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Molecular & Genomic Testing

Molecular Testing on a Biopsy: — What It Looks For

Molecular testing is often ordered before a treatment plan is confirmed, and the cost and waiting time can feel frustrating when you do not know what is being looked for. It reads the DNA and molecular markers inside your biopsy tissue to find specific changes that determine which treatments are most likely to work for your particular tumour.

Medically reviewed by Dr. Bharati Devi Gorantla, Medical Oncologist, MBBS · MD · DM (Adyar, Chennai) · ECMO · MRCP SCE (UK) · Last reviewed September 2026

  • Reads DNA, not just cell shape — Standard pathology identifies the cancer type under a microscope. Molecular testing reads the DNA to find the specific changes driving it.
  • Different from IHC — IHC tests for proteins on the cell surface. DNA sequencing reads the genetic code itself. Many workups use both.
  • Matches treatment to your tumour — The same cancer type can have different molecular drivers in different people. Molecular testing identifies which applies to you.
  • Your oncologist decides what to order — The relevant tests depend on your cancer type and what treatment options exist. Test selection is a clinical decision, not a standard checklist.
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Molecular testing reads your biopsy tissue to find specific DNA changes — mutations, fusions and expression levels — that guide treatment decisions. Standard pathology identifies what type of cancer it is. Molecular testing identifies how your specific tumour behaves, and which treatments it is most likely to respond to.

What does molecular testing look for?

Molecular testing looks for three types of changes in your biopsy tissue: mutations in specific genes, fusions where two genes have joined abnormally, and expression levels showing how much of a particular protein the cancer cells are producing.

Each of these changes can indicate which treatments are most likely to work for your specific tumour. Finding them before treatment begins is how the plan is matched to your particular cancer, rather than to the cancer type alone.

Your oncologist decides which tests to order based on your cancer type, stage and what treatment options are being considered.

What do the terms on your molecular testing report mean?

Mutation
A change in the DNA sequence of a cancer gene. Some mutations drive tumour growth; others point to specific treatment options.
Gene fusion
When parts of two genes join abnormally and produce a protein that drives cancer growth. Fusions are targeted by certain treatments in some cancer types.
Expression
Whether a particular protein is present on cancer cells and at what level. High or low expression of certain proteins predicts response to some treatments.
IHC (immunohistochemistry)
A staining test that detects proteins on tissue sections. Faster and cheaper than DNA sequencing, but measures protein presence rather than the DNA sequence itself.
NGS (next-generation sequencing)
A laboratory method that reads many genes at once in a single test. A comprehensive panel can report changes across hundreds of genes from one biopsy sample.
TMB (tumour mutational burden)
A count of how many mutations are present across the whole tumour. A high count may suggest the tumour is more likely to respond to immunotherapy.
MSI (microsatellite instability)
A sign that the tumour's DNA repair system is faulty. Tumours with high MSI have a distinct pattern of response to certain immunotherapy approaches.
Biomarker
Any measurable molecular feature — a mutation, a protein level, a gene count — used to guide a treatment or eligibility decision.

When do oncologists typically order molecular testing?

  • At initial diagnosis, before the treatment plan is finalised, for cancers where molecular features are known to change treatment decisions
  • When targeted therapy or immunotherapy is being considered
  • When the cancer has returned after earlier treatment, because a tumour's molecular profile can change over time
  • When the cancer type is unusual, metastatic, or the origin is uncertain
  • When eligibility for a clinical trial depends on a specific biomarker result
  • When a second opinion on treatment options is being sought

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How is molecular testing different from IHC and standard pathology?

Standard pathology and IHC look at what cells look like; molecular testing reads the DNA inside those cells. Standard pathology identifies cancer type and grade from cell structure. IHC detects specific proteins on the cell surface. DNA sequencing finds the mutations and fusions driving that particular cancer.

IHC is faster and cheaper than sequencing, so many workups begin with IHC and move to DNA testing when a more detailed result is needed, or when an IHC result is borderline.

Your oncologist may use all three in combination — pathology to confirm the diagnosis, IHC for specific proteins, and sequencing for the full molecular picture. The tests ordered depend on your cancer type and the treatment question being answered.

Did you know?

The WHO now classifies certain brain cancers and blood cancers primarily by their molecular features, not by how cells look under a microscope. Two tumours that appear identical under standard pathology can be different diseases requiring different treatment.

This is why molecular testing has moved from a specialist add-on to part of the standard diagnostic workup for an increasing number of cancers.

Source: WHO Classification of Tumours, 5th Edition

What else should you know about molecular testing?

How long does molecular testing take?

IHC results typically return within a few days of the biopsy being processed. Comprehensive DNA sequencing panels usually take two to three weeks, and sometimes longer if the sample must be sent to a specialist laboratory. Ask your team when the sample was sent and when results are expected. Starting treatment while awaiting a result that is likely to change the treatment plan is not generally recommended — clarify this directly with your oncologist.

How much does molecular testing cost?

Cost depends on which tests are ordered. A single IHC marker is considerably less expensive than a comprehensive NGS panel covering many genes. Some tests attract reimbursement under government health schemes, and foundational markers may be included in package pricing at some centres. Indicative figures change frequently — ask your team for current costs and whether any component is covered before you agree to the test.

Does my original biopsy sample have enough tissue for testing?

Molecular testing requires adequate, well-preserved tissue. If the original biopsy was small, or the sample was stored in conditions that degrade DNA, a repeat biopsy may be needed before sequencing can proceed. Your pathologist checks sample adequacy first and will inform your oncologist if more tissue is required. In some situations where repeat tissue biopsy is not feasible, liquid biopsy — testing circulating tumour DNA from a blood draw — is an alternative your oncologist can discuss with you.

Which cancers most often need molecular testing?

NCCN and ESMO guidelines recommend molecular testing as part of standard workup for lung adenocarcinoma, colorectal cancer, breast cancer, melanoma, cholangiocarcinoma and several other cancer types. For some of these, beginning certain treatments without prior molecular testing is explicitly not recommended. Testing is also relevant for cancers of unknown primary origin, where molecular patterns can help identify the site of origin. Your oncologist will tell you whether it is indicated for your specific diagnosis.

Is molecular testing on a biopsy the same as genetic testing for inherited risk?

No, and this distinction matters. Molecular testing on a biopsy looks at changes that occurred in the tumour itself — called somatic changes — which are not inherited and are not passed on to your children. Inherited risk testing looks at changes present in every cell of the body since birth, typically tested from a blood sample. Both answer different questions, use different samples, and are interpreted differently. Your treating team will make clear which type of testing you are being offered.

What if no actionable finding is identified?

A report with no actionable finding is a legitimate result. It means your oncologist will plan treatment based on your cancer type and stage using established approaches — which is the right path for many patients. It can also reflect that molecular changes are present but not yet matched to a known treatment option, which is different from finding nothing. Ask your oncologist to explain what was found, what was not, and how the treatment plan will be determined in the absence of an actionable result.

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Common questions

Frequently asked questions

Will molecular testing always change what treatment I receive?

Not always, and that does not mean the test was unnecessary. For some cancers and some results, the molecular profile confirms that standard treatment is the right choice. For others, it redirects the plan entirely toward a targeted approach that standard treatment would have missed. The purpose is to be certain you are receiving the treatment most likely to work for your specific tumour. Your oncologist will explain what the result showed and how it informed the recommendation.

My biopsy was done six months ago — can the stored sample still be tested?

Often yes. Biopsy tissue is preserved in a wax block called an FFPE block and can be stored for years. The laboratory checks whether the stored sample has enough intact DNA before proceeding. If the sample is degraded or too small, a repeat biopsy or a liquid biopsy may be discussed. Ask your oncologist to request the stored block from wherever the original biopsy was performed.

How do I know the report is being interpreted correctly?

Molecular reports are complex and require specialist interpretation alongside the full clinical picture. Your oncologist may discuss a difficult result with a molecular tumour board — a multidisciplinary group that reviews unusual or borderline findings. If you receive a result and are unsure what it means or how it changes your plan, it is entirely reasonable to ask for it to be explained in plain language, or to seek a second opinion on its interpretation from a specialist.

Can the molecular profile of a cancer change over time?

Yes. Tumours can acquire new mutations as they grow or in response to treatment — a process called clonal evolution. A result from the time of first diagnosis may not fully describe the cancer at the time of relapse or progression. This is one reason oncologists sometimes repeat molecular testing when a cancer comes back. Whether retesting is appropriate in your situation depends on your diagnosis and what treatment options are available at that point.

Does CION perform molecular testing?

Tissue samples collected at CION centres are sent to accredited pathology and molecular testing laboratories. Comprehensive NGS panels typically go to specialist laboratories, and turnaround time depends on the panel ordered. Your oncologist will explain which tests have been requested and when results are expected. Imaging for response assessment, including PET-CT, is coordinated with CION's partner imaging centres.

What should I ask my oncologist about the results?

Ask four things: what specific changes were found and in which genes; whether any finding is actionable — meaning it points to a specific treatment option; whether any finding has implications for your family's inherited cancer risk and whether a genetics referral is appropriate; and what the treatment plan will be and how the molecular result informed it. Writing the answers down helps, because these conversations are difficult to recall fully afterwards.

Full index

Browse all 701 biopsy topics

Every page in this section, grouped by the part of the journey it belongs to. Pick a group to see what is in it.

What Is a Biopsy?

What Is a Biopsy? Everything You Need to Know →

Types of Biopsy Compared

Which Biopsy Will You Have? Techniques Compared →

Preparing for a Biopsy

What to Expect on the Day of Your Biopsy →

Recovery and Aftercare

After a Biopsy: Recovery, Aftercare and Warning Signs →

Biopsy by Body Part

Biopsy by Body Part: What to Expect at Each Site →

Understanding Your Report

How to Read a Biopsy Report: Terms Explained →

IHC and Molecular Markers

IHC and Molecular Markers on a Biopsy: What They Mean →

Grading and Scoring Systems

Cytology & Prostate Scoring Systems Explained →

How Accurate Is a Biopsy?

How Accurate Is a Biopsy? Errors and Second Opinions →

If Your Result Is Benign

Your Biopsy Is Benign: What It Means and What Comes Next →

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