Path-iQ Guide · Specialty Focus
Molecular pathology applies DNA, RNA, and protein analysis to diagnose disease, guide treatment, and predict prognosis. This guide covers core techniques, clinical applications, companion diagnostics, and career development for molecular pathologists.
Molecular pathology is the subspecialty of pathology that uses nucleic acid and protein analysis to characterise disease. Where conventional histopathology examines tissue morphology under a microscope, molecular pathology interrogates the genetic and epigenetic changes that drive disease — particularly cancer.
Modern molecular pathology laboratories perform next-generation sequencing (NGS), fluorescence in situ hybridisation (FISH), polymerase chain reaction (PCR), immunohistochemistry (IHC), and liquid biopsy — providing the molecular information that oncologists, haematologists, and geneticists need to choose targeted therapies.
| Technique | What it detects | Common applications | Turnaround |
|---|---|---|---|
| Next-Generation Sequencing (NGS) | Point mutations, indels, CNV, fusions across hundreds of genes simultaneously | Tumour mutation profiling, TMB, MSI, hereditary cancer panels | 5–14 days |
| FISH | Gene amplification, deletion, translocation at chromosomal level | HER2 amplification, ALK/ROS1 rearrangement, MDM2/CDK4, BCR-ABL | 2–5 days |
| RT-PCR / qPCR | Specific fusion transcripts, mutation hotspots, MRD | BCR-ABL1 MRD, EGFR T790M, KRAS exon 2, NPM1 in AML | 1–3 days |
| IHC | Protein expression and localisation | PD-L1, MMR proteins, ER/PR/HER2, p53, Ki-67, ALK, ROS1 | 1–2 days |
| Liquid Biopsy (cfDNA) | Circulating tumour DNA mutations and copy number | Treatment monitoring, resistance mutation detection, early recurrence | 1–2 weeks |
| MLPA | Copy number variations across multiple loci | BRCA1/2 large deletions, DMD deletion/duplication, MLH1 methylation | 5–7 days |
| Methylation Analysis | Epigenetic silencing of specific gene promoters | MGMT promoter methylation in glioblastoma, MLH1 silencing in CRC | 3–5 days |
Companion diagnostics (CDx) are molecular tests required before prescribing specific targeted therapies. The FDA mandates CDx testing for many approved targeted agents.
| Biomarker | Cancer type | Test method | Drug class |
|---|---|---|---|
| EGFR mutation (exon 19/21) | Non-small cell lung cancer | NGS or real-time PCR | EGFR TKIs (osimertinib, erlotinib) |
| ALK rearrangement | NSCLC | FISH or NGS; IHC screen | ALK inhibitors (alectinib, lorlatinib) |
| HER2 amplification | Breast, gastric, CRC, lung | IHC + FISH; NGS | Anti-HER2 (trastuzumab, T-DM1, T-DXd) |
| KRAS/NRAS wild-type | Metastatic CRC | NGS or PCR | Anti-EGFR (cetuximab, panitumumab) |
| BRAF V600E | Melanoma, CRC, glioma, NSCLC | NGS or allele-specific PCR | BRAF/MEK inhibitors (vemurafenib, dabrafenib+trametinib) |
| PD-L1 expression | NSCLC, TNBC, gastric, HNSCC, bladder | IHC (22C3, SP142, SP263) | PD-1/PD-L1 inhibitors (pembrolizumab, atezolizumab) |
| MSI-H / dMMR | CRC, endometrial, pan-solid | PCR MSI or IHC MMR proteins | Pembrolizumab (pan-tumour approval) |
| BRCA1/2 mutation | Ovarian, breast, pancreatic, prostate | NGS (somatic + germline) | PARP inhibitors (olaparib, niraparib, rucaparib) |
| FGFR2/3 alteration | Urothelial, biliary tract | NGS or FISH | FGFR inhibitors (erdafitinib, infigratinib) |
| RET rearrangement | NSCLC, thyroid | NGS or FISH | RET inhibitors (selpercatinib, pralsetinib) |
Selected molecular pathologists at major international centres: