CGC Laboratory Genetics & Variant Interpretation 1 — Questions and Answers
Question 1: According to ACMG/AMP variant classification guidelines, variants are classified into how many categories?
- Three: pathogenic, benign, unknown
- Five: pathogenic, likely pathogenic, uncertain significance, likely benign, benign (Correct answer)
- Four: pathogenic, likely pathogenic, benign, likely benign
- Two: pathogenic and benign only
Correct answer: Five: pathogenic, likely pathogenic, uncertain significance, likely benign, benign
The 2015 ACMG/AMP guidelines established a five-tier classification system: pathogenic, likely pathogenic, VUS, likely benign, and benign.
Question 2: Which evidence criterion is classified as 'very strong pathogenic' (PVS1) in ACMG/AMP variant interpretation?
- The variant is observed in multiple unrelated affected individuals
- Null variant (nonsense, frameshift, canonical splice site) in a gene where loss of function is a known disease mechanism (Correct answer)
- The variant is absent from population databases
- Functional studies demonstrate a damaging effect
Correct answer: Null variant (nonsense, frameshift, canonical splice site) in a gene where loss of function is a known disease mechanism
PVS1 is assigned to null variants (loss-of-function) in genes where haploinsufficiency or loss-of-function is an established disease mechanism.
Question 3: Next-generation sequencing (NGS) gene panels in clinical genetics typically involve:
- Sequencing the entire genome at high depth
- Targeted sequencing of selected disease-relevant genes (Correct answer)
- Single-gene Sanger sequencing
- Cytogenetic karyotyping
Correct answer: Targeted sequencing of selected disease-relevant genes
Clinical gene panels use NGS to simultaneously sequence a curated set of genes known to cause a specific disease or disease category.
Question 4: Chromosomal microarray analysis (CMA) is MOST appropriate as a first-tier test for:
- Patients with a known familial pathogenic single-nucleotide variant
- Individuals with intellectual disability, autism spectrum disorder, or multiple congenital anomalies (Correct answer)
- Carrier screening in couples planning pregnancy
- Patients with suspected trinucleotide repeat disorders
Correct answer: Individuals with intellectual disability, autism spectrum disorder, or multiple congenital anomalies
CMA is recommended as first-tier testing for unexplained intellectual disability, autism, and multiple congenital anomalies due to its high diagnostic yield (~15–20%).
Question 5: Whole exome sequencing (WES) sequences:
- The entire genome including intergenic regions
- All protein-coding exons, approximately 1–2% of the genome (Correct answer)
- Only known disease-causing genes
- Mitochondrial DNA exclusively
Correct answer: All protein-coding exons, approximately 1–2% of the genome
WES captures and sequences the coding exons of all known genes, representing approximately 1–2% of the total genome but containing ~85% of known disease-causing variants.
Question 6: A mosaic pathogenic variant found in an individual means:
- Two different pathogenic variants are present in the same gene
- The pathogenic variant is present in some cells but not all cells of the individual (Correct answer)
- The variant was inherited from both parents
- The variant is present in a pseudogene
Correct answer: The pathogenic variant is present in some cells but not all cells of the individual
Mosaicism occurs when a variant arises post-zygotically, resulting in two or more cell populations with different genotypes within the same individual.
CGC Laboratory Genetics & Variant Interpretation 1
According to ACMG/AMP variant classification guidelines, variants are classified into how many categories?