# Molecular Pathology Diagnostics

> Molecular pathology in NEET-PG Pathology: PCR and FISH, BCR-ABL monitoring, PML-RARA, EGFR-ALK companion tests, MSI, CBNAAT for TB and liquid biopsy.

- Canonical URL: https://prepelephant.com/topics/neet-pg/pathology/molecular-pathology-diagnostics
- Exam / course: NEET-PG · Subject: Pathology
- Publisher: PrepElephant (https://prepelephant.com) — Prepared and reviewed by the PrepElephant Academic Review Team
- First published: 2026-10-02
- Last updated: 2026-10-02
- How to cite: "Molecular Pathology Diagnostics", PrepElephant, https://prepelephant.com/topics/neet-pg/pathology/molecular-pathology-diagnostics

## Direct answer

A BCR-ABL1 transcript number now steers chronic myeloid leukaemia therapy the way a haemoglobin once steered transfusion — molecular pathology quantifies disease, predicts drug response, and detects residual clones below any microscope's threshold. The toolkit is ordered by question: PCR (including quantitative RT-PCR) quantifies fusion transcripts and mutations; FISH localises targets in tissue — break-apart probes for sarcoma translocations, dual-fusion for leukaemia; next-generation sequencing screens many genes at once; Sanger sequencing confirms single variants. Companion diagnostics have made molecular testing mandatory before prescribing — ATRA-defining PML-RARA in acute promyelocytic leukaemia, EGFR, ALK and ROS1 testing in lung adenocarcinoma, HER2 in breast and gastric cancer, BRAF in melanoma, and mismatch-repair deficiency with microsatellite instability for immunotherapy response.

## What you must remember

- **Translocation-transcript pairs to memorise:** BCR-ABL1 p210 in CML (p190 in some Ph-positive ALL), PML-RARA t(15;17) in APL, RUNX1-RUNX1T1 t(8;21) and CBFB-MYH11 inv(16) in core-binding-factor AML, EWSR1-FLI1 t(11;22) in Ewing sarcoma, SYT-SS18 in synovial sarcoma, and ETV6-RUNX1 in childhood ALL.
- **Quantitative monitoring:** RT-PCR for BCR-ABL1 on the international scale defines milestones (10 per cent or lower at 3 months; 0.1 per cent, MR3, deeper), detects resistance — prompting kinase-domain testing, T315I the feared exit — and tracks molecular relapse before haematologic relapse.
- **Companion diagnostic set:** EGFR-sensitising mutations (exon 19 deletion, L858R) and ALK/ROS1 rearrangements before targeted therapy in lung adenocarcinoma; HER2 amplification (IHC 3+ or FISH) for trastuzumab; BRAF V600E for BRAF inhibitors in melanoma; KRAS G12C mutations now targetable in lung and colorectal cancer; JAK2 V617F calibrating myeloproliferative neoplasms.
- **Immunotherapy predictors:** mismatch repair protein loss (MLH1, MSH2, MSH6, PMS2) with microsatellite instability predicts checkpoint-inhibitor response; PD-L1 tumour proportionality scoring in non-small cell lung cancer, with 50 per cent the first-line monotherapy threshold.
- **Infectious-disease molecular armamentarium:** CBNAAT (Xpert MTB/RIF, and the more sensitive Ultra platform) detects Mycobacterium tuberculosis and rifampicin resistance within about two hours and is the first-line test under India's NTEP; viral load PCR guides HIV and hepatitis B and C management under the national programme.
- **Technique-trait matching:** FISH for structural rearrangements in archival tissue (ALK, HER2), PCR for known point mutations and fusions fast and cheap, NGS panels for broad tumour profiling, and array CGH for copy-number change.
- **Liquid biopsy:** circulating tumour DNA measured in plasma for EGFR T790M detection at progression, minimal residual disease assessment, and non-invasive tumour genotyping — a rising NEET-PG theme.
- **Quality caveats:** assays demand validated pre-analytics (fixation, tumour percentage); molecular classification of gliomas (1p/19q codeletion, MGMT methylation, IDH mutation) is now part of WHO grading itself.

## Choosing the right molecular test

Match the clinical question to the platform. A young patient with a pelvic small blue cell tumour: EWSR1 break-apart FISH on the biopsy, which works even in decalcified or archived material. In metastatic lung adenocarcinoma, an NGS panel for EGFR, ALK, ROS1, BRAF, MET, RET and KRAS — each result rewrites the prescription. Monitoring CML on imatinib: quantitative PCR on the international scale every three months; a rising transcript triggers ABL kinase-domain sequencing to find the mutation dictating second-generation inhibitor choice. Managing APL: t(15;17) at diagnosis, then PCR for PML-RARA to document molecular clearance — the original molecular-cure story, with ATRA and arsenic driving the clone to extinction. Screening a colorectal cancer family: MMR-protein IHC first, then MLH1 promoter methylation to separate sporadic from Lynch, with germline sequencing to confirm.

## How the exam frames it

One-liners test the pairing: drug with alteration — imatinib with BCR-ABL1, ATRA with PML-RARA, trastuzumab with HER2, vemurafenib with BRAF V600E, osimertinib with EGFR (including T790M), sotorasib with KRAS G12C. Monitoring questions ask what a rising BCR-ABL1 transcript means — loss of response, adherence problem, or resistance mutation — with kinase-domain sequencing as the next step. Technique questions contrast FISH and PCR: FISH sees structure in situ and tolerates poor tissue; PCR is faster and quantitative but needs known sequence and contamination control (amplicon carryover, dedicated areas, dUTP-UNG systems — a favourite). The Indian fixture is CBNAAT under NTEP — TB plus rifampicin resistance in about two hours; expect it whenever "rapid, molecular" appears.

## Frequently asked questions

### What is a major molecular response in CML and why does it matter?

A BCR-ABL1 transcript of 0.1 per cent or lower on the international scale, indicating deep suppression of the leukaemic clone and excellent long-term prognosis without progression.

### Which molecular test is first-line for suspected tuberculosis under NTEP?

Cartridge-based nucleic acid amplification testing (Xpert MTB/RIF or Ultra), which simultaneously detects M. tuberculosis complex and rifampicin resistance within about two hours.

### How do EGFR and ALK results change lung cancer treatment?

Sensitising EGFR mutations and ALK rearrangements mandate first-line tyrosine kinase inhibitors (erlotinib/osimertinib or crizotinib/alectinib generations) instead of chemotherapy — the archetype of companion diagnostics.

### What is liquid biopsy and its main applications?

Analysis of circulating tumour DNA from a blood draw, used for genotyping when tissue is unavailable (EGFR T790M at progression), minimal residual disease monitoring, and tracking resistance mutations.

### Why test mismatch repair proteins in colorectal carcinoma?

Loss of MLH1, MSH2, MSH6 or PMS2 identifies microsatellite-instability-high tumours — screening for Lynch syndrome and predicting strong response to PD-1 checkpoint immunotherapy.