Interpreting Genomic Profiling

1. What CGP platform was used (FoundationOne CDx, Tempus xT, Guardant360, MSK-IMPACT, institutional panel)? (Default: specify)
2. Was the sample tissue-based (tumor biopsy) or liquid biopsy (ctDNA)? (Default: specify)
3. What is the cancer diagnosis, stage, and treatment history? (Default: [VERIFY])
4. What is the specific clinical question (first-line treatment selection, resistance mechanism, trial matching)? (Default: treatment selection)
5. When was the sample collected relative to the last treatment? (Default: document date)
6. Is the tumor fraction/content adequate for the assay? (Default: check QC metrics on report)
7. Has prior molecular testing been performed? (Default: document)
8. Does the patient have a known germline mutation? (Default: assess family history)

Documents to Request

• Complete CGP report from the testing laboratory
• Pathology report confirming diagnosis and tumor content
• Treatment history with dates, agents, and response
• Prior molecular testing results (single-gene tests, smaller panels)
• Germline genetic testing results if performed
• Current NCCN guideline for the cancer type (molecular testing section)
• ClinicalTrials.gov search results for identified actionable alterations
• OncoKB, CIViC, or institutional molecular tumor board knowledgebase access

Step 1: Review Report Quality Metrics and Sample Adequacy

Before interpreting variants, assess report quality:

1. Tumor content/purity: Most tissue-based CGP requires ≥20% tumor content. Reports with low tumor content may have false-negative results.
2. Sequencing depth: Adequate coverage typically >500× for tissue, >2000× for ctDNA.
3. Specimen type: Tissue biopsy provides a more complete profile than liquid biopsy. Liquid biopsy may miss certain alterations (gene fusions, amplifications) at low tumor fraction.
4. Liquid biopsy ctDNA fraction: If ctDNA is not detected or very low (<0.5%), a negative result is not reliable — recommend tissue-based testing.
5. Microsatellite instability (MSI) and tumor mutational burden (TMB): Confirm these are reported — they are required for tumor-agnostic therapy eligibility.

Document any quality limitations that affect interpretation reliability.

Step 2: Classify Identified Alterations by Actionability

Use the OncoKB or AMP/ASCO/CAP tiered classification system:

AMP/ASCO/CAP Tier System:

Key actionable alterations by cancer type:

Step 3: Assess Resistance Mechanisms and Co-Mutations

For patients who have progressed on targeted therapy, interpret the CGP report for resistance:

• EGFR T790M after first/second-gen EGFR TKI → osimertinib (if not already used)
• EGFR C797S after osimertinib → clinical trial or combination approaches
• ALK resistance mutations (G1202R, compound mutations) → lorlatinib
• ESR1 mutations in ER+ breast cancer → resistance to aromatase inhibitors
• BRCA reversion mutations → loss of PARP inhibitor sensitivity
• MET amplification as bypass resistance in EGFR-mutant NSCLC → EGFR + MET combination

Document co-occurring mutations that affect prognosis or treatment selection:

• TP53 co-mutation worsens prognosis in EGFR-mutant NSCLC
• STK11/KEAP1 co-mutations in NSCLC predict poor response to immunotherapy
• PTEN loss may confer resistance to certain targeted therapies

Step 4: Generate the Interpretive Report

Structure the interpretation:

1. Report summary: Platform, specimen type, quality metrics, key findings
2. Tier I actionable findings: Each alteration with matched FDA-approved therapy, evidence level, and NCCN recommendation
3. Tier II findings: Clinical trial opportunities and emerging evidence
4. MSI/TMB status: Document for tumor-agnostic therapy eligibility
5. Resistance mutations: Identified mechanisms with clinical implications
6. Prognostic biomarkers: Co-mutations affecting prognosis or treatment response prediction
7. VUS: Listed for completeness but explicitly noted as not actionable
8. Germline implications: Flag pathogenic variants that may have germline significance (BRCA1/2, Lynch syndrome genes) and recommend confirmatory germline testing
9. Clinical trial matches: Specific NCT numbers for actionable alterations without on-label therapies
10. Recommended actions: Specific treatment changes, additional testing, or molecular tumor board referral

Checkpoint B: Post-Draft Alignment (Mandatory)

1. Are report quality metrics reviewed and any limitations documented?
2. Is each alteration classified using the AMP/ASCO/CAP tier system or OncoKB evidence levels?
3. Are actionable mutations matched to FDA-approved therapies with correct indications (on-label vs. tumor-agnostic)?
4. Have variants of uncertain significance been explicitly labeled as not actionable?
5. Are germline implications flagged for pathogenic variants in hereditary cancer genes?

Quality Audit

• CGP platform and specimen type documented
• Sample quality metrics reviewed (tumor content, sequencing depth, ctDNA fraction)
• Each alteration classified by actionability tier
• Tier I mutations matched to FDA-approved therapies with correct indication
• MSI-H/dMMR status reported and tumor-agnostic eligibility assessed
• TMB score reported with threshold for pembrolizumab eligibility (≥10 mut/Mb)
• NTRK fusion status assessed for tumor-agnostic therapy eligibility
• Resistance mutations interpreted in context of prior treatment
• Co-mutations affecting prognosis documented
• VUS explicitly noted as not actionable
• Germline implications flagged with recommendation for confirmatory testing
• Clinical trial matches identified for actionable alterations without on-label therapy
• Liquid biopsy limitations noted if ctDNA fraction is low
• Report reviewed by molecular tumor board or qualified genomic specialist

Guidelines

• Never recommend treatment based on a VUS — only Tier I and selected Tier II alterations are actionable
• Liquid biopsy with undetectable ctDNA is not the same as "no mutations found" — recommend tissue-based testing if liquid biopsy is negative in a patient with known active disease
• MSI-H/dMMR, TMB-H, and NTRK fusions are tumor-agnostic biomarkers — assess for every solid tumor patient regardless of cancer type
• Germline pathogenic variants detected on tumor profiling (especially BRCA1/2, MLH1, MSH2, MSH6, PMS2) require confirmatory germline testing and genetic counseling referral
• For NSCLC, NCCN requires broad molecular testing (EGFR, ALK, ROS1, BRAF, KRAS, MET, RET, HER2, NTRK) before first-line treatment selection — single-gene sequential testing is no longer acceptable
• Report interpretation should be updated if new FDA approvals or guideline changes create actionability for previously non-actionable findings
• Molecular tumor board review is recommended for complex cases with multiple actionable findings or uncertain actionability
• Document the date of the CGP report and the NCCN guideline version used for interpretation — both are time-sensitive