Introduction

In our previous article, we explored the different types of biomarkers and why they matter in cancer care. Biomarkers can signal disease risk, confirm a diagnosis, predict how a cancer will behave, and guide treatment decisions. But knowing that these biomarkers exist is only part of the story.

The next question is how these biomarkers are actually detected in clinical practice.

The answer lies in a set of diagnostic tests that translate biomarker science into actionable clinical information, helping physicians determine the right treatment for the right patient at the right time.

Not all tests are designed to answer the same question, and understanding the difference is key.

Immunohistochemistry: Reading Proteins in Tumour Tissue

When a tumour is biopsied or removed, a small sample can be examined under a microscope. Immunohistochemistry, or IHC, is a test that uses antibodies (proteins that bind to specific targets) to detect other proteins within that tissue.

These antibodies attach to a target protein and are made visible using a dye, allowing pathologists to see how much of the protein is present and where it is located in the cells.

A common example is HER2 testing in breast cancer. HER2 is a protein that, when present at high levels, can drive tumour growth. IHC helps determine whether HER2 is overexpressed, which can guide the use of targeted therapies. It is also widely used to assess hormone receptors, which helps determine whether hormonal treatments may be effective.

Because it is widely available, cost-effective, and works with standard tissue samples, IHC remains one of the most commonly used diagnostic tools in oncology.

Fluorescence In Situ Hybridization: Spotting Gene Abnormalities

While IHC focuses on proteins, fluorescence in situ hybridization, or FISH, looks at DNA, the genetic material inside our cells.

FISH uses small pieces of labelled DNA, called probes, that are designed to attach to specific genes. When these probes bind to their target, they light up under a special microscope.

By looking at the number and pattern of these signals, doctors can determine whether a gene is present in abnormal amounts or has been rearranged.

FISH is often used alongside IHC in HER2 testing when results are unclear, providing a more definitive answer. It is also used to detect gene changes, such as ALK rearrangements in lung cancer, which can help identify patients who may benefit from targeted therapies.

Next-Generation Sequencing Panels: A Comprehensive Look at the Genome

While IHC and FISH focus on specific targets, next-generation sequencing, or NGS, takes a broader approach.

NGS is a technology that allows scientists to read and analyze many genes at once. Instead of looking for one specific change, it scans across hundreds of genes to identify mutations and other alterations that may be driving cancer.

This matters because cancers are rarely caused by a single genetic change. Even within the same cancer type, tumours can differ significantly from one patient to another.

NGS panels can uncover changes that may be targeted with specific treatments. They can also measure features like tumour mutational burden (the number of mutations in a tumour) and microsatellite instability (a type of genetic instability), both of which can help predict response to certain therapies.

Because of the depth of information it provides, NGS has become a central tool in precision oncology, especially in more advanced disease.

Gene Expression Panels: Understanding Tumour Behaviour

While many tests focus on identifying what is present in a tumour, they do not always capture how that tumour is behaving.

Gene expression panels offer a different perspective by measuring how active specific genes are. Genes are present in every cell, but not all genes are “turned on” at the same time. Gene expression looks at which genes are active and how strongly they are being used.

These panels analyze patterns of gene activity to provide insight into tumour subtype, how aggressive a tumour may be, and how it may respond to treatment.

Tests such as Oncotype DX and MammaPrint in breast cancer use gene expression to estimate the risk of recurrence and guide decisions around chemotherapy. In some cases, this helps patients safely avoid unnecessary treatment.

Unlike tests that focus on individual mutations, gene expression panels capture the overall biological behaviour of a tumour, offering a more complete picture of how the cancer is functioning.

Circulating Tumour DNA Analysis: Monitoring Cancer Through a Blood Test

All of the approaches above rely on tumour tissue. Circulating tumour DNA, or ctDNA, analysis offers a different option by detecting tumour-derived DNA fragments in the bloodstream.

As tumours grow, they release small pieces of their DNA into the blood. These fragments carry the same genetic changes found in the tumour.

By analyzing a blood sample, doctors can identify these changes without needing an invasive biopsy. This is especially useful when tumour tissue is difficult to obtain.

ctDNA analysis can also be used over time to monitor how a tumour is responding to treatment, detect new mutations that may cause resistance, and identify early signs of recurrence.

This ability to track cancer through a simple blood test represents a meaningful shift in how cancer can be managed.

Conclusion

Precision oncology depends on more than identifying biomarkers. It requires reliable tools to detect them and translate that information into clinical decisions.

Each of these diagnostic approaches contributes a different layer of insight. Some identify specific molecular changes. Others confirm treatment eligibility or provide a broader view of tumour biology.

Not all tests offer the same level or type of insight, and understanding these differences is what allows precision oncology to move from data to truly informed decision-making.