ABPath Molecular Genetic Pathology 2 — Questions and Answers
Question 1: A patient's tumor shows microsatellite instability (MSI-high). Which pathway defect is most directly responsible?
- DNA mismatch repair deficiency (Correct answer)
- Nucleotide excision repair defect
- Homologous recombination deficiency
- Base excision repair defect
Correct answer: DNA mismatch repair deficiency
MSI results from loss of DNA mismatch repair function, commonly involving MLH1, MSH2, MSH6, or PMS2.
Question 2: Which method distinguishes germline BRCA1 mutations from somatic mutations in a tumor sample?
- Testing matched normal tissue such as blood (Correct answer)
- Increasing PCR cycle number
- Using a longer amplicon
- Adding more Taq polymerase
Correct answer: Testing matched normal tissue such as blood
A germline mutation is present in normal (blood) tissue, whereas a somatic mutation is confined to the tumor.
Question 3: The BCR-ABL1 fusion in chronic myeloid leukemia is best monitored for minimal residual disease using which assay?
- Quantitative real-time RT-PCR (Correct answer)
- Sanger sequencing
- Immunohistochemistry
- Karyotype alone
Correct answer: Quantitative real-time RT-PCR
Quantitative RT-PCR on the fusion transcript provides sensitive quantification of BCR-ABL1 for MRD monitoring.
Question 4: A Sanger sequencing electropherogram shows a double peak at a single position in a heterozygous sample. This most likely represents:
- A heterozygous single-nucleotide variant (Correct answer)
- A homozygous deletion
- A sequencing artifact requiring rejection
- A large chromosomal translocation
Correct answer: A heterozygous single-nucleotide variant
Two overlapping peaks at one position reflect two alleles with different bases, i.e., a heterozygous SNV.
Question 5: Which alteration is the primary target of EGFR tyrosine kinase inhibitor therapy in non-small cell lung cancer?
- EGFR exon 19 deletion (Correct answer)
- KRAS G12C alone
- TP53 missense mutation
- MYC amplification
Correct answer: EGFR exon 19 deletion
Exon 19 deletions and the L858R mutation are the classic activating EGFR alterations predicting TKI response.
Question 6: In a Fragile X (FMR1) analysis, which molecular feature defines a full mutation?
- More than 200 CGG repeats with hypermethylation (Correct answer)
- A point mutation in exon 1
- Deletion of the entire gene
- A balanced translocation at Xq27
Correct answer: More than 200 CGG repeats with hypermethylation
A full mutation is >200 CGG repeats, typically accompanied by promoter hypermethylation and gene silencing.
Question 7: Digital droplet PCR offers an advantage over qPCR primarily because it provides:
- Absolute quantification without a standard curve (Correct answer)
- Longer read lengths
- Direct protein detection
- Whole-genome coverage
Correct answer: Absolute quantification without a standard curve
By partitioning the sample into thousands of droplets, ddPCR counts target molecules absolutely without needing a standard curve.
ABPath Molecular Genetic Pathology 2
A patient's tumor shows microsatellite instability (MSI-high).
Which pathway defect is most directly responsible?