Next Generation Sequencing For Cancer - NGS Cancer Testing
Next generation sequencing reads hundreds of cancer genes from one biopsy or a blood sample to find the mutations, fusions and markers that decide targeted therapy and immunotherapy. ESMO recommends it for advanced lung, prostate, bowel, bile duct, ovarian and breast cancer. Our team explains the report, flags inherited findings, and patients abroad can send tissue blocks or blood by courier without traveling.
About This Department
Two cancers that look the same under the microscope can be driven by different genes. NGS reads those genes and points to the drug that fits.
Next generation sequencing, or NGS, is a laboratory test that reads the DNA, and in good panels the RNA, of a tumor across dozens to hundreds of genes at once. It looks for the mutations, fusions and amplifications that drive the cancer, and for markers such as microsatellite instability and tumor mutational burden that predict response to immunotherapy. Tissue from a biopsy or operation already done works, and so does blood. The European Society for Medical Oncology now recommends tumor NGS in routine care for ten groups of advanced cancer, among them lung, prostate, bowel, bile duct, ovarian and breast cancer (Mosele and colleagues, Annals of Oncology, 2024). A result can open the door to a targeted drug, show that one will not work, reveal an inherited mutation that matters to the family, or qualify a patient for a clinical trial. This page explains how NGS works, which cancers need it, treatments that follow a gene regardless of where the cancer began, tissue and blood testing, the steps and timeline, how to read the report, and how patients abroad can send samples to Biruni Hospital in Istanbul.
What NGS is
| Type of change | What it means | Example |
|---|---|---|
| Point mutation | One letter of the DNA code is changed | EGFR L858R in lung cancer, BRAF V600E |
| Fusion | Two genes break and join, making an abnormal protein | ALK, ROS1, RET and NTRK fusions |
| Amplification | Extra copies of a gene | HER2, MET |
| Genome-wide markers | Patterns across many genes | Microsatellite instability, tumor mutational burden, homologous recombination deficiency |
Panel size
| Test | Genes read | Typical use |
|---|---|---|
| Single gene test, PCR | One gene or a few hotspots | A quick answer for one question, such as EGFR |
| Targeted NGS panel | 50 to 500 genes | Standard care in advanced cancer |
| Whole exome or genome | All genes | Research and selected rare cases |
A comprehensive panel on one sample replaces a chain of single tests, saves tissue and gives the full picture before the first treatment decision.
Which cancers need it
| Cancer | Main genes and markers | Treatments they open |
|---|---|---|
| Non-squamous lung cancer | EGFR, ALK, ROS1, BRAF, KRAS G12C, MET, RET, NTRK, HER2 | Osimertinib, alectinib, lorlatinib and other targeted tablets |
| Prostate cancer | BRCA1, BRCA2 and other repair genes | Olaparib and other PARP inhibitors |
| Bowel cancer | RAS, BRAF, MSI, HER2 | Anti-EGFR antibodies, encorafenib, immunotherapy |
| Bile duct cancer | IDH1, FGFR2, BRAF, HER2, MSI | Ivosidenib, FGFR inhibitors |
| Ovarian cancer | BRCA1, BRCA2, homologous recombination deficiency | PARP inhibitors |
| Breast cancer | PIK3CA, ESR1, AKT1, PTEN, BRCA | Alpelisib, capivasertib, elacestrant |
| GIST, sarcoma, thyroid cancer, cancer of unknown primary | KIT, PDGFRA, RET, BRAF, NTRK and others | Imatinib, selpercatinib and others |
ESMO recommends tumor NGS in advanced non-squamous lung, prostate, colorectal, bile duct and ovarian cancer, and since 2024 also in advanced breast cancer and in rare tumors such as gastrointestinal stromal tumors, sarcoma, thyroid cancer and cancer of unknown primary (Mosele and colleagues, 2024).
Treatments for any cancer type
Tumor-agnostic approvals
| Finding | Drug | Frequency |
|---|---|---|
| NTRK fusion | Larotrectinib, entrectinib, repotrectinib | Under 1 percent of common cancers, very common in some rare ones |
| MSI-high or mismatch repair deficiency | Pembrolizumab, dostarlimab | Around 4 percent of advanced cancers, more in womb and bowel |
| High tumor mutational burden | Pembrolizumab | Varies widely by cancer type |
| BRAF V600E | Dabrafenib with trametinib | Common in melanoma and thyroid, rare elsewhere |
| RET fusion | Selpercatinib | One to two percent of lung cancers, rare elsewhere |
The overall response rate to larotrectinib was 75 percent in 55 patients with 17 unique TRK fusion-positive tumor types, ranging in age from 4 months to 76 years (Drilon and colleagues, 2018).
Why one test instead of many
Tissue runs out fast.
A lung biopsy taken with a needle may yield a few millimeters of tumor, and every single-gene test cuts slices from the same block. Testing EGFR, then ALK, then ROS1, then PD-L1 one after another can exhaust the sample before the last question is answered, and a second biopsy means another procedure and weeks of delay while the cancer grows. Time is lost too. Sequential testing also takes longer overall, because each result prompts the next request. One broad panel ordered at diagnosis answers every current question at once, and the laboratory rereads the stored data when a new drug is approved for a gene that was already on the panel. Studies in lung cancer have found that single-gene strategies miss a share of targetable changes that a broad panel catches, simply because the relevant gene was never tested.
The saving in time matters most in cancers that grow fast.
Tissue or blood
| Feature | Tissue NGS | Liquid biopsy |
|---|---|---|
| Sample | Biopsy or surgical block | Two tubes of blood |
| Turnaround | About two weeks | About one week |
| Fusions and copy changes | Detected well | Detected less reliably |
| A negative result | Reliable when tumor content is adequate | Does not rule out a mutation if the tumor sheds little DNA |
| Best use | First choice at diagnosis | When tissue is scarce, a biopsy is risky, or to track resistance |
When blood is used
Can a blood test replace a biopsy?
How the test works
Timeline
| Step | Time | Note |
|---|---|---|
| Block retrieval or shipping | One to five days | Longer when the block is held at another hospital |
| Extraction and sequencing | Five to seven days | A failed run is repeated if tissue allows |
| Analysis and report | Two to four days | Complex findings go to the molecular tumor board |
Reading the report
| Term | Meaning | Why it matters |
|---|---|---|
| Variant allele frequency | The share of DNA reads carrying the change | Around 50 percent can hint at an inherited mutation |
| Variant of uncertain significance | A change whose effect is unknown | Not acted on, may be reclassified later |
| Tumor mutational burden | Mutations per million DNA letters | 10 or more may predict response to immunotherapy |
| MSI-high | Loss of the DNA spelling-check system | Strong response to immunotherapy |
| Actionable | Linked to an approved drug or a trial | The findings that change treatment |
- The alterations found, ranked by how much evidence links them to a treatment.
- Matched drugs and trials.
- Genome-wide markers, and a note if the sample was too small to assess them.
Levels of evidence
| Tier | Meaning | Action |
|---|---|---|
| I | Proven benefit in this cancer | Use the matched drug |
| II | Promising evidence awaiting confirmation | Consider, usually in a trial |
| III | Proven in another cancer type | Trial or off-label discussion |
| IV to X | Laboratory evidence only, or none | No action outside research |
Inherited findings
Of 1,040 patients with advanced cancer, 182 (17.5 percent) had clinically actionable mutations conferring cancer susceptibility, and 101 (9.7 percent) would not have had these mutations detected using clinical guidelines (Mandelker and colleagues, JAMA, 2017).
When nothing is found
No actionable change
What if the test fails?
Tests NGS does not replace
| Test | Cancer | Why it is separate |
|---|---|---|
| Estrogen and progesterone receptors, HER2 | Breast, stomach | Protein levels measured by staining the tissue |
| PD-L1 | Lung, stomach, head and neck, cervix, others | Guides immunotherapy, measured by staining |
| Mismatch repair proteins | Bowel, womb, others | A quick staining screen that complements MSI by NGS |
| HER2-low and ultralow | Breast | Staining grades that decide trastuzumab deruxtecan |
NGS reads genes. Staining measures proteins. Both are needed to plan modern cancer treatment.
Repeating the test
A cancer changes under treatment.
When a targeted drug stops working, a new test finds the reason, a second mutation in the same gene or a switch to another pathway, and points to the next drug. A liquid biopsy suits this well. A new tissue biopsy of a growing deposit gives the fullest answer when safe.
Timing matters as well. Testing at diagnosis sets the first treatment. Testing again at progression sets the second, and in lung cancer with an EGFR mutation, looking for the resistance change called C797S or a new MET amplification has become part of routine follow-up at centers that treat patients over many years of targeted therapy.
For patients abroad
Sending samples without traveling
One coordinator from the international patients office handles arrangements from the first message through discharge and answers the same WhatsApp number once you are back home. The office works in English, Arabic, French, Russian, Serbian, Romanian and Spanish and books interpreters for other languages, and it arranges the visa invitation letter, airport transfers, daily transport and accommodation near the hospital. Halal, vegetarian and diabetic meals, a prayer room on site, and a female physician on request wherever the rota allows.
Cost
| Item | Included | Priced separately |
|---|---|---|
| The test | Sequencing of the agreed panel, DNA and RNA where specified | A second run on another block, liquid biopsy |
| Interpretation | Molecular pathologist report, tumor board review of complex findings | Genetic counseling and blood confirmation of inherited findings |
| Consultation | Explanation of the result by an oncologist | Treatment that follows |
The price depends on the size of the panel, whether RNA is read and whether blood is sequenced alongside the tumor.
A cheaper small panel that misses the relevant gene costs more in the end.
References
- Mosele MF, Westphalen CB, Stenzinger A, et al. Recommendations for the use of next-generation sequencing (NGS) for patients with advanced cancer in 2024. A report from the ESMO Precision Medicine Working Group. Ann Oncol. 2024;35(7):588-606.
- Drilon A, Laetsch TW, Kummar S, et al. Efficacy of larotrectinib in TRK fusion-positive cancers in adults and children. N Engl J Med. 2018;378(8):731-739.
- Mandelker D, Zhang L, Kemel Y, et al. Mutation detection in patients with advanced cancer by universal sequencing of cancer-related genes in tumor and normal DNA vs guideline-based germline testing. JAMA. 2017;318(9):825-835.
- Zehir A, Benayed R, Shah RH, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med. 2017;23(6):703-713.
Editor's note
Written by the Biruni Hospital medical editorial team. Reviewed by Prof. Dr. Özcan YILDIZ, Medical Oncology.
Medically reviewed by
Prof. Dr. Özcan YILDIZ
Medical Oncology
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