Chromosomal microarray, exome and genome sequencing — branching viva

Opening stem

You are the paediatric registrar in clinical genetics clinic. A four-year-old with unexplained global developmental delay has a normal chromosomal microarray. The parents ask what testing comes next. Talk me through your approach. ^[1]

Branch A — The resolution ladder

Examiner: What is the resolution ladder, and why does it matter? ^[1]

Strong answer: The platforms climb a resolution ladder. A karyotype resolves whole chromosomes at the megabase level and remains the test for a balanced rearrangement. A chromosomal microarray resolves copy-number variants down to tens of kilobases but misses single-base changes. Whole-exome sequencing reads the coding single-nucleotide variants; whole-genome sequencing reads the entire genome including non-coding, structural and repeat-expansion variants. Resolution rises as you climb, and so does the burden of variants of uncertain significance. The ladder matters because each platform answers a different question and has a different blind spot. ^{[1] [2]}

Branch B — Why a normal microarray is not the end

Examiner: The microarray is normal. Does that exclude a genetic cause? ^[1]

Strong answer: No. A normal microarray excludes only the common copy-number causes. It does not detect single-nucleotide variants, repeat expansions such as fragile X, deep intronic or regulatory variants, structural variants, or low-level mosaicism. I would not reassure the family that there is no genetic cause; I would explain what the test excluded and keep the door open for sequencing. ^{[1] [3]}

Branch C — Escalating to sequencing

Examiner: What is your next test, and what yield do you quote? ^[2]

Strong answer: I escalate to whole-exome or whole-genome sequencing, ideally as a trio — the child and both parents — which resolves de novo status and inheritance and lifts the yield. I quote a diagnostic yield of roughly thirty to forty percent for trio exome or genome sequencing after a normal microarray, supported by the 2021 ACMG guideline and the 2019 meta-analytic consensus. Before testing I consent the family on the variant of uncertain significance and the secondary-findings opt-out. ^{[2] [3]}

Branch D — Interpreting the result

Examiner: The exome returns a variant of uncertain significance. How do you handle it? ^[6]

Strong answer: I interpret every variant against the clinical phenotype, because a variant that does not match the picture should not be over-called. The variant of uncertain significance is classified by the ACMG/AMP five-tier framework — pathogenic, likely pathogenic, uncertain significance, likely benign, benign — and only pathogenic and likely pathogenic variants are diagnostic. I arrange segregation testing of the parents to see whether the variant is de novo or inherited, which may move the classification, and I do not build a management plan on a variant of uncertain significance that does not fit the phenotype. ^[6]

Branch E — The critically ill infant

Examiner: Now picture a critically ill neonate in intensive care with a suspected monogenic disorder. How does your approach change? ^[7]

Strong answer: In the critically ill infant the tier collapses. The test of choice is rapid whole-genome sequencing, which can return a diagnosis within days — the timeframe in which a diagnosis can change acute management. The NSIGHT1 randomised trial showed that rapid whole-genome sequencing increases the proportion of infants receiving an etiologic diagnosis within a clinically useful timeframe, and the Farnaes cohort showed decreased morbidity and cost. A diagnosis may escalate a specific therapy, withdraw futile treatment, or redirect to palliative care. I refer through the local rapid-genomics pathway and consent the family that a rapid result may change the goals of care. ^{[7] [8]}