Your child's neurologist just recommended genetic testing. The referral says "chromosomal microarray" but when you called to schedule, the genetic counselor asked if you'd considered whole genome sequencing instead. Now you're trying to figure out whether the $300 test is enough or if you should fight your insurance for the $3,000 one.

The short answer: it depends on what you're trying to find, what your insurance will cover, and how much uncertainty you can live with while you wait for answers.

What Each Test Detects

Chromosomal microarray (CMA) looks for chunks of DNA that are missing or duplicated. It catches deletions and duplications as small as 50,000 base pairs, which is enough to identify most chromosome disorders. CMA is the test that finds conditions like 22q11.2 deletion syndrome or Angelman syndrome when a child has autism, developmental delays, or unexplained intellectual disability.

Whole exome sequencing (WES) reads the protein-coding portions of your child's genome, about 1-2% of the total. It's good at finding point mutations (single-letter changes in DNA) that cause disease. If your child has a rare genetic condition caused by one broken gene, WES is more likely to catch it than CMA.

Whole genome sequencing (WGS) reads all 3 billion base pairs. It's the most comprehensive option and catches everything WES does plus mutations in non-coding regions that regulate how genes work. It also produces the highest volume of variants of uncertain significance (VUS), meaning results your doctors can't interpret yet.

CMA won't find single-gene mutations. WES won't find large deletions or duplications unless they happen to disrupt a gene. WGS finds nearly everything but costs more and takes longer to analyze.

Diagnostic Yield: What the Numbers Mean

CMA identifies a genetic cause in roughly 10% of children with autism, developmental delays, or intellectual disabilities. WGS pushes that number to about 34% in some studies, but a 34% diagnostic yield means 66% of families still leave without an answer. Understanding Genetic Testing for Autism, Cerebral Palsy, and Developmental Disabilities: A Parent's Guide breaks down why genetic causes are identified in fewer than 25% of autism cases even with comprehensive testing.

The yield depends heavily on your child's symptoms. Children with multiple congenital anomalies, severe developmental delays, and dysmorphic features (facial or physical characteristics that suggest a syndrome) have higher diagnostic yields across all test types. A child whose only symptom is mild speech delay and social communication differences will have a much lower yield.

Your genetic counselor should help you estimate where your child falls on that spectrum before you commit to a $3,000 test.

Cost and Insurance Coverage

CMA typically costs $300 to $1,000 out of pocket if insurance doesn't cover it. Most insurers do cover CMA as a first-tier test when a child has developmental delays, intellectual disability, or autism spectrum disorder. The American Academy of Pediatrics (AAP) updated its 2025 guidelines to recommend CMA as first-tier evaluation for global developmental delay (GDD) and intellectual disability (ID).

WES runs $500 to $2,500. WGS runs $1,000 to $5,000 or higher depending on the lab and analysis depth. Insurance coverage for sequencing tests varies widely. Some plans cover WES after CMA comes back negative. Others require prior authorization and documented clinical criteria before they'll approve sequencing at all. A few cover it as first-tier testing for children with complex presentations.

If you're paying out of pocket, the cost difference matters. A $300 CMA that finds an answer saves you $2,700. A $300 CMA that doesn't find anything means you're back at square one, but you're only $300 in.

Sequential testing (start with CMA, move to WES or WGS if negative) spreads the cost over time and avoids paying for comprehensive sequencing when a simpler test would have worked. Concurrent testing (run CMA and WES or WGS at the same time) gets you to a diagnosis faster if there is one to find, but you're paying for both tests whether or not the cheaper one would have been enough.

The American College of Medical Genetics and Genomics (ACMG) recommends CMA as the first-tier test for patients with developmental delays, intellectual disabilities, or autism of unknown cause. Sequential testing is the standard approach unless your child's presentation is severe enough to justify skipping straight to sequencing.

When to Start With CMA

Start with CMA if your child's symptoms are relatively straightforward: autism without other medical issues, mild to moderate developmental delays, or isolated intellectual disability. If the presentation suggests a chromosomal disorder (multiple affected systems, physical features that suggest a syndrome, growth delays), CMA is the right first step.

CMA is also the right choice if you're working within insurance constraints and need to demonstrate that first-tier testing was negative before your insurer will approve sequencing.

If CMA comes back with a pathogenic variant (a known disease-causing deletion or duplication), you have your answer. If it comes back normal or with a VUS (variant of uncertain significance), you and your genetic counselor can decide whether to pursue WES or WGS based on how much the lack of diagnosis is affecting treatment planning.

When to Push for Sequencing

Push for WES or WGS as a first-line test if your child has a severe or complex presentation: multiple organ systems affected, seizures that don't respond to standard medications, regression (loss of previously acquired skills), or a combination of symptoms that don't fit a known syndrome.

If your child has already had CMA and it came back negative, sequencing is the logical next step. Ending the Diagnostic Odyssey: How Whole Genome Sequencing Is Changing Rare Disease Diagnosis covers how WGS is shortening the years-long search for answers in rare disorder cases.

If multiple family members are affected (siblings with developmental delays, parents with learning disabilities or psychiatric conditions), sequencing may catch inherited variants that CMA would miss.

WGS is also the better choice when time matters. If your child is declining or if a genetic diagnosis would change immediate medical management (medication choices, surgical planning, enrollment in a clinical trial), paying for comprehensive testing upfront may be worth it.

What Happens After You Get Results

A positive result (pathogenic variant identified) gives you a diagnosis, which may:

• Explain your child's symptoms
• Connect you to condition-specific support groups and research
• Change medication or therapy recommendations
• Open access to clinical trials
• Inform family planning decisions

A negative result (no pathogenic variants found) doesn't mean your child doesn't have a genetic condition. It means the test didn't find it. Sequencing technologies improve every year. Labs reanalyze stored samples as new disease genes are discovered. A test that comes back negative in 2026 may turn positive in 2028 when researchers publish new findings.

A VUS result (variant of uncertain significance) is the hardest outcome. You found something, but no one knows yet whether it causes disease. Some VUSs get reclassified as pathogenic or benign as more data comes in. Others stay uncertain indefinitely.

Your genetic counselor is essential before and after testing. They help you understand what the results mean, whether a VUS warrants further investigation, and when it makes sense to retest as technology improves.

The Test Does Not Diagnose Autism or Cerebral Palsy

Genetic testing identifies a potential cause, not a diagnostic confirmation. A child with autism and a pathogenic variant in a gene associated with autism still has autism, but now you know why. A child with cerebral palsy and a negative genetic test still has cerebral palsy.

The value of the test is in what it opens up: targeted therapies, clinical trial eligibility, answers for siblings who may be carriers, or simply the end of the diagnostic odyssey. Navigating a Rare Disorder Diagnosis: From Genetic Testing to Building a Care Team walks through what happens after you get a genetic diagnosis and how to build a care team around it.

For some families, not knowing is harder than knowing the answer is unfixable. For others, the cost and emotional energy of testing isn't worth the low probability of finding an actionable result.

Making the Decision

Ask your genetic counselor these questions before you choose a test:

Based on my child's presentation, what's the realistic diagnostic yield for CMA vs. WGS?

If your counselor says CMA has a 5% chance and WGS has a 15% chance, you're looking at a 10-percentage-point difference on a test that costs five times as much. You're paying $2,700 more for a 10% better shot at an answer.

If we find a genetic cause, will it change treatment?

Some genetic diagnoses unlock specific therapies or clinical trials. Others just give you a name for what you already knew. Know which scenario you're in before you test.

Does our insurance require CMA first, or can we go straight to sequencing?

If your insurance won't cover WGS without a negative CMA, start with CMA. Fighting your insurer for months while your child goes undiagnosed helps no one.

What happens if we get a VUS?

Ask whether the lab offers reanalysis as new data becomes available, and whether that reanalysis costs extra.

You don't have to choose the most comprehensive test. You have to choose the test that makes sense for your child, your family's financial situation, and what you'll do with the results once you have them.