Molecular Genetic Pathology Flashcards

A 15% variant allele fraction is reported for a somatic mutation in a tumor with 40% tumor cellularity. This VAF is most consistent with:

Answer: A heterozygous mutation in the tumor cells

With ~40% tumor content, a heterozygous somatic mutation is expected around ~20% VAF, so 15% fits a heterozygous clonal event.

Which control is essential to confirm that a negative PCR result is not due to amplification failure?

Answer: An internal amplification (endogenous) control

An internal/endogenous control confirms amplifiable DNA is present, ruling out inhibition or failed extraction behind a true-negative call.

FISH break-apart probes are most useful for detecting:

Answer: Gene rearrangements with variable partners such as ALK

Break-apart FISH detects rearrangement of a gene regardless of the fusion partner by separating flanking probes.

Which is the most common cause of a false-positive low-level variant call in FFPE-derived DNA?

Answer: Formalin-induced cytosine deamination artifacts

Formalin fixation causes cytosine deamination producing C>T/G>A artifacts that mimic low-VAF variants.

In next-generation sequencing, 'read depth' at a position primarily determines:

Answer: Sensitivity for detecting low-frequency variants

Higher coverage improves confidence and sensitivity for calling low variant allele fraction mutations.

A KRAS mutation in metastatic colorectal cancer predicts:

Answer: Resistance to anti-EGFR monoclonal antibody therapy

Activating KRAS mutations downstream of EGFR confer resistance to cetuximab and panitumumab.

Multiplex ligation-dependent probe amplification (MLPA) is best suited to detect:

Answer: Copy number changes such as exon-level deletions or duplications

MLPA quantifies relative copy number and readily detects single- or multi-exon deletions and duplications.