PRECISION ONCOLOGY &
NGS TESTING: COMPLETE PATIENT GUIDE

Precision oncology asks a fundamentally different diagnostic question: not 'where did this cancer start?' but 'what is uniquely wrong at the molecular level inside this patient's cancer cells — and what can we do about it?' By adding genomic profiling to the traditional tissue-of-origin diagnosis, treatment can be matched to tumour biology with far greater specificity.

“Precision oncology means the right drug, the right dose, the right combination — matched to the right tumour biology, eliminating medications unlikely to work and finding drugs that actually target the molecular driver.”

• Comprehensive Genomic Profiling (NGS)

  Identifies the mutations, amplifications, fusions, deletions, MSI status, TMB, and HRD that drive a specific tumour — producing a molecular blueprint that guides treatment matching.

• Targeted Therapy Matching

  Drugs designed to block the specific mutated proteins or pathways identified by NGS — EGFR inhibitors for EGFR mutations, ALK inhibitors for ALK fusions, PARP inhibitors for BRCA1/2 or HRD, BRAF inhibitors for BRAF V600E.

• Biomarker-Guided Immunotherapy

  PD-L1 expression, MSI-H/dMMR status, and TMB-H are biomarkers that predict immunotherapy response — now with tumour-agnostic FDA approvals for pembrolizumab across any solid tumour type.

• Clinical Trial Matching + Liquid Biopsy Monitoring

  NGS identifies clinical trials matched to a patient's specific mutation profile. Serial liquid biopsy using blood-based ctDNA tracks treatment response and detects resistance mutations in real time — without repeated invasive procedures.

NGS simultaneously sequences millions of DNA and RNA fragments — producing a comprehensive genomic profile (CGP) of the cancer in a single test that previously would have required dozens of individual gene tests.

1. 1

   Sample Collection

   A tissue sample is obtained from a biopsy, surgical specimen, or archived FFPE tumour block — or a blood sample is collected for liquid biopsy (ctDNA/cfDNA). Sample quality and tumour cellularity directly affect result quality.

2. 2

   DNA / RNA Extraction

   DNA (and sometimes RNA for fusion detection) is extracted from the sample in a certified, accredited molecular laboratory. FFPE tissue requires additional processing steps due to formalin-induced DNA fragmentation.

3. 3

   Library Preparation & Sequencing

   The extracted genetic material is prepared into a sequencing library and loaded onto a high-throughput sequencing platform. Millions of DNA fragments are read simultaneously and mapped against the reference human genome.

4. 4

   Bioinformatics Variant Calling

   Sophisticated bioinformatics software identifies variants — mutations (SNVs, indels), copy number alterations (amplifications, deletions), gene fusions, and rearrangements — while filtering out sequencing errors and germline background noise.

5. 5

   Clinical Interpretation

   Clinically trained molecular pathologists and oncologists interpret variants against curated databases of known actionable alterations — classifying each by evidence tier (Tier I–IV) and clinical significance.

6. 6

   Structured Clinical Report Generation

   A comprehensive report is generated listing: identified alterations, evidence tier classification, potentially matched approved therapies (by tumour type and tumour-agnostically), and relevant open clinical trials.

The most important question after receiving an NGS report: how many findings are actionable? An actionable alteration can be matched to an approved drug, clinical trial, or treatment decision.

NGS testing is relevant across all solid tumours in advanced disease — but the density of actionable findings varies significantly by cancer type. These are the highest-priority indications.

• Non-Small Cell Lung Cancer (NSCLC) — Essential

  NGS is mandated by NCCN, ESMO, and IASLC guidelines at diagnosis of advanced NSCLC. EGFR, ALK, ROS1, BRAF, KRAS G12C, MET exon 14, RET, NTRK, HER2, PD-L1, and TMB are all matched to approved targeted agents or immunotherapy. The most biomarker-rich solid tumour in oncology.

• Colorectal Cancer — Essential

  KRAS, NRAS, BRAF V600E, HER2, MSI/MMR, and NTRK testing guide anti-EGFR therapy eligibility (requires RAS wild-type), BRAF inhibitor use, immunotherapy eligibility (MSI-H), and emerging HER2-directed strategies.

• Breast Cancer — Strongly Recommended

  PIK3CA, HER2, BRCA1/2, HRD, ESR1 (acquired resistance mutation), and NTRK are actionable in metastatic breast cancer. Critical for metastatic HR+ disease (PI3K inhibitors) and TNBC (PARP inhibitors for BRCA-mutated; immunotherapy for PD-L1+).

• Ovarian Cancer — Strongly Recommended

  BRCA1/2 somatic and germline testing plus HRD scoring guide PARP inhibitor eligibility and maintenance therapy selection — one of the most clinically impactful biomarker relationships in oncology. NTRK testing adds additional actionable potential.

• Prostate Cancer — Strongly Recommended (Metastatic)

  BRCA1/2, CDK12, MSI/MMR, and AR pathway alterations guide PARP inhibitor eligibility (olaparib, rucaparib) and immunotherapy consideration in metastatic castration-resistant disease. Germline BRCA testing has family implications.

• Cholangiocarcinoma — High Impact

  FGFR2 fusion (in ~15% of intrahepatic CCA), IDH1 mutation, and NTRK are all matched to approved targeted agents. Cholangiocarcinoma has one of the highest actionable mutation rates relative to its rarity — NGS is particularly high-yield here.

• Any Solid Tumour — Tumour-Agnostic Targets

  MSI-H/dMMR, TMB-H (≥10 mut/Mb), and NTRK fusions have tumour-agnostic FDA approvals — meaning any patient with these findings, regardless of cancer type, is eligible for pembrolizumab (MSI-H, TMB-H) or larotrectinib/entrectinib (NTRK). NGS is the only way to identify these.

NGS is no longer reserved for patients who have exhausted all standard options. It is increasingly recommended at diagnosis of advanced disease to ensure no targeted or trial option is missed from the start.

NGS reports are technically complex and can be overwhelming for patients and even oncologists unfamiliar with molecular oncology. Understanding the structure and evidence tier system is essential for informed decision-making.

• Tier I — Strong Clinical Evidence

  Alterations with approved therapy in this specific tumour type, or diagnostic/prognostic significance per professional guidelines. These are the most immediately actionable findings — an approved drug exists for your mutation in your cancer type.

• Tier II — Potential Clinical Significance

  Alterations with approved therapy in a different tumour type (off-label), or strong pre-clinical evidence. These require specialist interpretation — the drug may work in your cancer but has not been validated in your specific tumour type through a randomised trial.

• Tier III — Variants of Unknown Significance (VUS)

  Alterations with uncertain significance based on current evidence. These are detected but should NOT drive therapy without further specialist review. A VUS today may become actionable tomorrow — reclassification as evidence evolves is common and legitimate.

• Tier IV — Benign Variants

  Variants classified as benign or likely benign — not clinically significant. Also typically included in reports: MSI status, TMB score, HRD score, and (for comprehensive panels) germline findings flagged for genetic counselling referral.

Receiving an NGS report is the first step — not the last. Translating genomic data into a treatment plan requires molecular oncology expertise. This is where a molecular tumour board (MTB) is essential.

1. 1

   Molecular Tumour Board (MTB) Review

   In leading cancer centres, NGS results are reviewed by a multidisciplinary team: medical oncologists, molecular pathologists, genomic scientists, radiologists, and clinical trial specialists. For patients not at MTB-equipped centres, CancerFax arranges virtual MTB consultations with precision oncology specialists globally.

2. 2

   Identify All Actionable Tier I & II Alterations

   List every finding with approved or potential matched therapy. Tier I (approved for your tumour type) takes priority. Tier II (approved for a different cancer type) may be accessible through off-label use or clinical trials.

3. 3

   Assess Co-Mutation Context

   Co-mutations can negate or reduce the benefit of a matched therapy. For example: KRAS co-mutation abolishes anti-EGFR benefit in colorectal cancer; TP53 co-mutations reduce the efficacy of certain targeted therapies. A Tier I match is not automatically the right choice without assessing the co-mutation landscape.

4. 4

   Review MSI, TMB & PD-L1 for Immunotherapy Eligibility

   Alongside targeted therapy matching, assess whether the patient's MSI-H/dMMR or TMB-H status qualifies them for tumour-agnostic checkpoint inhibitor approvals — potentially unlocking immunotherapy as an option regardless of cancer type.

5. 5

   Screen for Open Clinical Trials

   NGS results unlock access to mutation-matched clinical trials. Many Phase II/III trials for precision oncology agents require specific mutations as eligibility criteria. CancerFax continuously monitors global trial registries and matches patients to open studies for which they are genomically eligible.

6. 6

   Incorporate into Full Treatment Sequence

   NGS findings must be integrated with the patient's current performance status, prior treatment history, organ function, and treatment goals. The result is a personalised treatment sequence — not just a single matched drug, but a planned pathway that anticipates resistance and next-line options.

Liquid biopsy is one of the most significant advances in precision oncology — enabling comprehensive genomic profiling from circulating tumour DNA (ctDNA) shed into the bloodstream, without invasive tissue biopsy.

• Baseline Profiling When Tissue Is Unavailable

  When tumour tissue is insufficient, inaccessible, or unsafe to biopsy, liquid biopsy provides genomic profiling as an alternative. FDA-approved platforms include Guardant360 CDx and FoundationOne Liquid CDx — validated against tissue NGS.

• Real-Time Treatment Monitoring

  Serial liquid biopsies track changes in ctDNA levels over time — reflecting tumour response or progression earlier than imaging in some settings. Rising ctDNA can signal emerging resistance before it becomes visible on a CT or PET scan.

• Resistance Mutation Detection

  When a targeted therapy stops working, liquid biopsy identifies resistance mutations that guide next-line treatment. The landmark example: T790M mutation detection in EGFR-mutated NSCLC after first-generation TKI failure — qualifying patients for osimertinib.

• Key Limitation: Lower Sensitivity than Tissue NGS

  Liquid biopsy has lower sensitivity than tissue NGS — particularly for small, low-shedding tumours or early-stage disease where ctDNA levels are very low. A negative liquid biopsy does NOT exclude a targetable mutation. Tissue testing should follow if clinical suspicion is high.

NGS is a transformative technology — but it has real limitations patients should understand. Setting realistic expectations is as important as understanding what it can detect.

Precision oncology does not replace standard oncology — it adds a critical additional layer of information to every treatment decision. Most patients today benefit from both approaches in combination.

• 40–70%Solid Tumour Patients with an Actionable NGS FindingVaries by cancer type — NSCLC and cholangiocarcinoma have the highest actionability rates.
• 10–21 daysTurnaround Time — Tissue NGSLiquid biopsy (ctDNA) turnaround is faster: 7–14 days. Plan treatment timing accordingly.
• 3Tumour-Agnostic FDA Approvals Based on NGS BiomarkersMSI-H/dMMR, TMB-H (≥10 mut/Mb), and NTRK fusions — pembrolizumab and larotrectinib/entrectinib.
• 500+Genes Covered by Comprehensive NGS PanelsFoundationOne CDx, Guardant360 CDx, and equivalent platforms cover hundreds of cancer-related genes in a single test.

Explore in-depth guides on every aspect of precision oncology and NGS testing.

Frequently Asked Questions

The most common questions from patients and families exploring precision oncology and NGS testing.