Molecular Pathology and Cytogenetics
Core concepts
Molecular questions test the central dogma in diagnostic terms: DNA/RNA structure, replication, transcription, and translation, plus the technologies that exploit them (PCR, RT-PCR, Sanger sequencing, next-generation sequencing, FISH, karyotyping, microarray). Know the difference between germline and somatic variants, variant classification (pathogenic, likely pathogenic, VUS, likely benign, benign), and the meaning of variant allele fraction. Understand cytogenetic nomenclature (ISCN), common translocations (t(9;22) BCR-ABL1, t(15;17) PML-RARA, t(8;21)), and the difference between constitutional and acquired abnormalities. Know molecular oncology concepts: driver mutations, tumor suppressor loss (two-hit hypothesis), and pharmacogenomic markers (e.g., TPMT, CYP2C19).
Traps
A frequent trap is confusing a VUS with a pathogenic variant-VUS results should not drive clinical management. Another is misinterpreting low variant allele fraction as germline when it may reflect somatic mosaicism or tumor heterogeneity. Questions may ask about test selection: karyotype for balanced rearrangements, FISH for targeted loci, microarray for copy-number changes, sequencing for point mutations. Do not assume a negative test excludes a diagnosis when the assay has limited sensitivity or does not cover the variant.
Worked example / rule of thumb
For a suspected balanced translocation, order a karyotype; for a suspected deletion/duplication, order a microarray; for a known point mutation, order targeted sequencing. Rule of thumb: choose the assay by the type of variant you expect-structural, copy-number, or sequence-level.