Molecular Diagnostics and Tumour Markers
Why it matters
Molecular results now determine eligibility, drug choice and prognosis. Understand the purpose before the technique: a screening test needs high sensitivity, a diagnostic or confirmatory test needs high specificity, and a companion diagnostic must reliably identify likely responders.
Core statistics
Sensitivity = TP/(TP+FN); specificity = TN/(TN+FP); positive predictive value = TP/(TP+FP); negative predictive value = TN/(TN+FN). Predictive values change with prevalence; sensitivity and specificity do not.
Technologies
PCR and real-time PCR for hotspot mutations and fusion transcript quantification; Sanger sequencing for single genes with limited sensitivity (variant allele fraction roughly 15 to 20%); allele-specific PCR for very high sensitivity; FISH for translocations and amplifications; immunohistochemistry as a protein surrogate; next-generation sequencing panels needing adequate tumour cellularity; and ctDNA liquid biopsy, which is minimally invasive but prone to false negatives in low-shedding disease.
Tumour markers
AFP (hepatocellular carcinoma, non-seminomatous germ cell tumours), hCG and LDH (germ cell), CA125 (ovarian, mainly monitoring), CA19-9 (pancreatobiliary), CEA (colorectal monitoring), PSA, calcitonin (medullary thyroid carcinoma). Markers are generally for monitoring and prognosis, not diagnosis.
Traps
Pre-analytical variables: fixation time, decalcification, tumour cellularity and turnaround. Germline versus somatic reporting matters because a germline variant requires genetic counselling; variants of uncertain significance should not change management.
Rule of thumb
No tumour marker is diagnostic in isolation: a normal CEA does not exclude colorectal cancer, whereas a rising CEA after resection is highly informative.