General pathology · The pathology laboratory
Molecular pathology: PCR, FISH, sequencing and liquid biopsy !
- Technique
Molecular tests read the genes of a tumour or a microbe to confirm the diagnosis and choose the treatment.
Updated 2026-11-01
What it is
Molecular pathology studies DNA, RNA and chromosomes in tissue, blood or cells. In oncology it answers three questions: which tumour it is (by its typical translocation), which targeted treatment may work (by its mutations) and how it is responding (by how much of the alteration remains). It also identifies microorganisms and their resistance. Its quality depends on enough tumour and good fixation.
Step by step
- The pathologist picks the block with the most tumour and marks the area for nucleic acid extraction.
- DNA or RNA is extracted; formalin fragments DNA and strong-acid decalcification destroys it.
- The technique is chosen by the question: a translocation, one mutation or many at once.
- The result is analysed and a tumour (somatic) change is told apart from an inherited (germline) one.
- The report integrates the finding with morphology and states whether a targeted treatment is linked to it.
- A pathogenic germline variant leads to genetic counselling for the family.
Which technique answers which question
| Technique | What it detects | Example |
|---|---|---|
| Real-time (quantitative) PCR | The amount of a specific RNA or DNA | BCR-ABL1 transcript to follow treatment response |
| FISH | Translocations, amplifications and deletions in intact nuclei | HER2 amplification; t(9;22); MYCN amplification |
| Next-generation sequencing (panels) | Many mutations at once | EGFR, ALK, ROS1, KRAS and BRAF in lung adenocarcinoma |
| Microsatellite instability | Failure of mismatch repair | Colorectal cancer and Lynch syndrome |
| Flow cytometry | Surface proteins on live cells in suspension | Kappa or lambda light-chain restriction in a B-cell lymphoma |
| IGH and TCR clonality | A single lymphocyte population | Lymphoma versus a benign reaction |
| Liquid biopsy | Circulating tumour DNA in plasma | Resistance mutations in lung cancer |
| PCR for microorganisms | The agent's DNA and resistance genes | Tuberculosis and rifampicin resistance |
Clinical notes
- Chronic myeloid leukaemia: the Philadelphia chromosome t(9;22) is confirmed by cytogenetics, FISH or PCR, and quantitative PCR follows the response to tyrosine kinase inhibitors.
- Advanced lung adenocarcinoma: EGFR, ALK and other alterations are sought before treatment is chosen.
- Liquid biopsy: useful when there is no tissue or to detect resistance; a negative result does not exclude the alteration.
- Neuroblastoma: MYCN amplification indicates a poor prognosis.
Test yourself
Think of the answer, then tap the question to see it.
Which molecular test is used to follow treatment response in chronic myeloid leukaemia?
Quantitative PCR for the BCR-ABL1 transcript in blood.
Which technique detects HER2 amplification by counting signals in intact nuclei?
Fluorescence in situ hybridisation (FISH).
What separates a somatic mutation from a germline one?
A somatic mutation is only in the tumour; a germline one is in every cell, is inherited and calls for testing the family.
What limits a negative liquid biopsy?
There may be very little tumour DNA in plasma; a negative result does not exclude the mutation and tissue may be needed.
Related
- Oncogenes: RAS, MYC, HER2, BCR-ABL and the table to know
- Tumour suppressor genes: RB, TP53, APC, BRCA and the two-hit hypothesis
- Translocations, amplifications and epigenetic changes in cancer
- Genomic instability: mismatch repair, BRCA and xeroderma pigmentosum
- Hereditary cancer syndromes: the table to know
- Immunohistochemistry: the principle and the markers to know
Related conditions
- Chronic myeloid leukaemia
- Lung cancer
- Breast cancer
- Colorectal cancer
- Melanoma
- Neuroblastoma
- Ewing sarcoma
- Lynch syndrome (hereditary non-polyposis colorectal cancer)
- Hereditary breast and ovarian cancer syndrome (BRCA1/BRCA2)
- Non-Hodgkin lymphoma
- Acute leukaemia (AML and ALL)
- Gastrointestinal stromal tumour (GIST)
- Tuberculosis
Elsewhere in DurgiPedia
- Polymerase chain reaction (PCR)
- FISH (fluorescence in situ hybridization)
- DNA sequencing
- Flow cytometry and the CD4 count
- Types of mutations
- Oncogenes and tumour suppressor genes
- DNA microarrays
Microorganisms
Educational content on the mechanisms of disease; not a diagnostic or treatment guide and no substitute for a health professional's advice. No doses are given.
Sources: Biomarker Testing for Cancer Treatment (National Cancer Institute, 2024); Pathology Reports (National Cancer Institute, 2023); Testing for HER2 in Breast Cancer: A Continuing Evolution (Pathology Research International (PMC), 2011).
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Representative model, for educational purposes only.