Next-Generation Sequencing (NGS) in GI Cancers: When and Why Is It Recommended?

Introduction

Next-Generation Sequencing (NGS) is an advanced laboratory method used to examine multiple cancer-related genes simultaneously. In gastrointestinal (GI) cancers, it can identify molecular alterations—changes in the tumour’s DNA or RNA—that may help explain how a cancer behaves and whether a specific targeted treatment, immunotherapy, or clinical trial may be suitable.

NGS is an important component of precision oncology: treatment decisions are increasingly based not only on the organ in which a cancer began, but also on the individual molecular features of the tumour. However, NGS is not necessary for every patient with every GI cancer, and its value depends on the cancer type, stage, tissue availability, prior treatment, and the likelihood that a result will change management.

What Is Next-Generation Sequencing (NGS)?

Next-Generation Sequencing is a technology that allows a laboratory to analyse many genes, or selected parts of genes, in a single test. It can identify different types of molecular changes, including:

• Mutations: small changes in the DNA sequence of a gene
• Gene amplifications: extra copies of a gene that may drive tumour growth
• Gene fusions or rearrangements: abnormal joining of two genes
• Biomarkers such as microsatellite instability (MSI) and tumour mutational burden (TMB), depending on the test used

Traditional molecular tests often assess one biomarker at a time. In contrast, an NGS panel can evaluate several clinically relevant biomarkers from one tumour sample and, in some settings, from a blood sample. This approach can be particularly useful when tissue is limited or when multiple biomarkers need to be assessed before selecting systemic therapy.

NGS may also be described as tumour genomic profiling, molecular profiling, or comprehensive genomic profiling. The exact genes and biomarkers included vary between laboratories and test panels.

How Does NGS Work in GI Cancers?

NGS is usually performed on tumour tissue obtained during a biopsy or cancer surgery. The pathology laboratory selects an appropriate tumour-containing sample, extracts DNA—and sometimes RNA—and analyses it using a validated sequencing panel. Results are then interpreted alongside the pathology report, imaging findings, cancer stage, previous treatments, and the patient’s overall health.

In some situations, NGS can be performed on a blood sample. This is often called a liquid biopsy or circulating tumour DNA (ctDNA) test. Liquid biopsy may be useful when obtaining a tissue biopsy is difficult, unsafe, or likely to delay treatment. However, a blood-based test may not detect all tumour alterations, especially when the amount of tumour DNA circulating in the blood is low. A negative liquid-biopsy result does not always rule out an actionable mutation, and tissue testing may still be needed.

The report may identify:

• An alteration that has an approved targeted treatment or immunotherapy option
• A biomarker that predicts lack of benefit from a particular treatment
• A mutation that may make a patient eligible for a clinical trial
• A possible inherited cancer-risk finding that requires confirmation with a separate germline blood or saliva test

Importantly, not every molecular alteration found on NGS is clinically actionable. Results should ideally be reviewed by a multidisciplinary cancer team, with genetic counselling when appropriate.

When Is NGS Recommended for GI Cancer Patients?

NGS is most often considered for patients with advanced, recurrent, unresectable, or metastatic GI cancers, particularly when the result could influence systemic treatment selection. Current precision-oncology recommendations support tumour NGS in advanced colorectal cancer and cholangiocarcinoma, and increasingly in selected metastatic cancers where matched therapies are accessible.

Your oncology team may recommend NGS in the following situations:

The cancer is advanced, recurrent, or has spread to distant organs

Standard treatment options have been used, are unsuitable, or have stopped working

There is a need to assess several biomarkers at the same time before starting treatment

The tumour type has known actionable molecular alterations

A clinical trial or targeted therapy may be available based on the result

Tissue is limited, and a broader panel may avoid repeated testing

The patient is young, has multiple cancers, or has a significant family history suggestive of an inherited cancer predisposition syndrome

The role of NGS differs between GI cancers:

Colorectal cancer: In metastatic disease, testing for RAS genes, BRAF, mismatch-repair deficiency/MSI status, and HER2 is clinically important. Broader NGS can also identify rare but actionable alterations, including NTRK fusions. Universal mismatch-repair or MSI testing is recommended in newly diagnosed colorectal cancer because it can influence treatment and help identify possible Lynch syndrome.

Biliary tract cancer/cholangiocarcinoma: Broad molecular profiling is particularly valuable in advanced disease because alterations such as IDH1 mutations, FGFR2 fusions or rearrangements, HER2 alterations, BRAF V600E mutations, MSI-high status, and NTRK fusions may influence targeted-treatment options.

Gastric and gastro-oesophageal junction cancer: Essential biomarkers in advanced disease commonly include HER2, PD-L1, MSI/MMR status, and CLDN18.2. NGS may be helpful in selected patients, particularly later in the treatment course or when broader profiling is needed, but some biomarkers are often best assessed using immunohistochemistry or in-situ hybridisation rather than NGS alone.

Pancreatic cancer: Tumour profiling may identify selected actionable alterations, while all patients with pancreatic adenocarcinoma should also be considered for germline genetic testing because inherited mutations can affect treatment, family counselling, and screening recommendations for relatives.

Gastrointestinal stromal tumour (GIST): Molecular testing is important for identifying KIT or PDGFRA mutations. NGS is especially useful when routine testing does not identify these common drivers or when resistance to treatment develops.

For patients with early-stage, potentially curable GI cancers, NGS is not routinely required in every case. More focused biomarker testing may be more appropriate, depending on the cancer type and treatment plan.

Why Is NGS Important in GI Cancer Care?

NGS can provide a more detailed molecular profile of a tumour and may help personalise treatment. Rather than assuming that two cancers from the same organ will respond in the same way, molecular testing helps identify clinically meaningful differences between tumours.

The potential benefits include:

• Identifying patients who may benefit from targeted therapies
• Identifying biomarkers that support the use of immunotherapy, such as MSI-high or mismatch-repair-deficient tumours
• Helping avoid treatments that are unlikely to be effective, such as anti-EGFR therapy in certain RAS-mutated colorectal cancers
• Detecting rare but actionable alterations that may otherwise be missed with single-gene testing
• Supporting eligibility for biomarker-driven clinical trials
• Providing information that may prompt evaluation for an inherited cancer syndrome
• NGS does not replace standard cancer care. Decisions about surgery, chemotherapy, radiotherapy, immunotherapy, targeted therapy, and supportive care should be made by a multidisciplinary team and tailored to the individual patient.

Benefits and Limitations of NGS in GI Oncology

NGS can be extremely useful, but it is important to have realistic expectations. A test is valuable when its result has a reasonable chance of changing treatment, clarifying prognosis, or identifying a trial option.

Benefits:

1. Evaluates multiple clinically relevant genes and biomarkers in a single test
2. May reduce the need for repeated testing when adequate tissue is available
3. Helps identify targeted therapy and immunotherapy options in selected patients
4. Can detect rare alterations that may qualify a patient for tumour-agnostic treatments or clinical trials
5. May identify findings that warrant formal germline genetic counselling and testing
6. Can support more informed treatment discussions between the patient and multidisciplinary cancer team

Limitations:

1. Not every mutation is a treatment target, and not every target has an accessible or approved medicine
2. A molecular alteration may be biologically interesting without being clinically actionable
3. The test may not provide useful information if the tissue sample has too few viable tumour cells or poor-quality DNA
4. Results can take time, although turnaround varies by laboratory
5. Some tests may be costly, and reimbursement or insurance coverage can vary
6. A blood-based liquid biopsy can miss alterations that may be detected in tissue

Results require expert interpretation; treatment should not be chosen on the basis of an NGS report alone

A tumour-only NGS report may suggest an inherited mutation, but this must be confirmed by dedicated germline testing from blood or saliva before making conclusions about family cancer risk

What to Expect During NGS Testing

Your oncologist will first explain why NGS is being considered and how the result may affect your treatment plan. The test is usually performed using tissue that has already been collected during a biopsy or surgery. If suitable tissue is not available, a repeat biopsy or a blood-based liquid biopsy may be considered.

The general process includes:

• Sample selection: A pathologist reviews the tumour tissue to ensure that it is adequate for testing.
• Laboratory analysis: DNA, and sometimes RNA, is extracted and analysed using a validated NGS panel.
• Reporting: The laboratory provides a report describing relevant molecular findings and their potential clinical significance.
• Clinical interpretation: Your cancer specialist reviews the report in the context of your diagnosis, stage, prior treatment, general fitness, and locally available therapies or clinical trials.
• Genetic counselling when required: If a finding raises concern for an inherited cancer predisposition, a genetic counsellor or specialist may recommend separate germline testing.

Most patients do not need special preparation if an existing tissue sample is being used. For a blood-based test, the procedure is similar to a routine blood draw.

Frequently Asked Questions about NGS in GI Cancers

Is NGS safe?

Yes. When performed on an existing biopsy or surgical specimen, NGS does not involve any additional procedure for the patient. If a new biopsy is needed, the safety considerations relate to the biopsy itself, not to the sequencing test.

Will NGS find all cancer risks?

No. Tumour NGS primarily studies changes within the cancer. It may occasionally raise suspicion of an inherited mutation, but it does not replace formal germline genetic testing for hereditary cancer syndromes.

Is NGS covered by insurance?

Coverage depends on the insurer, the type and stage of cancer, the test selected, and local policy. Your treating centre can help clarify expected costs and documentation requirements before testing.

Can NGS help with all GI cancers?

NGS can be useful across many GI cancers, but its clinical value varies. It is generally most helpful in advanced cancers where molecular findings may guide targeted therapy, immunotherapy, or clinical-trial enrolment. In some cancers, focused tests for specific biomarkers may be more appropriate than a broad panel.

Where can I get NGS testing?

NGS is available through many tertiary cancer centres and accredited molecular pathology laboratories. The most important step is not simply obtaining the test, but ensuring that the result is interpreted by an experienced oncology team and incorporated into an appropriate treatment plan.

Conclusion

Next-Generation Sequencing has become an important tool in modern GI cancer care. By identifying clinically relevant molecular alterations, it can help select targeted therapies, identify patients who may benefit from immunotherapy, and open access to suitable clinical trials.

However, NGS is not a one-size-fits-all test. Its value is greatest when ordered for the right patient, at the right time, using an appropriate test panel, and interpreted in the context of multidisciplinary cancer care. If you or a loved one has a GI cancer, consult a GI cancer specialist, such as Dr. Anshul Verma, to understand whether molecular profiling or NGS is appropriate for your individual diagnosis and treatment plan.