Basics of Chromosomal Microarray Analysis (CMA)
Chromosomal Microarray Analysis (CMA) is one of the most powerful genetic diagnostic tools available today — capable of detecting chromosomal abnormalities at a resolution far beyond what traditional karyotyping can achieve. It is now recommended as a first-line genetic test for children with developmental delay, intellectual disability, autism spectrum disorder, and multiple congenital anomalies.
What Is CMA?
CMA is a laboratory technique that scans the entire genome for copy number variants (CNVs) — deletions or duplications of chromosomal segments. These CNVs can disrupt gene function and cause a wide range of genetic conditions. CMA can detect CNVs as small as a few kilobases — far smaller than the 5–10 megabase threshold of traditional karyotyping.
Types of CMA
Array CGH (Comparative Genomic Hybridisation) — compares the patient’s DNA to a reference genome to identify gains and losses of chromosomal material
SNP array — detects CNVs and also identifies regions of homozygosity (ROH), which can indicate consanguinity or uniparental disomy (UPD)
When Is CMA Recommended?
Children with unexplained developmental delay or intellectual disability
Children with autism spectrum disorder (ASD)
Children with multiple congenital anomalies
Prenatal diagnosis when ultrasound findings are abnormal
Recurrent pregnancy loss (RPL) investigation
Advantages Over Traditional Karyotyping
Detects submicroscopic CNVs invisible to karyotyping
Covers the entire genome in a single test
Higher diagnostic yield (15–20% in children with developmental delay vs. 3–5% for karyotyping)
Does not require cell culture, so results are faster
Limitations
Cannot detect balanced chromosomal rearrangements (translocations, inversions)
Variants of uncertain significance (VUS) may be identified, requiring careful interpretation by a genetic counsellor
Cannot detect single gene mutations or trinucleotide repeat expansions
Expert Genetic Counselling for CMA and Chromosomal Testing
MapmyGenome’s certified genetic counsellors provide expert guidance for families navigating chromosomal microarray results, developmental delay, ASD, and congenital anomaly diagnoses. Available online across India.
