Chromosomal Microarray

Chromosomal Microarray Analysis (CMA) is a high-resolution genetic testing method that detects submicroscopic chromosomal imbalances, making it a valuable tool for diagnosing developmental disorders, autism, and congenital anomalies. 

By identifying copy number variants (CNVs) with far greater precision than traditional karyotyping, CMA has become a first-line genetic test in both postnatal and prenatal diagnostic settings.

What is Chromosomal Microarray Analysis (CMA)?

Chromosomal Microarray Analysis (CMA) is a powerful genetic testing technique that has significantly advanced the diagnostic capabilities of clinicians in various specialties, particularly in genetics and developmental medicine. 

Unlike a standard karyotype (a visual map of chromosomes used to detect abnormalities), which typically detects imbalances on the order of several megabases, CMA can detect much smaller changes, in the kilobases – roughly 1000-fold finer resolution.​​

In practice, CMA is performed either by array-comparative genomic hybridization (aCGH) or by single-nucleotide polymorphism (SNP) arrays. In an aCGH-based CMA, a patient's DNA and a normal reference DNA are differentially labeled and co-hybridized, with the ultimate goal of comparing a patient's DNA to reference DNA. 

By analyzing consecutive probes showing an imbalance, the size and genomic position of a chromosomal deletion/duplication can be determined.​

SNP-array CMA platforms similarly detect copy-number changes and can additionally provide genotype information, which helps detect regions of absence of heterozygosity or triploidy when present​.

Thus, CMA is a preferred tool compared to karyotyping for clinicians and families who want to uncover submicroscopic chromosomal abnormalities that were previously undetectable by traditional cytogenetics.

CMA Detects Copy Number Variants

A copy number variant (CNV) is a genomic alteration involving the deletion or duplication of DNA segments detectable by chromosomal microarray analysis (CMA). Depending on size and location, it can range from benign to pathogenic and may impact gene function.

The types of CNVs that CMA can detect include:

• Deletions: Loss of a segment of DNA.
• Duplications: Gain of a segment of DNA.
• Copy-Neutral Loss of Heterozygosity (CN-LOH): this occurs when an individual inherits two copies of a chromosome segment from one parent and none from the other. This can increase the risk of recessive genetic conditions.

CMA offers higher resolution than traditional karyotyping and can identify smaller CNVs that karyotyping may miss. However, karyotyping still remains useful for detecting larger chromosomal rearrangements, such as translocations and inversions, that CMA cannot.

Clinical Indications: Who Should Consider CMA?

CMA may be considered in the following scenarios:

Postnatal (Pediatric) Indications

CMA has become a first-tier diagnostic test for individuals with unexplained developmental or congenital disorders. Both research evidence and professional guidelines support using CMA as the initial genetic test (replacing the routine karyotype) in the evaluation of:

Developmental Delay (DD) / Intellectual Disability (ID)

Children with global developmental delays or intellectual disability of unknown cause are prime candidates for CMA testing​. The American Academy of Pediatrics (AAP) has designated chromosomal microarray as a first-line test in these cases, replacing the standard karyotype (and older subtelomere FISH tests) for children with intellectual disability without a known etiology​. 

However, because CMA does not detect the DNA repeat expansion that causes Fragile X syndrome, Fragile X testing is still recommended in parallel as an initial test for children (especially males) with unexplained ID​.

Autism Spectrum Disorder (ASD)

For individuals with autism or autism spectrum disorders, especially when accompanied by developmental delays or dysmorphic features, CMA is indicated as a first-tier genetic test​. 

Many autism spectrum disorder cases have subtle chromosomal microdeletions or duplications contributing to the phenotype. Studies summarized by the International Standard Cytogenomic Array Consortium found a significant portion of patients with ASD and/or ID have pathogenic copy-number variants detectable by CMA, supporting its routine use in the diagnostic workup​.

Multiple Congenital Anomalies or Dysmorphic Features

Patients with multiple congenital anomalies (MCA) (e.g. a child with several birth defects or dysmorphic physical features suggestive of an underlying syndrome) should undergo CMA as a first-line test​.

The technology's high resolution allows the detection of microdeletion syndromes and other genomic imbalances that underlie many syndromic conditions. 

In fact, a consensus statement in the American Journal of Human Genetics concluded that chromosomal microarray outperforms G-banded karyotype for individuals with unexplained developmental disabilities or congenital anomalies and should be used as the initial cytogenetic test in such evaluations​.

Prenatal Indications

CMA is also a valuable tool in prenatal diagnostics, particularly when fetal anomalies are suspected:

Ultrasound-detected Fetal Anomalies

If one or more structural anomalies are identified on prenatal ultrasound (for example, heart defects, brain malformations, cleft palate, etc.), chromosomal microarray is recommended on invasive prenatal samples (chorionic villus or amniotic fluid). 

The American College of Obstetricians and Gynecologists (ACOG) and Society for Maternal-Fetal Medicine (SMFM) issued guidelines advising that CMA should replace or supplement karyotyping for fetuses with major structural abnormalities​.

Routine Prenatal Diagnosis (in absence of anomalies)

For pregnancies undergoing invasive testing due to other indications (such as advanced maternal age or positive aneuploidy screening), CMA may also be offered as an alternative to karyotype. Guidelines state that all pregnant women should have the option of diagnostic testing regardless of age or screening, and either karyotype or microarray can be used.​

In fetuses without ultrasound abnormalities, the added diagnostic yield of CMA over karyotype is smaller but still present (approximately 1–2% of such cases had clinically significant CNVs detected by CMA that were not apparent on karyotype)​.

Therefore, some couples opt for CMA in prenatal testing to maximize detection of any genetic issues. It should be noted that CMA, like karyotype, requires fetal DNA from an invasive sample (amniocentesis or CVS)​; noninvasive screening tests (e.g. cell-free DNA screening) cannot replace diagnostic CMA since they do not offer the same resolution or breadth of genomic information.

What Do Clinically Significant CNVs Detected by CMA Mean?

Clinically significant CNVs detected by CMA indicate submicroscopic genomic imbalances that may impact fetal development, but their effects vary. 

Some are clearly pathogenic, while others have uncertain or mild clinical consequences. CMA identifies additional findings in 1% of structurally normal pregnancies and 6% of those with ultrasound anomalies, including conditions with variable expressivity, such as neurodevelopmental disorders. 

Given the potential for uncertain results, genetic counseling is essential to guide interpretation, further testing, and reproductive decisions.

What Do Normal CMA Results Mean?

While CMA is an excellent tool for identifying CNVs, it is important to understand that a normal CMA result does not rule out all genetic conditions. CMA is only capable of detecting CNVs; it does not detect single-gene mutations or balanced chromosomal rearrangements, which may also be responsible for certain genetic conditions. 

Therefore, if a clinician strongly suspects a genetic condition despite normal CMA results, further testing such as single-gene testing, exome sequencing, or karyotyping might be warranted.