different tests may use different technologies, thresholds and validation approaches.
NCI explicitly notes that even when a biomarker matches a treatment, the therapy may not work because other cancer or patient characteristics can influence response, and because not all tumor cells necessarily share the same biomarkers.
Companion Diagnostics
A companion diagnostic is a diagnostic test developed or used to help determine whether a particular patient is likely to benefit from a specific medical product, or whether a particular safety risk exists. In oncology, companion diagnostics are an important bridge between a biomarker, a diagnostic test, patient selection, and the eventual therapy. The FDA recognizes companion diagnostics as an important component of personalized medicine and maintains information on cleared and approved companion diagnostic devices.
Biomarkers and Clinical Trials
Biomarkers increasingly determine who can participate in cancer clinical trials. A trial may require a specific mutation, a gene fusion, a protein-expression threshold, MSI-H or dMMR status, a particular TMB range, HER2 positivity, a specific resistance mutation, or a particular immune phenotype.
Some trials are basket trials, in which patients with different cancer types are grouped according to a shared molecular alteration. Others are umbrella trials, where patients with one cancer type are assigned to different treatment strategies according to their molecular profiles. NCI notes that some trials enroll patients based on biomarkers rather than the anatomical location where the cancer began. This is one reason comprehensive genomic testing can sometimes be useful even when an immediately actionable mutation is not found.
How Biomarkers Connect to Treatment: 5 Questions
A useful way to interpret any report is to work through five questions:
- What cancer do I have? The same biomarker can have different implications in different cancers.
- What is the stage? Localized, locally advanced, metastatic and recurrent disease can require very different strategies.
- What biomarkers were detected? Identify alterations with established, emerging or investigational relevance.
- What treatment have I already received? A biomarker that initially predicts sensitivity may later become associated with resistance after treatment.
- What is the evidence level? An FDA-approved therapy supported by clinical trials is fundamentally different from an experimental treatment supported only by laboratory evidence.
Therefore: Biomarker ≠ Drug. More accurately: Biomarker + Cancer Context + Evidence + Treatment History → Clinical Interpretation.
How SmartCancer Grades Evidence
SmartCancer uses an evidence-oriented framework to distinguish established clinical knowledge from emerging and experimental concepts:
- E0 – Hypothesis: theoretical or mechanistic idea without meaningful human evidence.
- E1 – Preclinical: laboratory, cellular or animal evidence.
- E2 – Early human evidence: preliminary clinical or early-phase human data.
- E3 – Comparative clinical evidence: stronger evidence from comparative studies and clinical trials.
- E4 – Established clinical evidence: substantial evidence supporting clinical use in appropriate settings.
- E5 – Guideline / standard-of-care evidence: incorporated into authoritative clinical practice recommendations or established standards.
This framework is particularly important when reading a genomic report, because commercial laboratory reports may list approved therapies, investigational therapies and theoretical associations in the same document.
SmartCancer rule: The more exciting a biomarker-treatment connection sounds, the more important it is to ask — what level of evidence supports it, and does that evidence apply to this cancer and this patient?
SmartCancer Biomarker Knowledge Graph
This is where the Biomarkers pillar becomes a central component of the wider SmartCancer Oncology Knowledge Graph.
Core SmartCancer biomarker nodes: EGFR · ALK · ROS1 · KRAS · BRAF · MET · RET · NTRK · HER2 · BRCA1/2 · PIK3CA · IDH1/2 · MSI-H · dMMR · PD-L1 · TMB · PSMA · HRD · ctDNA · CTCs
| Cancer | Biomarker | Biological Type | Potential Clinical Role | Connected SmartCancer Node |
|---|---|---|---|---|
| Lung | EGFR | Mutation | Targeted therapy | EGFR inhibitors → resistance |
| Lung | ALK | Fusion | Targeted therapy | ALK inhibitors → resistance |
| Lung | PD-L1 | Protein | Immunotherapy selection | Checkpoint inhibitors |
| Breast | HER2 | Amplification / expression | Targeted therapy / ADCs | HER2 therapeutics |
| Colorectal | MSI-H / dMMR | Genomic phenotype | Immunotherapy / hereditary assessment | Immuno-oncology |
| Multiple | NTRK fusion | Gene fusion | Targeted therapy | Tissue-agnostic oncology |
| Multiple | BRCA1/2 | DNA-repair alteration | Selected targeted therapy | DNA damage response |
| Multiple | TMB | Genomic measure | Selected immunotherapy decisions | Immune biomarkers |
| Prostate | PSMA | Cell-surface protein | Imaging / radioligand therapy | Theranostics |
The Future of Cancer Biomarkers
The next generation of oncology biomarkers will increasingly move beyond static DNA mutations:
- Multi-omics – combining genomic, transcriptomic, proteomic, metabolomic and other biological layers.
- Dynamic biomarkers – measuring how tumor biology changes during treatment.
- ctDNA monitoring – using circulating tumor DNA to investigate treatment response, molecular recurrence and resistance.
- Single-cell analysis – studying individual tumor and immune cells rather than averaging across a tumor.
- Spatial biology – mapping molecular characteristics according to their location within the tumor.
- AI biomarker discovery – using machine learning to identify complex patterns associated with diagnosis, prognosis or treatment response.
- Digital pathology – computational analysis of tissue images and molecular features.
- Adaptive biomarkers – biomarker strategies that evolve alongside tumor treatment and resistance.
The long-term direction is toward increasingly dynamic models of cancer biology rather than a single molecular snapshot.
Frequently Asked Questions
What is a cancer biomarker?
A cancer biomarker is a measurable biological characteristic that provides information about a cancer, its behavior, its molecular characteristics, or its potential response to treatment.
What is biomarker testing?
Biomarker testing analyzes tissue, blood or another biological sample for genes, proteins or other molecules that may help with diagnosis, treatment selection, prognosis or monitoring.
What is the difference between a genomic report and a biomarker report?
A genomic report primarily describes DNA or RNA alterations, whereas a biomarker report can include genomic findings plus protein expression, immune biomarkers, hormone receptors, ctDNA and other measurements.
Are biomarkers the same as tumor markers?
Not exactly. Tumor markers traditionally refer to substances associated with cancer, while the modern biomarker concept includes genomic, molecular, protein, cellular and other biological characteristics.
Why are biomarkers important in precision oncology?
They can help identify biological differences between cancers and guide treatment toward therapies that target specific characteristics.
Does every cancer have an actionable biomarker?
No. Some cancers have multiple clinically actionable alterations, while others may have no currently actionable biomarker.
Does finding a mutation mean there is a treatment for it?
No. Some alterations are actionable, some have emerging evidence, some are useful mainly for diagnosis or prognosis, and others have no established treatment implication.
What does VUS mean?
VUS means variant of uncertain significance. There is not enough evidence to determine its clinical significance confidently, and it should not automatically be treated as a disease-causing or treatment-directing mutation.
What does VAF mean?
Variant allele frequency describes the proportion of sequencing reads containing a particular variant. It should not automatically be interpreted as the percentage of tumor cells carrying the mutation.
Does a biomarker guarantee that a treatment will work?
No. A biomarker may increase the likelihood of benefit in a particular clinical context, but treatment response is influenced by many other factors.
Can biomarkers change over time?
Yes. Tumor biology can evolve over time, particularly under treatment pressure, and a previous test may not always represent the current tumor biology.
Can a blood test (liquid biopsy) replace a tumor biopsy?
Not always. Liquid biopsy can be extremely useful, but sensitivity depends on tumor shedding, assay characteristics and the specific alteration. A tissue biopsy may still be necessary.
What does a negative or “not detected” result mean?
It means the tested assay did not detect the specified alteration. It does not necessarily prove that the alteration is absent from every cancer cell.
What is a companion diagnostic?
A companion diagnostic is a diagnostic test used to help determine whether a particular medical treatment is appropriate for a patient based on a relevant biological characteristic.
Can biomarkers identify clinical trials?
Yes. Some cancer clinical trials use specific biomarkers as eligibility criteria, including basket and umbrella trial designs, allowing patients to be matched to investigational therapies based on tumor biology rather than only the organ where the cancer began.
Should every cancer patient have comprehensive genomic testing?
Not necessarily. The value of testing depends on cancer type, stage, treatment setting, available tissue, clinical guidelines, and the likelihood that results could affect management. Discuss testing with the treating oncology team.
Conclusion: Biomarkers Are the Language of Precision Oncology
The future of cancer treatment is increasingly about understanding which cancer is present, what biological mechanisms are driving it, how those mechanisms change, and which treatment is most appropriate at a particular point in time. Biomarkers — and the reports that document them — provide part of that language.
↓
PATHOLOGY
↓
STAGE
↓
BIOMARKER TESTING
↓
MOLECULAR PROFILE
↓
ACTIONABLE FINDINGS
↓
TREATMENT MATCH
↓
RESPONSE MONITORING
↓
PROGRESSION / RESISTANCE
↓
RETEST WHEN CLINICALLY APPROPRIATE
↓
NEXT TREATMENT / CLINICAL TRIAL
But the most important principle is this: a biomarker is not a treatment. A biomarker is information that may change the probability that a particular diagnosis, prognosis, treatment or clinical trial is relevant — and a report is only as useful as the clinical context it is read within. That distinction is central to responsible precision oncology.
The SmartCancer Biomarker pillar therefore connects directly to the broader oncology ecosystem: Biomarkers → Genomic Reports → Cancer Types → Molecular Pathways → Targeted Therapy → Immunotherapy → Resistance → Monitoring → Clinical Trials → Next-Generation Treatments.
Precision Oncology • Molecular Profiling • Genomic Report Interpretation • Immunotherapy • Targeted Therapy • Cancer Clinical Trials
Publisher: SmartCancer.org | Topic: Cancer Biomarkers, Genomics & Precision Oncology | Audience: Cancer patients, caregivers, families and health professionals seeking evidence-based, patient-friendly explanations | Last reviewed/updated: September 2026 (merged and expanded from two prior SmartCancer.org articles)
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