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]

SAQ 2 (10 marks)

A term newborn in the neonatal intensive care unit has refractory seizures, hypotonia, and lactic acidosis. A metabolic disorder is suspected but no specific diagnosis has been reached despite 72 hours of conventional investigation. The family is distressed and asking whether anything else can be done. [7] [8]

a) State the most appropriate genetic test for this infant and justify why the usual tiered pathway does not apply. (3 marks) [7] [8]

b) Summarise the evidence from the NSIGHT1 randomised controlled trial that supports this test in critically ill infants. (3 marks) [7]

c) Describe three ways in which a rapid molecular diagnosis could change the acute management of this infant. (2 marks) [7] [8]

d) Outline the elements of the consent discussion you would have with these parents before sending this test. (2 marks) [2] [10]

Model answers

a. The most appropriate test is rapid whole-genome sequencing. In a critically ill infant with a suspected monogenic disorder, the usual tiered pathway (microarray then exome or genome) does not apply because the value of a diagnosis is measured in days, not weeks. Rapid whole-genome sequencing interrogates the entire genome — coding, non-coding and structural variants — and can return a result within days, which is the timeframe in which a diagnosis can change acute management in the intensive care unit. [7] [8]

b. The NSIGHT1 randomised controlled trial compared rapid whole-genome sequencing against standard genetic testing in critically ill infants. It showed that rapid whole-genome sequencing increased the proportion of infants receiving an etiologic diagnosis within a clinically useful timeframe, and that a diagnosis was reached in a substantial proportion of infants. Subsequent cohorts (the Farnaes study and the PICU studies) extended this to show decreased morbidity and cost of hospitalisation and clinical utility in the paediatric intensive care population. This is the evidence that justifies bypassing the tier. [7] [8]

c. A rapid molecular diagnosis could: institute a specific therapy targeted to the confirmed disorder (for example a tailored metabolic regimen, cofactor, or dietary manipulation); redirect care away from invasive curative-intent interventions toward palliative or comfort-focused care when the diagnosis is a lethal neurodegenerative or metabolic condition; and guide withdrawal of harmful or futile treatment. It also informs reproductive counselling for the parents for future pregnancies. [7] [8]

d. Consent the parents that the result may arrive within days and may change the goals of care, including the possibility that the diagnosis is a severe or life-limiting condition. Explain that a variant of uncertain significance may be returned and will be interpreted against the clinical picture, that secondary findings in actionability genes may be reported unless they opt out, and that the result will inform recurrence risk for future pregnancies. Consent is a conversation held in parallel with, not after, the test. [2] [10]