Liqomics Evidence-Based Liquid Biopsy Knowledge
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Melanoma

Circulating Tumor DNA for Minimal Residual Disease Detection & Molecular Profiling

Clinical Overview

Cutaneous melanoma represents one of the most well-studied applications of ctDNA testing in solid tumors. While early-stage melanoma has excellent prognosis following surgical resection, approximately 20-30% of patients with stage II-III disease experience recurrence. Molecular profiling has revealed actionable BRAF mutations in approximately 50% of patients, enabling targeted therapy selection between BRAF/MEK inhibitor combinations and immunotherapy approaches.

Recent advances in immunotherapy with anti-PD-1 antibodies and targeted therapy with BRAF/MEK inhibitor combinations have transformed melanoma treatment. However, determining which patients require adjuvant therapy after surgical resection, and which patients will benefit from treatment intensification, remains a clinical challenge. Circulating tumor DNA has demonstrated prognostic value in identifying high-risk patients with molecular evidence of residual disease.

Clinical Impact: Multiple prospective studies have established ctDNA as a prognostic biomarker in melanoma, with hazard ratios ranging from 3.5 to 38 for recurrence depending on disease stage and testing timepoint. Lead times of 5.5-8.7 months before radiographic progression enable potential early intervention, though prospective trials testing whether ctDNA-guided treatment improves survival are ongoing.

Understanding ctDNA Testing Methodology

What is Circulating Tumor DNA (ctDNA)?

Circulating tumor DNA (ctDNA) represents fragments of tumor-derived DNA that are released into the bloodstream when cancer cells die. These DNA fragments carry the same genetic alterations present in the tumor, making them detectable through a simple blood draw rather than invasive tissue biopsy.

How ctDNA Testing Differs from Other Methods

ctDNA vs Tissue Biopsy

  • Sample collection: Blood draw vs surgical/needle biopsy
  • Risk profile: Minimal risk vs procedural complications
  • Tumor heterogeneity: Captures DNA from all tumor sites vs single location
  • Serial monitoring: Easy repeat testing vs limited repeat procedures

ctDNA vs Cellular Blood Tests

  • Target: Cell-free DNA fragments vs intact circulating tumor cells
  • Sensitivity: Detects 0.01-0.001% tumor fraction vs 0.1-1% requirement
  • Processing: Plasma separation vs cell isolation techniques
  • Clinical applications: MRD detection and monitoring vs enumeration only

Testing Approaches: Tumor-Informed vs Tumor-Agnostic

Tumor-Informed (Baseline-Based) Approach

How it works: Uses a baseline sample (tissue biopsy OR baseline plasma/blood) to identify the patient's tumor mutations, then tracks those specific mutations at MRD timepoints

Advantages:

  • Ultra-high sensitivity (0.001-0.01% tumor fraction)
  • Tracks patient's known mutations from baseline
  • Validated for MRD detection in melanoma

Best used for:

  • Post-surgical MRD detection
  • Monitoring during adjuvant therapy
  • Early relapse detection in surveillance

Requirements: Baseline sample (tissue from surgery or blood sample) for initial mutation identification

Tumor-Agnostic (No Baseline) Approach

How it works: Tests directly at MRD timepoint without prior baseline profiling, using panels covering common melanoma mutations (BRAF, NRAS, KIT, TERT)

Advantages:

  • No baseline sample required
  • Faster turnaround (5-7 days vs 2-3 weeks)
  • Can detect mutations emerging during treatment

Best used for:

  • Advanced/metastatic disease monitoring
  • Treatment selection based on actionable mutations
  • Cases where baseline profiling was not performed

Limitations: Lower sensitivity for MRD (0.1-0.5% tumor fraction)

Clinical Decision Points for Melanoma

When to Use Each Approach

Clinical Scenario Recommended Approach Rationale
Post-surgical MRD detection (Stage IIB-IV) Tumor-informed Maximum sensitivity needed; uses baseline profiling from surgery
Adjuvant therapy decision Tumor-informed Clinical trials used baseline-informed approach for risk stratification
BRAF V600E genotyping Either approach Can be detected with or without baseline profiling
Treatment resistance monitoring Either approach Can track emerging mutations with or without baseline
Surveillance (years 0-2) Tumor-informed Highest sensitivity using baseline mutation tracking

MRD Detection Clinical Utility

Prognostic Value in Resected Melanoma

Multiple prospective studies have demonstrated strong prognostic value of ctDNA detection after surgical resection in stage II-IV melanoma patients. Detection of molecular residual disease identifies patients at dramatically higher risk of recurrence.

BRIM-8 Trial: Largest Prospective Analysis

Study Design: Prospective analysis of 420 patients with resected stage IIB-IV BRAF V600 mutant melanoma

ctDNA Detection Rates by Stage:

  • Stage IIB-IIC: 10-15% ctDNA-positive
  • Stage IIIA-IIIB: 20-25% ctDNA-positive
  • Stage IIIC-IV: 35-45% ctDNA-positive

Recurrence Risk by ctDNA Status:

  • Hazard Ratio: 1.85 for relapse-free survival (95% CI 1.39-2.46, p<0.0001)
  • Stage-dependent HR: HR 3.5-6.2 depending on stage
  • Clinical Significance: ctDNA status remained prognostic independent of stage

Sensitivity and Specificity for MRD Detection

Test Performance Characteristics:

  • Sensitivity for future recurrence: 77-92% depending on stage and method
  • Specificity: 94-98% (low false-positive rate)
  • Positive Predictive Value: 65-80% depending on disease stage
  • Negative Predictive Value: 85-95% (8-15% of ctDNA-negative patients still recur)

Lead Time Before Imaging Detection

Early Detection Performance:

  • Median Lead Time: 5.5-8.7 months before radiographic recurrence (range 1-24 months)
  • Clinical Implication: Molecular detection precedes clinical/imaging progression
  • Intervention Window: Sufficient time for treatment modification or clinical trial enrollment
  • Surveillance Frequency: Testing every 3 months during first 2 years captures most relapses

Prognostic Value by Testing Timepoint

Post-Surgical Timepoint (4-8 weeks)

Immediate Post-Surgical Assessment:

  • Hazard Ratio: 6.8-11.5 for recurrence if ctDNA-positive
  • Detection Rate: 15-25% of patients depending on stage
  • Clinical Use: Identifies highest-risk patients for adjuvant therapy consideration

End-of-Treatment Timepoint

After Adjuvant Therapy Completion:

  • Hazard Ratio: 12-38 for recurrence if ctDNA-positive
  • Detection Rate: 5-10% of patients who completed adjuvant therapy
  • Clinical Significance: Extremely high-risk population requiring intensification

Longitudinal Monitoring During Surveillance

Serial Testing Performance:

  • Conversion from negative to positive: HR 15-25 for recurrence
  • Persistently negative: 90-95% remain recurrence-free at 2 years
  • Optimal Frequency: Every 3 months during years 1-2, then every 6 months years 3-5

Comparison with Traditional Risk Factors

ctDNA vs Clinical Staging:

Risk Factor Hazard Ratio for Recurrence Independent Prognostic Value
ctDNA positivity (post-surgical) 6.8-11.5 Yes - independent of stage
Stage IIIC vs IIIA 2.5-3.2 Yes
Ulceration present 1.8-2.1 Yes
Breslow thickness >4mm 2.0-2.5 Yes
Tumor mutational burden (high) 1.2-1.5 No - not independent of ctDNA

Key Finding: ctDNA status is the strongest prognostic factor, outperforming traditional clinical and molecular biomarkers.

Clinical Application: Post-surgical ctDNA testing identifies patients at high risk of recurrence who may benefit from adjuvant therapy or treatment intensification. The 5.5-8.7 month lead time before radiographic progression provides a window for early intervention, though prospective trials are ongoing to determine whether ctDNA-guided treatment improves survival outcomes.

Genotyping for Targeted Therapy Selection

Beyond MRD detection, ctDNA enables non-invasive genotyping for actionable mutations guiding treatment selection in melanoma. Molecular profiling has become essential for distinguishing patients eligible for targeted therapy versus immunotherapy approaches.

BRAF V600 Mutations: BRAF/MEK Inhibitor Combinations

Clinical Context and Treatment Options

Prevalence and Detection:

  • Frequency: 50% of cutaneous melanoma (V600E most common, V600K 15-20%)
  • ctDNA-Tissue Concordance: >95% for BRAF V600E detection
  • Clinical Advantage: Non-invasive testing enables rapid treatment selection

BRAF/MEK Inhibitor Combination Therapy:

  • First-line regimens: Dabrafenib + trametinib, encorafenib + binimetinib, vemurafenib + cobimetinib
  • Response Rate: 60-70% objective response rate
  • Median PFS: 11-15 months with combination therapy
  • Median OS: 25-33 months depending on regimen

Adjuvant Setting: COMBI-AD Trial Results

Phase III RCT in Resected Stage III BRAF-Mutant Melanoma:

  • Treatment: Dabrafenib + trametinib vs placebo for 12 months
  • 5-Year Relapse-Free Survival: 52% vs 36% (HR 0.51, 95% CI 0.42-0.61)
  • 5-Year Overall Survival: 65% vs 57% (HR 0.80, 95% CI 0.62-1.01)
  • Distant Metastasis-Free Survival: 65% vs 54% (HR 0.55)
  • Clinical Significance: Statistically significant improvement in relapse-free survival

NRAS Mutations: Limited Targeted Options

Clinical Characteristics:

  • Frequency: 28% of cutaneous melanoma
  • Common sites: Q61R, Q61K most frequent
  • Mutually exclusive: NRAS mutations rarely co-occur with BRAF
  • Targeted therapy: Binimetinib (MEK inhibitor) shows modest benefit
  • Response Rate: 15-20% with MEK inhibitor monotherapy
  • Standard approach: Immunotherapy preferred for NRAS-mutant melanoma

c-KIT Mutations: Rare but Actionable

Clinical Context:

  • Frequency: <5% overall, enriched in acral (15-20%) and mucosal (20-25%) melanoma
  • Targeted therapy: Imatinib, dasatinib
  • Response Rate: 20-30% with imatinib in c-KIT mutant/amplified tumors
  • Testing indication: Acral, mucosal, or chronically sun-damaged melanomas
  • ctDNA utility: Non-invasive detection avoids repeat biopsy in advanced disease

PD-L1 Expression and TMB: Immunotherapy Selection

Biomarkers for Checkpoint Inhibitor Therapy

PD-L1 Expression:

  • Testing method: Immunohistochemistry on tissue (not ctDNA)
  • Adjuvant pembrolizumab: HR 0.65 for recurrence-free survival (KEYNOTE-054)
  • Clinical note: Benefit seen regardless of PD-L1 status in adjuvant setting

Tumor Mutational Burden (TMB):

  • High TMB (>10 mutations/Mb): 60-70% of melanomas
  • Association: Higher TMB correlates with improved immunotherapy response
  • Response Rate: 40-50% in TMB-high vs 15-25% in TMB-low
  • ctDNA assessment: TMB can be estimated from plasma ctDNA panels
  • Limitation: TMB alone insufficient for treatment selection decisions

Comprehensive Genotyping Strategy

Recommended Testing Algorithm:

  1. All advanced melanoma patients: BRAF V600, NRAS mutation testing at baseline
  2. Acral/mucosal/CSD melanoma: Add c-KIT mutation testing
  3. BRAF V600E-positive:
    • Adjuvant: Consider dabrafenib + trametinib based on stage and risk
    • Metastatic: BRAF/MEK combination vs immunotherapy based on disease burden
  4. BRAF wild-type: Immunotherapy (anti-PD-1 ± anti-CTLA-4) first-line
  5. Resistance monitoring: Repeat ctDNA genotyping at progression to identify resistance mechanisms

Treatment Selection by Molecular Profile

Molecular Profile Prevalence Preferred Treatment Response Rate
BRAF V600E/K 50% BRAF/MEK inhibitor combination 60-70%
NRAS mutant 28% Anti-PD-1 immunotherapy 40-50%
c-KIT mutant (acral/mucosal) 15-25% Imatinib or immunotherapy 20-30%
BRAF/NRAS wild-type 20% Anti-PD-1 immunotherapy 40-45%
TMB-high (any genotype) 60-70% Immunotherapy preferred 40-50%

Clinical Summary and Practice Considerations

Melanoma ctDNA testing demonstrates clinical utility with:

  1. Strong Prognostic Value: HR 3.5-38 for recurrence depending on timepoint and stage
  2. High Sensitivity and Specificity: 77-92% sensitivity, 94-98% specificity for MRD detection
  3. Meaningful Lead Time: 5.5-8.7 months before radiographic progression
  4. Actionable Genotyping: BRAF V600 (50%), NRAS (28%), c-KIT (rare) guide targeted therapy
  5. Clinical Validation: Multiple prospective studies with >2,000 patients across stage II-IV disease
  6. Evidence Gap: Prospective trials testing whether ctDNA-guided treatment improves survival are ongoing

Evidence-Based Application Strategy

Recommended Clinical Pathway:

  1. Stage IIB-IV melanoma: Consider baseline ctDNA 4-8 weeks post-surgery for risk stratification
  2. BRAF genotyping: All advanced melanoma patients for treatment selection
  3. High-risk patients: Serial ctDNA monitoring every 3 months during years 0-2
  4. ctDNA-positive during surveillance: Confirm with imaging, consider treatment intensification or clinical trial
  5. Resistance monitoring: Repeat genotyping at progression on targeted therapy

Clinical Perspective: Melanoma represents one of the most extensively studied applications of ctDNA testing, with strong prognostic data demonstrating risk stratification capability. The technology provides valuable molecular information for treatment selection through BRAF genotyping and identifies high-risk patients through MRD detection. While the prognostic value is well-established, prospective interventional trials are needed to demonstrate that ctDNA-guided treatment decisions improve patient outcomes. Current use should focus on genotyping for treatment selection and risk stratification in stage IIB-IV disease, ideally within clinical trials or research protocols.

References

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  3. Syeda MM, Wiggins JM, Corless BC, et al. Circulating tumor DNA in patients with advanced melanoma treated with dabrafenib or dabrafenib plus trametinib: a clinical validation study. Nat Commun 2021;12:1-12.
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Evidence summary as of January 2026 | Document Version: 2.0

This educational resource incorporates the latest clinical trial data for ctDNA testing in melanoma