Chromosome microarray (CMA)

What it detects

Chromosome microarray (CMA) detects copy number variants (deletions and duplications) across the genome at much higher resolution than conventional karyotype, making it the first-tier test for many genetic indications
Now first-line genetic testing (ahead of conventional karyotype) for unexplained developmental delay/intellectual disability, autism spectrum disorder, and multiple congenital anomalies, reflecting its substantially higher diagnostic yield for these indications

CMA compares the patient's DNA to a reference genome across thousands of probes spanning the genome, detecting submicroscopic deletions/duplications (microdeletion/microduplication syndromes) too small to be visible on conventional karyotype, which only resolves changes down to ~5-10 million base pairs

CMA detects copy number changes but not balanced rearrangements (balanced translocations, inversions) or single-gene point mutations - conventional karyotype remains useful specifically for suspected balanced rearrangements (e.g. in recurrent miscarriage workup), and sequencing-based tests are needed for point mutations
Diagnostic yield for unexplained developmental delay/intellectual disability with CMA substantially exceeds that of conventional karyotype, which is why CMA has become the first-tier test for this indication

A detected copy number variant requires interpretation against population databases and known pathogenic/benign CNV catalogues - many CNVs are benign population variants, and (as with sequence variants) some remain of uncertain significance
Parental testing is often needed to determine whether a CNV found in the patient is inherited (more likely benign, if also present in an unaffected parent) or de novo (more likely pathogenic)

Developmental delay/intellectual disability workup, autism spectrum disorder, multiple congenital anomalies, recurrent miscarriage (balanced rearrangement workup uses karyotype instead)

CMA has substantially increased diagnostic yield in unexplained developmental disorders compared with the karyotype-only era, though a normal CMA still does not exclude a genetic cause - single-gene disorders and balanced rearrangements require different, complementary testing

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