CMA vs Sequencing
CMA vs Sequencing in Autism Diagnostics
When to Use CMA vs Gene Sequencing in Clinical Evaluations
Genetic testing plays a growing role in autism and developmental evaluations. Two of the most commonly used tools, Chromosomal Microarray (CMA) and genetic sequencing serve different purposes and are often used sequentially rather than interchangeably.
Understanding when to use each test helps Autism Centers, ABA programs, developmental pediatricians, neurologists and behavioral health providers build clearer diagnostic pathways and manage expectations.
What CMA Is Designed to Detect
Chromosomal Microarray (CMA) identifies copy number variations (CNVs), including:
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Microdeletions
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Microduplications
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Small chromosomal gains or losses
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These genomic changes are strongly associated with differences in:
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Development
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Learning
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Behavior
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Neurological function
Because of its broad screening capability, CMA is widely recommended as the first-line genetic test for children with autism, developmental delays or intellectual disability.
What Sequencing Is Designed to Detect
Sequencing tests (such as Whole Exome Sequencing / WES) analyze the DNA sequence of individual genes to identify:
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Single nucleotide variants (SNVs)
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Gene-level mutations
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Rare inherited or de novo variants
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Sequencing is most useful when:
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CMA results are normal or inconclusive
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Clinical features suggest a single-gene disorder
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Neurologic symptoms are complex or progressive
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Family history indicates inherited conditions
Key Clinical Differences
CMA
Genome-wide detection of CNVs
First-line test in autism diagnostics
Faster turnaround
Lower overall cost
Strong yield for structural variation
Sequencing
Gene-level mutation detection
Typically second-line testing
Longer turnaround
Higher cost
Strong for rare or targeted conditions
Bottom line: CMA establishes the foundation. Sequencing adds depth when needed.
Why CMA Remains the First-Line Test
CMA is recommended first because it:
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Captures clinically significant CNVs
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Frequently impacts care planning and referrals
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Provides actionable insights quickly
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Fits well into structured diagnostic workflows
Sequencing is powerful but most effective after CMA, not before.
Why Centers Start With CMA Labs
Autism and pediatric centers often prioritize CMA because:
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Space requirements are modest
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Workflow design is simpler
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Equipment needs are lower
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Turnaround times improve dramatically
What This Means for Providers
Autism and pediatric centers often prioritize CMA because:
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Space requirements are modest
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Workflow design is simpler
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Equipment needs are lower
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Turnaround times improve dramatically
Learn More or Explore CMA Implementation for Your Center
If your organization wants faster access to CMA results or is planning a diagnostic expansion, we can help.
Your center delivers answers.
We help you deliver them faster.