NGS Tumour Testing: How Cancer Gene Sequencing Works

Next-generation sequencing (NGS) tumour testing extracts DNA from a cancer biopsy, reads dozens of genes at once and reports the alterations driving that tumour, so the oncologist can confirm the diagnosis and choose a targeted drug. Dr. Shrinidhi Nathany, Consultant Molecular Hematology & Oncology, Fortis Memorial Research Institute, Gurgaon, India, recommends testing at least 50 genes, and her laboratory returns reports within three to four days.

That turnaround, and the clinical gains it unlocks, were the practical heart of her masterclass. This article follows a sample from the biopsy block to the report, sets out which genes are tested and what the guidelines say, and uses her stage 4 lung cancer example to show what precision medicine has changed. The wider picture, from the WHO classification to genomics outside oncology, is in the Genomics Revolution in Cancer complete guide.

What NGS tumour testing is

Next-generation sequencing is a technology that reads the order of the DNA letters in many genes, or many samples, in parallel, rather than one gene at a time as older methods did. Dr. Nathany used "genome sequencing" and "next generation sequencing" interchangeably for the cancer test. Asked by an attendee what genomic sequencing is all about, she reduced it to its purpose: across all the genes in the body that can cause a genetic disease or a cancer, the laboratory works out the sequence of each gene.

In a tumour, those changes are somatic: acquired by the cancer cells, not inherited. A somatic mutation that drives the growth of the cancer is called a driver mutation, and when a drug exists that blocks the product of that gene, the mutation becomes actionable. The distinction from inherited (germline) testing is set out in the hereditary cancer article.

From biopsy block to report

The test starts with material the pathologist already has. Dr. Nathany described the sequence:

1. The biopsy block. The tissue removed on suspicion of cancer is processed into a block, conventionally formalin-fixed and embedded in paraffin wax, which is the same material used for the microscopic diagnosis.
2. DNA extraction. The laboratory takes DNA out of that block.
3. Automated preparation and sequencing. The tumour DNA goes into the sequencer, where a robotic arm performs the test. Answering a question about the robot's role, she explained that it prepares the sample inside the machine and helps detect which gene alteration is present. It does not decide treatment; that remains a clinical decision informed by the report.
4. Data processing. The machine produces raw data, which the team processes with analysis software.
5. The report. The processed result is issued to the treating doctor as a molecular report.

The same platform is not limited to tissue. Dr. Nathany noted that blood, tumour tissue and other body fluids can all be processed on it.

NGS turnaround time: three to four days against three weeks

An NGS tumour report from Dr. Nathany's laboratory takes three to four days, against about three weeks, or 21 days, internationally. Speed was the point she pressed hardest. Her sequencer completes a run in a maximum of 18 hours, which allows the laboratory to deliver a report within three days, and the team's commitment is never to exceed four days. At the time of the masterclass, the laboratory had processed more than 500 samples on the machine.

For a patient with advanced cancer, the difference between four days and three weeks is the time spent waiting before a matched treatment can begin.

How many genes an NGS panel should test, and what the guidelines say

Asked which markers are tested routinely, Dr. Nathany's answer was a number rather than a list: the recommendation is to test at least 50 genes, and she offered to share her gene list with doctors through Jivo Healthcare. She added that the US FDA has approved drugs linked to at least 10 different genes, and that anyone reading the NCCN guidelines for a given tumour today will find molecularly directed, or genomic-directed, therapy within them. In her view, every cancer should undergo at least a basic genomic sequencing, citing the NCCN and ESMO guidelines.

The published guidance is most detailed for advanced lung cancer. For metastatic non-small cell lung cancer, the NCCN guidelines recommend broad molecular profiling that covers EGFR, ALK, ROS1, BRAF, KRAS, MET, RET, NTRK and ERBB2 (HER2), alongside PD-L1 testing for immunotherapy. ESMO's 2020 recommendations advise routine tumour NGS for advanced non-squamous non-small cell lung cancer, prostate cancer, ovarian cancer and cholangiocarcinoma; for many other cancers, single-gene tests or smaller panels remain acceptable where they answer the clinical question. Testing many genes in one panel avoids a sequence of single-gene tests that each consume tissue and time.

Stage 4 lung cancer: what precision medicine changed

For patients with stage 4 lung cancer whose tumour carries a targetable alteration, Dr. Nathany put median survival on matched oral therapy at 36 months. She chose advanced lung cancer to show how genomics and precision medicine work in practice, because the change there has been so large.

Before targeted therapy. She recalled that a patient with stage 4, or last-stage, lung cancer was once expected to live no more than six months. In the era of chemotherapy alone, she noted, only about 30% of patients opted for any kind of chemotherapy. Median overall survival with standard platinum-based chemotherapy for advanced non-small cell lung cancer was typically under a year.

After genome sequencing. With the US FDA approving many molecules targeting at least 10 genes, oral medicines are now available for patients whose tumour carries one of those alterations. Dr. Nathany was careful about the 36-month figure: it is the median, meaning the middle patient lives at least 36 months, not the average.

The gain depends entirely on the test. A patient whose tumour is never sequenced cannot receive the medicine matched to it.

Targeted therapy: treating the driver, not the organ

Targeted therapy aims at the gene, or the molecule that gene produces, that is driving the disease, rather than at every dividing cell as chemotherapy does. Dr. Nathany called it bullseye therapy. That is why the same lung cancer can need entirely different tablets in two patients, and why the label "lung cancer" alone no longer determines treatment.

Her conclusion followed directly. Precision medicine needs genomics, and genomics needs a molecular pathologist: the specialist who designs the test, interprets the variants and writes a report the oncologist can act on.

Liquid biopsy: where it is proven and where it is still research

Liquid biopsy is a blood test that detects circulating tumour DNA (ctDNA), the fragments of DNA that tumours shed into the bloodstream. Dr. Nathany presented it as the genetic complement to imaging in cancer screening, and in the discussion an attendee asked her to clarify which part she had called research.

Her answer drew a clear line. Using liquid biopsy to catch cancer at an early stage is, overall, still under research. In lung cancer, she said, its use is already recommended by guidelines and proven; in other cancers, it is still being studied. In established practice, the guideline-endorsed role in lung cancer is plasma ctDNA testing to find targetable mutations in advanced disease, particularly when tissue is scarce or a repeat biopsy is not feasible. Screening for lung cancer itself still relies on low-dose CT, and blood-based multi-cancer early detection tests remain under evaluation in clinical trials.

For a referring doctor, the practical message is that a blood-based genomic test can stand in for tissue in some advanced cancers, but a negative blood screening test cannot yet rule cancer out. The same discussion is recorded in the Live Discussion from this masterclass.

NGS test cost and access to targeted drugs

An NGS tumour test costs about US$300 to $400 for a basic test and up to about $1,000 for broader tests, according to Dr. Nathany. Few governments and few insurance companies cover them, so in most countries the patient pays out of pocket.

Asked whether that cost is justified by the outcome, and whether it is affordable for middle-income countries, she said it is: the cost is relatable to the outcome, the targeted therapies themselves can be obtained at much lower cost in middle-income countries, and patient access programmes, run to reduce the price of these medicines, lower it further.

Referring samples for NGS testing

Doctors in other countries can send samples to Dr. Nathany's team for NGS and discuss the results jointly. She also offered to help partner institutions set up their own centre of excellence for sequencing, and the medical genetics and oncology specialties list the partner teams working in this field.

The family and prevention side of genomic testing, including BRCA, cascade testing and gene therapy, is in hereditary cancer testing, BRCA and prevention. For the treating oncologist's view of the same shift, see precision oncology, targeted therapy and immunotherapy and personalised cancer treatment, from chemotherapy to NGS; the surgical oncologist's perspective on NGS and ctDNA is in recent trends in surgical oncology.