A Practical Guide to Biomarkers for Cutaneous Melanoma

Melanoma starts in pigment cells, but the story it tells is written in its biomarkers. These are the measurable clues that help a care team diagnose, stage, and track the disease, and decide which treatments have the best odds of working.¹ Think of biomarkers as the metadata on a digital photo. The image might look similar at a glance, but the details behind it can change everything.

This guide translates the key melanoma biomarkers into plain language, with clear examples, what they can and cannot tell you, and how they fit together. It is kept grounded in current guidelines and real data, and calls out limits where the science is still evolving.

What qualifies as a melanoma biomarker?

Biomarkers can be found in tissue, blood, or imaging reports. They can be molecular, like a gene mutation, or clinical, like tumor thickness.² In melanoma, the most useful biomarkers do at least one of three jobs: confirm the diagnosis under the microscope, refine the risk of spread and recurrence, or predict which therapies are likely to help. No single marker does it all. The strongest insights come from combining them.

Diagnosis under the microscope: the pathologist's toolkit

Most melanomas are diagnosed on a skin biopsy. A pathologist looks at the tissue and often adds immunohistochemistry, which uses antibodies to detect proteins inside the cells. These are diagnostic biomarkers. They help separate melanoma from look-alikes when the appearance is tricky.

Common diagnostic markers you might see on a report:

• S100 and SOX10: highly sensitive markers for melanocytic cells; strong positives support melanoma but are not specific by themselves³
• Melan-A (MART-1) and HMB-45: more specific for melanocytic lineage; often used in combination with S100 or SOX10³
• PRAME: a newer marker often upregulated in melanoma compared with benign nevi; helpful in ambiguous cases, though not perfect
• Ki-67: a proliferation marker; a high index supports malignancy when interpreted with morphology

These tests are like color filters on a camera. They bring features into focus but must be interpreted in context. Inflammatory skin diseases, sun damage, and some benign moles can mislead if each stain is read in isolation. Final diagnosis is made by synthesizing the microscopic architecture with these markers and the clinical picture.

Your pathology report: the core prognostic biomarkers

Once melanoma is confirmed, certain features of the tumor predict its behavior. These clinicopathologic biomarkers power the AJCC eighth edition staging system used worldwide.²

Key items and why they matter:

• Breslow thickness: the measured depth of the melanoma in millimeters; the single strongest predictor of risk;⁴ thicker tumors carry higher odds of lymph node spread and recurrence
• Ulceration: a break in the skin over the tumor; signals a more aggressive biology independent of thickness²
• Mitotic rate: the count of dividing cells per square millimeter; higher rates reflect faster growth dynamics⁵
• Microsatellites: small nests of melanoma cells near the main tumor; associated with a higher risk of nodal and distant spread
• Margins: whether the biopsy or excision completely removed melanoma at the edges; positive margins do not change biology but matter for surgical planning
• Lymphovascular or perineural invasion: melanoma cells seen in small vessels or nerves; less common but associated with higher risk when present

Two items deserve special attention because they fundamentally change staging and downstream decisions: sentinel lymph node status and ulceration. Sentinel node evaluation is a surgical sampling of the first draining lymph node basin.⁶ It is not a treatment, but a staging biomarker that uncovers microscopic spread that imaging cannot see. Ulceration upgrades stage within thickness categories because it tracks with more aggressive behavior in large population studies.²

Staging as a biomarker: translating features into risk

AJCC stage groups are not just labels. They are validated risk categories built from tens of thousands of patients.² Broadly, Stage I and II refer to localized tumors, Stage III to nodal involvement, and Stage IV to distant metastases. Lactate dehydrogenase (LDH) in the blood is included in Stage IV classification because high LDH correlates with tumor burden and worse prognosis.¹ Staging pulls together all the core biomarkers to estimate the baseline risk and to guide surveillance intensity and systemic therapy decisions in advanced settings.

Predictive tissue biomarkers: mutations that matter

Melanoma's DNA often carries signature ultraviolet damage. Within that landscape, several mutations carry clinical weight. They are predictive biomarkers because they inform therapy choice.⁷

• BRAF mutations: present in roughly 40 to 50 percent of cutaneous melanomas; most are V600E, with V600K the next most common; these mutations activate the MAPK pathway, and their presence predicts response to combined BRAF and MEK inhibition in advanced disease⁷
• NRAS mutations: present in about 15 to 20 percent; activate similar pathways but do not currently have approved targeted therapies; they can influence trial eligibility and prognostic discussions
• NF1 alterations: more common in older adults; lead to MAPK pathway activation; no approved targeted therapy yet, but they shape tumor biology
• KIT mutations: more often seen in acral and mucosal subtypes and chronically sun-damaged skin; selected activating mutations can be actionable⁸
• TERT promoter mutations: frequent across melanomas; associated with tumor progression, but not yet a routine therapy guide

How the testing is done matters. BRAF can be assessed by immunohistochemistry using the VE1 antibody, which detects the V600E protein with high sensitivity and rapid turnaround, but it will not catch non-V600E variants like V600K. PCR-based assays detect common hotspots quickly. Next-generation sequencing (NGS) surveys multiple genes in one run, capturing rarer variants and co-mutations that can influence clinical trials and prognosis.⁷ Sample quality, tumor content, and prior decalcification of tissues can affect accuracy. When a result does not match the clinical picture, confirmation by an alternate method is reasonable.

Immune biomarkers: PD-L1, TMB, and the nuance problem

Immunotherapy changed outcomes in advanced melanoma, and naturally everyone asks which immune biomarkers predict benefit. Here is the current, honest state of play:

• PD-L1 expression by immunohistochemistry: higher levels can correlate with response probabilities in some cancers; in melanoma, benefit from PD-1 blockers occurs across PD-L1 levels, so testing is not required to use these drugs;⁹ different antibody clones and scoring systems add variability, and tumor samples can be heterogenous
• Tumor mutational burden (TMB): melanoma tends to be TMB-high due to UV damage, which supports immunotherapy responsiveness at a population level;¹⁰ for an individual, TMB is a probabilistic signal rather than a yes or no; assay cutoffs and platforms differ across labs
• MMR/MSI status: mismatch repair deficiency is uncommon in cutaneous melanoma; when present, it may predict immunotherapy sensitivity, but routine testing is not standard for all melanomas

In short, the immune biomarkers you hear about are helpful trend lines, not gatekeepers.⁹ Clinical trials and large real-world datasets show that many patients with low PD-L1 still respond, and some with high PD-L1 do not. Results are best used as part of a broader mosaic.

Blood biomarkers: what a simple tube can and cannot tell you

Blood tests offer convenience, but they have limits. The main serum biomarkers are LDH, S100B, and, in some centers, circulating tumor DNA.

LDH: This is an enzyme released by many tissues. In metastatic melanoma, a high LDH correlates with tumor burden and worse outcomes, which is why it is part of Stage IV classification.¹ But LDH is nonspecific. Hemolysis during blood draw, liver injury, or intense exercise can raise it. Elevated LDH should be interpreted alongside imaging and clinical context, not in isolation.

S100B: Widely used in parts of Europe for surveillance in higher-risk melanoma, S100B can rise with disease recurrence and broadly tracks with tumor load.¹ It is not melanoma-specific. Brain injury, stroke, seizures, and even vigorous activity have been associated with transient elevations. Its role varies by region and guideline, and it is best viewed as a supportive signal when used.

Gene expression profiles: promise, controversy, and careful use

You may hear about multigene expression assays that categorize primary melanomas into lower or higher risk groups. These tests analyze RNA patterns in the tumor to forecast recurrence or sentinel lymph node positivity. They can be appealing because they offer a seemingly simple risk label. However, professional societies have been cautious.¹¹ Validation studies show mixed performance, integration with AJCC staging is inconsistent, and prospective utility to change outcomes has not been definitively proven. If used, they should be adjunctive rather than replacements for established clinicopathologic factors.

Sentinel lymph node biopsy: a staging biomarker with real weight

A sentinel lymph node (SLN) biopsy removes one or a few first-draining nodes to look for microscopic melanoma.⁶ It does not improve survival by itself, but it improves risk stratification and guides access to adjuvant therapies in appropriate stages. The likelihood of a positive SLN rises with Breslow thickness and ulceration.⁶ Procedural nuances matter: adequate mapping, experienced surgical teams, and meticulous pathology with step sections and immunohistochemistry help minimize false negatives. SLN status is one of the most impactful pieces of prognostic information in localized melanoma.¹²

Imaging as a biomarker adjunct

Imaging does not detect microscopic spread from a thin primary, but in higher-stage disease, PET-CT and high-quality CT or MRI establish the anatomic extent of melanoma. PET uptake reflects glucose metabolism, which correlates with active tumor in many cases, but inflammation can also light up. Imaging findings are best read alongside tissue diagnosis and blood markers like LDH. Serial imaging is a practical biomarker for response and progression in advanced disease.

Subtypes and special contexts that shift biomarker meaning

Cutaneous melanoma is a family of diseases. Subtype and patient context influence biomarker patterns.

• Acral lentiginous melanoma: more common on palms, soles, and under nails; relatively less UV-driven, with fewer BRAF mutations and more KIT alterations;⁸ often diagnosed later because lesions can be hidden by calluses or nail pigment
• Chronically sun-damaged skin melanomas in older adults: fewer BRAF mutations, more NF1 alterations; tumors may be thicker at diagnosis due to subtle early signs
• Younger adults: BRAF V600E is more prevalent; immune system vigor and tumor genetics can differ from older patients
• Skin of color: melanoma is less common but often presents at acral sites or mucosal surfaces; delays in diagnosis drive worse outcomes; biomarker patterns mirror the subtype distribution
• Pregnancy: current data do not show that pregnancy worsens melanoma prognosis when matched for stage; management is coordinated to balance maternal and fetal safety

These differences do not change the fundamentals of staging, but they do shape which molecular tests are most informative and how results are interpreted.

Assay details and practical caveats that matter

Two blood draws with different tubes or two tumor tests from different labs can give different answers if the methods differ. Here are common, real-world caveats that improve interpretation and avoid whiplash.

• IHC variability: PD-L1 assays use different antibody clones and scoring rules; BRAF VE1 IHC detects V600E but not V600K; PRAME thresholds are not fully standardized
• Tumor heterogeneity: a small biopsy might miss a subclone with a targetable mutation; repeat sampling or NGS on a larger specimen can clarify
• Sample handling: decalcification can damage DNA; heavily pigmented or necrotic tissue may reduce yield for molecular tests
• Cutoffs and units: LDH reference ranges differ by lab; S100B has assay-specific cutoffs; TMB thresholds are platform-dependent⁵

If a result seems out of step with the clinical course, it often helps to confirm with an orthogonal method or repeat at a reference lab with validated melanoma panels.

Putting biomarkers to work: example scenarios

Scenario 1: A 0.6 mm melanoma without ulceration is excised with clear margins. The most meaningful biomarkers here are Breslow thickness and ulceration status. The risk of sentinel node positivity is low, and systemic blood biomarkers are not informative at this stage. Care focuses on complete surgical removal and skin surveillance based on stage and individual risk factors.

Scenario 2: A 1.3 mm melanoma with ulceration. Sentinel lymph node biopsy becomes a high-yield staging tool.⁶ If the node is negative, the tumor remains localized but carries higher risk than a non-ulcerated tumor of the same thickness. Molecular testing on the primary is not strictly necessary for staging, but if nodal disease is found, BRAF and NGS become relevant for potential adjuvant therapy options in advanced stages.

Scenario 3: Resected Stage III melanoma. This is where predictive biomarkers earn their keep. BRAF status guides eligibility for targeted adjuvant therapy versus immunotherapy options. Baseline LDH is documented for context. Some centers add ctDNA monitoring during follow-up to complement imaging, recognizing that a negative ctDNA does not exclude recurrence and a positive result warrants correlation with scans and clinical findings.¹³

Scenario 4: Metastatic disease with elevated LDH. LDH reinforces that the tumor burden is significant and prognosis is more guarded. BRAF, NRAS, KIT, and broader NGS inform targeted options and clinical trial eligibility.⁷ PD-L1 can be reported but does not control access to PD-1–based regimens. Serial imaging and, where available, ctDNA help track response dynamics.¹³

How to read your report without getting lost

Pathology and molecular reports can feel like alphabet soup. Here is a simple way to parse them.

• Start with the diagnosis line: confirms melanoma and subtype
• Find Breslow thickness and ulceration: anchor your stage risk⁴
• Look for mitotic rate and margins: they refine risk and guide surgery⁵
• Check for sentinel lymph node results: yes or no to microscopic spread⁶
• Read the molecular section: BRAF first, then broader mutations and any notes on assay method⁷
• Note any blood biomarkers: LDH, S100B values with dates and reference ranges¹

If you compare across reports, line up dates and methods. A BRAF result from an IHC test on an older biopsy and an NGS report from a new metastasis might legitimately differ if the tumor evolved. That is biology, not necessarily an error.

Where lifestyle fits with biomarkers

Biomarkers do not replace healthy behaviors, but they explain why certain choices matter. Ultraviolet exposure creates the DNA damage signature that drives melanoma's high mutational burden. Sunscreen and shade reduce that mutational load at the source. Exercise and balanced nutrition influence systemic inflammation and immune tone, which can affect how the body handles residual disease. Think of it like optimizing your phone's operating system so the apps run better. These are supportive, not curative, and they do not substitute for evidence-based treatment decisions built on the biomarkers above.

What the research horizon looks like

Several lines of investigation are moving quickly. Minimal residual disease detection with highly sensitive ctDNA is being tested to personalize adjuvant therapy duration.¹³ Spatial profiling of immune cells within the tumor microenvironment may refine immunotherapy prediction beyond PD-L1. Liquid biopsy panels that track multiple mutations at once are improving detection rates. These advances are exciting, but they need prospective validation to prove that acting on the signals actually improves outcomes.

Common misconceptions to sidestep

• A high PD-L1 score guarantees immunotherapy response: it does not; it is a probability tilt⁹
• A normal LDH means no metastasis: many patients with metastatic melanoma have normal LDH¹
• BRAF-negative means no targeted options: KIT or other alterations may still be actionable in select subtypes⁸
• One negative ctDNA test rules out recurrence: sensitivity depends on tumor volume and assay; serial trends are more informative than single data points¹³
• Gene expression tests replace staging: they do not; AJCC features remain the backbone² ¹ ¹

Quality and equity: why access to good testing matters

Accurate melanoma biomarker testing depends on sample handling, validated assays, and teams experienced in interpretation. That is a resources issue as much as a science issue. Equitable access to skilled dermatopathology, molecular diagnostics, and guideline-based care is a public health priority, especially for populations that present later or have atypical subtypes. In practical terms, the most impactful "biomarker upgrade" can be getting tissue read by a melanoma-experienced pathologist and ensuring molecular testing is performed with appropriate methods.

Practical questions you can answer with biomarkers

Biomarkers are not trivia. They answer specific, practical questions.

• Is this lesion melanoma or a benign nevus? Diagnostic IHC and morphology answer this³
• How risky is this melanoma? Breslow thickness, ulceration, mitotic rate, and SLN status quantify risk² ¹ ⁴
• Has it spread microscopically? SLN biopsy detects early nodal involvement⁶
• Which systemic treatment is most rational if needed? BRAF, KIT, and broader NGS guide targeted options; immune biomarkers provide supportive context⁷
• How is treatment working over time? Imaging, LDH trends, and, where available, ctDNA dynamics offer complementary views¹³

A brief note on numbers without the noise

It is tempting to anchor on a single metric. Resist that. In melanoma, composite views are consistently more reliable. The AJCC system is built on multivariable models for a reason.² An individual PD-L1 or S100B level is informative when it is layered on top of the clinical stage, imaging, and molecular profile. That is how large datasets turn into wise, tailored decisions.

Bottom line

Melanoma biomarkers turn a diagnosis into a navigable map. Diagnostic markers confirm what it is.³ Clinicopathologic features like thickness, ulceration, and sentinel node status frame the risk.² ¹ ⁶ Molecular testing clarifies options for targeted and immune-based treatments.⁷ Blood tests and imaging help track the journey. Each marker has limits and quirks, and the most reliable answers come from integrating them rather than chasing a single number. When you understand what each biomarker can tell you, and what it cannot, you are better equipped to engage in a clear, levelheaded plan that reflects the best of current science.