ABPath Molecular Genetic Pathology 3

Question 1

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

Accepted Answer

A heterozygous mutation in the tumor cells

Answer

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

Question 2

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

Accepted Answer

An internal amplification (endogenous) control

Answer

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

Question 3

FISH break-apart probes are most useful for detecting:

Accepted Answer

Gene rearrangements with variable partners such as ALK

Answer

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

Question 4

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

Accepted Answer

Formalin-induced cytosine deamination artifacts

Answer

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

Question 5

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

Accepted Answer

Sensitivity for detecting low-frequency variants

Answer

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

American Board of Pathology (ABPath) Practice Test