--- module: 096-03 language: en chapter: 96 title: "General and Diagnostic Pathology: Patterns, Specimens, and Clinicopathological Reasoning" module_title: "Specimens, diagnostic methods, and clinicopathological reasoning" source_sha256: 8591edd7861d15aca4178a92cb7cc1fc1abefce0d353c125ffc307110de011e0 --- # Specimens, methods, and clinicopathological reasoning ## Clinical question and pre-analytical phase ### Diagnosis begins before the laboratory ### Question sets site, speed, medium, handling #### Sterile, unfixed, frozen, or light-protected ### Right test on wrong specimen fails ### Integrate history, site, imaging, treatment ### Ischaemic time alters molecules and detail ### Crush, cautery, drying, contamination artefacts ### Small biopsy may miss a focal lesion #### May capture only necrosis or reactive tissue ### Auditable chain of identity and orientation ### Allocate scarce tissue in advance ## Gross examination ### Size, weight, colour, consistency, margins ### Ink margins, open, slice, map nodes ### Blocks from tumour, interface, deepest invasion ### Photographs preserve spatial relationships ### Sampling trade-off #### More blocks cost time and tissue #### Too few give false reassurance ## Fixation and processing ### Fixation limits autolysis and putrefaction ### Formalin cross-links proteins #### Delayed or excessive fixation alters assays ### Decalcification harms antigens and nucleic acids ### Paraffin processing and thin sections ### Frozen sections: rapid but less definitive #### Ice artefact and limited sampling ## Morphology on routine stains ### Haematoxylin: nuclei; eosin: cytoplasm, matrix ### Architecture, polarity, stroma, necrosis first ### Then nuclear and cytoplasmic detail ### Atypia is not malignancy #### Repair, infection, radiation, degeneration ## Special stains and immunohistochemistry ### Special stains answer narrow questions #### Organisms, mucin, iron, amyloid #### Sensitivity depends on burden and preservation ### Other modalities add artefacts and limits ### Immunohistochemistry localises proteins #### Lineage, origin, proliferation, receptors #### No marker is perfectly specific #### Staged panel beats broad unguided panel ## Specimen types ### Cytology: minimally invasive, little architecture #### Cell blocks add histology and immunostains ### Core biopsy preserves architecture and grade ### Excision shows boundaries and heterogeneity ### Resection permits pathological staging ### Least invasive is not always least costly ## Haematopathology and molecular tests ### Integrate counts, smears, marrow, genetics ### Flow cytometry detects subtle populations ### Chromosome analysis: large changes ### In situ hybridisation targets selected loci ### Polymerase chain reaction and sequencing ### Interpret against sensitivity and tumour fraction #### Clonal change without overt malignancy ### Marker roles must not be conflated #### Diagnostic names a disorder #### Prognostic estimates outcome #### Predictive estimates therapy response #### Monitoring tracks a known clone ### Negative result may reflect too few cells ## Tumour reporting ### Grade is differentiation, stage is extent ### Type, size, depth, invasion, margins, nodes ### Positive margin meaning depends on context ### Preoperative treatment causes regression changes ## Correlation, uncertainty, and quality ### Patterns have differentials, not final answers ### Discordance triggers review of identity and sampling ### State certainty explicitly in reports #### Definitive, favoured, indeterminate, inadequate ### Urgent findings need direct communication ### Predictive values depend on prevalence ### Selection and verification bias ### Consensus is more honest than false precision ## Autopsy and the diagnostic chain ### Autopsy audits cause, mechanism, treatment ### Cause of death as a causal sequence ### Sampling constrains morphology, morphology directs tests ### Confidence never exceeds specimen adequacy