Genetic and metabolic test selection — formative SAQs

SAQ 1 (10 marks)

A 4-year-old boy is referred to your general paediatric clinic with global developmental delay and mild dysmorphism. He walked at 22 months and speaks in two-word phrases. His chromosomal microarray, requested by the general practitioner a year ago, is normal. Both parents are available and willing to provide blood. [1] [2]

1. State the next genetic test of choice, the platform, and the sample strategy, and defend the choice against the alternatives of repeating the microarray and requesting a karyotype. (4) [1]
2. Explain why a trio sample (child and both parents) is preferred over a proband-only sample, and quantify the expected effect on the diagnostic yield. (3) [2]
3. The exome returns a pathogenic variant in BRCA1, reported as an incidental actionable secondary finding. Outline the consent that should have been taken before the test, the post-test counselling, and the rules around testing this child's siblings. (3) [11]

Model answer — SAQ 1

(1) Next test of choice and defence (4). The next test is whole-exome sequencing as a trio (the child and both parents). The chromosomal microarray is the first-tier test for unexplained developmental delay and detects copy-number variants with a yield of around 10 to 20 percent, but a normal microarray does not exclude a genetic diagnosis — it directs the next step. Repeating the microarray is not indicated because it will not find a new class of variant. A karyotype is the wrong test for developmental delay because its resolution (5 to 10 megabases) is too low; it is reserved for suspected aneuploidy or a known familial balanced rearrangement. The exome is the platform that answers the question a normal microarray raises — a single-nucleotide variant or small indel in a coding gene — and Yang and colleagues' series gives a diagnostic yield of around 25 percent in ambulant children with a suspected monogenic disorder. [1] [2]

(2) Trio over proband-only (3). The single most powerful signal in exome interpretation is the de novo variant — a variant present in the affected child and absent from both unaffected parents, which arose in the germline of one parent or in early embryogenesis. A trio sample lets the bioinformatician filter the roughly 20,000 coding variants found in a typical child down to the small handful that are de novo and plausibly disease-causing. A proband-only sample leaves a much larger variant list that the laboratory must prioritise by phenotype alone. The effect on yield is large — trio sampling roughly doubles the diagnostic yield of exome over proband-only testing. Both parents should have their blood drawn at the same time as the child's, and the family structure documented on the request form. [2]

(3) Incidental actionable secondary finding (3). Before the test, the consent must have recorded the family's opt-in or opt-out for the ACMG secondary-findings list, which in the v3.2 update stands at 81 reportable genes covering hereditary cancer and cardiovascular risk syndromes among others. The family should have been told that an exome can return a diagnostic finding, a variant of uncertain significance, an incidental actionable secondary finding, or an unexpected finding such as non-paternity, and that the secondary finding is a family finding, not the child's finding. Post-test, the counselling frames the BRCA1 variant as an actionable risk rather than a diagnosis: predictive testing is offered to at-risk adult relatives; a minor is not tested for an adult-onset condition without a childhood intervention, so the siblings would not be tested now; and the child is referred, when an adult, to a familial cancer service for their own predictive testing and surveillance. The discussion is documented. [11]