Laboratory Testing Strategy: Choosing the Right Test First
Match the test to the variant class
Test selection is a reasoning exercise: identify the suspected variant class, then choose the assay that detects it reliably. Chromosomal microarray detects copy-number variants and is first-tier for developmental delay, intellectual disability, and multiple congenital anomalies. Karyotype remains appropriate for suspected balanced rearrangements, mosaicism, and aneuploidy. FISH is targeted and limited. MLPA detects exon-level deletions and duplications in specific genes. Sanger sequencing confirms known familial variants. Next-generation sequencing panels, exome, and genome sequencing detect single-nucleotide variants and small insertions or deletions, with copy-number detection that varies by platform. Repeat-expansion disorders require specialized PCR or Southern blot. Imprinting and methylation disorders require methylation-specific testing. Enzyme assays and metabolite panels remain first-line for many biochemical disorders.
Consider test characteristics: diagnostic yield, sensitivity and specificity, variant-of-uncertain-significance rate, turnaround, cost, and tissue source. Blood is standard, but buccal or skin fibroblasts may be needed when a hematologic malignancy or mosaicism is a concern. Prenatal options include chorionic villus sampling, amniocentesis, and cell-free DNA screening, which is screening rather than diagnosis.
Traps
Ordering exome sequencing for fragile X syndrome or a methylation disorder; using a karyotype to look for a microdeletion; ordering cell-free DNA as a diagnostic test; and failing to reflex to parental testing when a proband result is uncertain.
Rule of thumb
Copy-number variant, choose microarray. Single-nucleotide variant, choose sequencing. Repeat expansion, choose targeted expansion testing. Methylation defect, choose methylation analysis. Enzyme deficiency, start with biochemical testing.