Chromosomal microarray, exome and genome sequencing — formative SAQs

SAQ 1 (10 marks)

A three-year-old boy is referred for global developmental delay. He walked at 22 months and has a vocabulary of fewer than fifteen words. There are no dysmorphic features on examination, and a chromosomal microarray has returned normal. The parents ask why more testing might be needed. ^{[1] [3]}

a) Explain why a normal chromosomal microarray does not exclude a genetic cause, naming two specific variant classes the microarray cannot detect. (3 marks) ^[1]

b) State the diagnostic yield of chromosomal microarray and of trio whole-exome sequencing in this population, and define what a "trio" strategy means. (3 marks) ^{[1] [3]}

c) Describe how you would counsel the family before proceeding to whole-exome or whole-genome sequencing, covering the variant of uncertain significance and secondary findings. (2 marks) ^{[6] [10]}

d) Name two targeted tests you would send alongside or before exome sequencing in this boy, regardless of the microarray result. (2 marks) ^[1]

Model answers

a. A normal microarray reduces but does not eliminate the probability of a genetic cause because microarray detects only copy-number variants (deletions and duplications) and regions of homozygosity. It does not detect single-nucleotide variants or small indels in coding genes — the variant class behind most monogenic intellectual disability and developmental disorders. It also does not detect repeat expansions (such as the FMR1 CGG expansion in fragile X syndrome), balanced rearrangements, deep intronic or regulatory variants, or low-level mosaicism below its detection threshold. A normal microarray excludes the common copy-number causes and nothing more. ^{[1] [3]}

b. Chromosomal microarray yields a pathogenic copy-number variant in roughly fifteen to twenty percent of children with unexplained developmental delay or intellectual disability. Trio whole-exome sequencing — sequencing the child and both parents — adds a further diagnostic increment and reaches roughly thirty to forty percent. A trio means the child's variants are interpreted in the light of parental genotypes, which resolves whether a variant is de novo (strong evidence of pathogenicity), inherited from an unaffected carrier (which weakens pathogenicity), or inherited from an affected parent, and it lifts the yield compared with proband-only testing. ^{[1] [3]}

c. Before sequencing, counsel the family that the test may return a variant of uncertain significance — a real finding whose clinical meaning is not yet known, which must not be over-interpreted as a diagnosis, and which may be reclassified over time. Address the secondary-findings opt-out: the laboratory may report pathogenic variants in a curated list of actionability genes (for example hereditary cancer genes such as BRCA1 and BRCA2, or potentially lethal cardiac genes) unrelated to the child's presentation, and the family may choose whether to receive these. Explain data storage, the possibility of future re-analysis, and that a negative result does not fully exclude a genetic cause. ^{[6] [10]}

d. FMR1 repeat testing (PCR for repeat size and Southern blot for methylation), because microarray does not detect the fragile X expansion and fragile X is the most common inherited cause of intellectual disability in boys. A karyotype if a balanced rearrangement is suspected (for example a family history of recurrent miscarriages), because microarray misses balanced translocations. ^[1]