DraftUnitedHealthcarePolicy CS017ID.B

Chromosome Microarray Testing (Non-Oncology Conditions) (for Idaho Only)

Defines medical necessity and coverage for chromosome microarray testing (aCGH/SNP array) for non-oncology indications for members in Idaho, including Idaho Medicaid Plus.

Policy Summary

PayerUnitedHealthcare

PolicyChromosome Microarray Testing (Non-Oncology Conditions) (for Idaho Only)

Policy CodePolicy CS017ID.B

Change TypeRevisions to covered indications, counseling language, and state-specific guidance

Effective DateAug 1, 2025

Next Review DateN/A

Key ActionCheck Idaho Medicaid Provider Handbook Chapter 4.8 and submit required medical documentation when requesting covered chromosome microarray testing.

SourceLink

POLICY UPDATE CHANGES

Added instruction to refer to the Idaho Medicaid Provider Handbook, Laboratory Services, Chapter 4.8: Genetic Testing for medical necessity clinical coverage criteria for genetic testing.

Removed language indicating pre-test genetic counseling was strongly recommended as a policy requirement for individual patients.

Revised list of proven and medically necessary evaluations for chromosome microarray testing; removed evaluation of embryo/fetus for intrauterine fetal demise or stillbirth and testing products of conception following pregnancy loss, and removed evaluation of biological parent or sibling of a fetus or child with an abnormal or equivocal CMA finding.

Added language that medical records documentation may be required to assess whether the member meets the clinical criteria for coverage but does not guarantee coverage; refers to guidelines titled Medical Records Documentation Used for Reviews.

Removed ICD-10 diagnosis codes P02.9, R62.0, R62.50, and R62.51 from the Applicable Codes section.

Updated Clinical Evidence and References sections to reflect the most current information.

Idaho only

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Coverage Criteria — Chromosome Microarray Testing (CMA)

Medically necessary indications

Covered when ALL of the following are met for the indicated populations:

Prenatal evaluation (invasive sampling): Chromosome microarray testing using aCGH and/or SNP array is proven and medically necessary for evaluation of an embryo/fetus in individuals undergoing invasive prenatal testing (amniocentesis, chorionic villus sampling, or fetal tissue sampling).

Requires invasive prenatal sample (amniocentesis, CVS, or fetal tissue sampling).

Postnatal indications: Chromosome microarray testing using aCGH and/or SNP array is proven and medically necessary for individuals with one or more of the following: autism spectrum disorder (ASD); isolated severe congenital heart disease; multiple anomalies not specific to a well-delineated genetic syndrome and not identifiable by clinical evaluation alone; developmental delay/intellectual disability when a specific syndrome is not suspected.

Clinical rationale and limitations

Clinical use and considerations:

Clinical context: CMA (aCGH or SNP array) detects genome-wide copy number variations (deletions and duplications) and is used for diagnostic evaluation of chromosomal abnormalities in fetuses, newborns, and children with developmental disorders; diagnostic prenatal CMA requires invasive sampling such as amniocentesis or CVS.

Descriptive guidance — informational only.

Test limitations: CMA may detect variants of uncertain significance and false positives that require further testing; CMA cannot reliably detect balanced chromosomal rearrangements (no net gain/loss) and may require additional assays or parental studies and database curation for interpretation.

Informational only; consider reflex testing or parental segregation as appropriate.

Guideline-based indications and sequencing

Professional society recommendations summarized below provide the rationale for testing sequencing and when CMA is preferred:

ACMG guidance: ACMG recommends CMA as the first-tier test in evaluation of individuals with neurodevelopmental disability and congenital anomalies; CMA may not detect balanced cytogenomic abnormalities or UPD and additional testing may be required to clarify mechanism and inheritance.

ACMG clinical practice report (Waggoner et al., 2018).

ACMG on NIPS follow-up: ACMG practice resource: CMA on CVS or amniocentesis may be used to confirm abnormal NIPS results or as a reflex when karyotype is normal; CMA should be used for follow-up when small CNVs are reported on NIPS.

Prenatal structural anomaly testing

Systematic review evidence supporting prenatal CMA for fetuses with structural anomalies:

Systematic review findings: Systematic reviews and meta-analyses report that CMA is considered a first-tier test for fetuses with structural anomalies identified on ultrasound, with overall diagnostic yields that vary by anomaly type (mixed anomalies ~5.72% overall; higher yields for multiple structural anomalies), and that parental segregation and karyotyping should be used as appropriate; WES may provide higher incremental yield in selected cases.

Mastromoro et al. 2022c systematic review summarized diagnostic yields and VUS rates; WES has higher incremental yield for some indications.

Fetal congenital heart defects

Evidence and meta-analyses regarding congenital heart defects (CHD):

CMA for fetal CHD: Multiple studies and meta-analyses demonstrate increased diagnostic yield of CMA compared with karyotype in fetuses with congenital heart defects (example: single-center study reported CMA yield 15.3% vs karyotype 8.3%); yields are higher in non-isolated CHD and when extracardiac anomalies are present, supporting CMA as a first-tier test for CHD or when karyotype/FISH is normal.

Consider CMA especially for non-isolated CHD and certain subtypes (e.g., septal defects) where chromosome abnormality rates are higher.

POC and pregnancy loss

Products of conception (POC) and pregnancy loss context and evidence:

CMA for POC/pregnancy loss: Meta-analyses of CMA on products of conception report substantially higher diagnostic yields for chromosomal abnormalities compared with karyotype (overall chromosomal abnormalities ≈49.9% in pooled POC series) and identify miscarriage-associated CNVs and candidate regions; CMA may improve success rates on nonviable tissue and detect pCNVs implicated in pregnancy loss.

Peng et al. 2023 and Wang et al. 2020 provide pooled yields and recurrent CNV regions associated with miscarriage.

Prenatal and stillbirth indications

Covered prenatal and stillbirth indications and society recommendations:

Prenatal/stillbirth indications: Specialty societies (ACMG, ACOG/SMFM, SMFM) recommend that CMA be offered or used when fetal structural abnormalities are detected on ultrasound in patients undergoing invasive diagnostic testing, that CMA can replace karyotype for these indications, and that CMA is preferred for stillbirth evaluation because of higher yield and better performance on nonviable tissue.

ACOG/SMFM and SMFM statements support offering CMA for structural anomalies and stillbirth workup; CMA should be available to patients choosing invasive testing.

NIPS follow-up and discordant sex: Guidelines recommend CMA for follow-up/confirmatory testing after abnormal NIPS findings (including small CNVs) and when NIPS sex determination is discordant with fetal/physical findings.

ACMG practice resource and ACOG guidance.

Postnatal neurodevelopmental indications

Postnatal and neurodevelopmental indications referenced by professional guidance:

Postnatal neurodevelopmental indications: ACMG recommends CMA as the first-tier test for evaluation of individuals with neurodevelopmental disabilities and congenital anomalies (including developmental delay/intellectual disability and ASD), recognizing CMA may not detect balanced rearrangements or UPD and additional testing may be necessary.

ACMG clinical practice report (Waggoner et al., 2018).

Genetic counseling and consent

Counseling and testing process requirements:

Genetic counseling and informed consent: Comprehensive pretest and posttest genetic counseling from a provider with genetics expertise is recommended; informed consent should address the potential for findings of uncertain significance, incidental findings (including non-paternity and consanguinity), and reporting preferences for adult-onset conditions. CMA should not be ordered without informed consent that includes discussion of these issues.

ACOG/SMFM and SMFM guidance stress the need for counseling by qualified providers and informed consent prior to CMA.

Chromosome microarray testing (aCGH and/or SNP array) is considered proven and medically necessary for the specific indications listed in this policy (prenatal diagnostic testing via invasive sampling and defined postnatal neurodevelopmental and congenital indications). Use of CMA for populations or conditions not specifically listed in the covered indications is considered unproven and not medically necessary due to insufficient evidence of efficacy.

Chromosome microarray analysis has intrinsic detection limits: CMA identifies copy number variations (deletions and duplications) across the genome but cannot detect certain abnormalities such as balanced chromosomal rearrangements (no net gain or loss of chromosomal material). Results may include variants of unknown significance (VUS) and false positives that require additional evaluation.

CMA (aCGH or SNP array) detects genome-wide copy number variants but has important limitations for clinical interpretation. Laboratories and clinicians may encounter VUS that require database review and possible parental testing to clarify significance. Additionally, because CMA measures copy number, it is not suitable for detecting balanced translocations or other balanced rearrangements; such findings will not be identified by CMA and may necessitate karyotype or other cytogenetic testing for detection and characterization.

Policy revisions removed prior language listing CMA for evaluation of intrauterine fetal demise, stillbirth, or routine testing of products of conception (POC) following pregnancy loss from the list of proven and medically necessary evaluations. Providers should note these indications are no longer included among covered usages in this policy update.

Any proposed use of chromosome microarray testing outside the specified covered indications (for example, conditions or populations not enumerated in this policy) is considered unproven and not medically necessary. Requests for CMA for such unlisted purposes may be subject to coverage denial.

Language that previously referenced CMA for certain pregnancy loss evaluations and for testing of relatives (biological parent or sibling) was removed in this revision, indicating these are no longer enumerated as covered indications in the current policy.

Diagnostic evaluation of chromosomal abnormalities

Diagnostic evaluation context:

Diagnostic evaluation: CMA (aCGH and/or SNP array) is indicated for diagnostic evaluation of chromosomal abnormalities in fetuses, newborns, and children with developmental delay, intellectual disability, dysmorphic features, congenital anomalies, or other neurodevelopmental disorders; prenatal diagnostic CMA requires invasive sampling.

Informational; follow-up testing and parental studies may be needed to interpret CNVs.

Evaluation and follow-up after abnormal NIPS

Evaluation and sequencing considerations for developmental delay, congenital anomalies, and abnormal NIPS:

Evaluation and follow-up testing: ACMG and systematic review evidence support CMA as a first-tier test for individuals with developmental delay, intellectual disability, congenital anomalies, and fetuses with structural anomalies identified on ultrasound; CMA may be used to follow up abnormal NIPS results and small CNV findings, and WES may be considered for selected cases with higher incremental yield.

Parental segregation, karyotype, or additional molecular testing may be required depending on findings.

Testing of products of conception (POC) and pregnancy loss

Testing of products of conception (POC) and analysis in pregnancy loss:

POC testing: CMA of products of conception yields higher informative rates and identifies miscarriage-associated chromosomal abnormalities and pCNVs; systematic reviews report high pooled diagnostic yields and identify recurrent CNV regions associated with miscarriage, supporting use of CMA in POC analysis algorithms.

Clinical context: CMA often outperforms karyotype for nonviable tissue.

Prenatal diagnosis for structural anomalies and stillbirth

Prenatal diagnosis when fetal structural anomalies are identified on ultrasound or for stillbirth evaluation:

Prenatal diagnosis for structural anomalies/stillbirth: When fetal structural anomalies are identified on ultrasound and an invasive diagnostic procedure is performed, CMA is recommended and may replace karyotype; CMA is also preferred for stillbirth evaluation due to higher diagnostic yield and better performance on nonviable tissue.

Society guidance: ACOG/SMFM and SMFM statements support CMA as primary testing modality in these contexts.

ACMG first-tier recommendation for neurodevelopmental disabilities

ACMG first-tier recommendation summarized for postnatal evaluation:

ACMG first-tier recommendation: ACMG recommends chromosome microarray analysis as the first-tier test for evaluation of individuals with neurodevelopmental disabilities and congenital anomalies in the postnatal setting.

Waggoner et al., 2018.

Coding — Procedure and Diagnosis Codes

Procedure/CPT/HCPCS codesmixed

0156U	Copy number (e.g., intellectual disability, dysmorphology), sequence analysis.
0209U	Cytogenomic constitutional (genome-wide) analysis, interrogation of genomic regions for copy number, structural changes, and areas of homozygosity for chromosomal abnormalities.
81228	Cytogenomic (genome-wide) analysis for constitutional chromosomal abnormalities; interrogation of genomic regions for copy number variants, comparative genomic hybridization [CGH] microarray analysis.
81229	Cytogenomic (genome-wide) analysis for constitutional chromosomal abnormalities; interrogation of genomic regions for copy number and single nucleotide polymorphism (SNP) variants, comparative genomic hybridization (CGH) microarray analysis.
81349	Cytogenomic (genome-wide) analysis for constitutional chromosomal abnormalities; interrogation of genomic regions for copy number and loss-of-heterozygosity variants, low-pass sequencing analysis.
81479	Unlisted molecular pathology procedure
S3870	Comparative genomic hybridization (CGH) microarray testing for developmental delay, autism spectrum disorder and/or intellectual disability

Diagnosis/ICD-10 codes (selected examples from list)ICD-10

F70	Mild intellectual disabilities.
F71	Moderate intellectual disabilities.
F72	Severe intellectual disabilities.
F73	Profound intellectual disabilities.
F78.A1	SYNGAP1-related intellectual disability.
F78.A9	Other genetic related intellectual disability.
F79	Unspecified intellectual disabilities.
F80.0	Phonological disorder.
F84.0	Autistic disorder.
N96	Recurrent pregnancy loss.

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Applicable ICD-10 Diagnosis CodesICD-10

O35.10X0	Maternal care for (suspected) chromosomal abnormality in fetus, unspecified, not applicable, or unspecified.
O35.10X1	Maternal care for (suspected) chromosomal abnormality in fetus, unspecified, fetus 1.
O35.11X0	Maternal care for (suspected) chromosomal abnormality in fetus, Trisomy 13, not applicable or unspecified.
O35.12X0	Maternal care for (suspected) chromosomal abnormality in fetus, Trisomy 18, not applicable or unspecified.
O35.13X0	Maternal care for (suspected) chromosomal abnormality in fetus, Trisomy 21, not applicable or unspecified.
O35.14X0	Maternal care for (suspected) chromosomal abnormality in fetus, Turner Syndrome, not applicable or unspecified.
O35.15X1	Maternal care for (suspected) chromosomal abnormality in fetus, sex chromosome abnormality.
O35.19X0	Maternal care for (suspected) chromosomal abnormality in fetus, other chromosomal abnormality, not applicable or unspecified.
O35.2XX0	Maternal care for (suspected) hereditary disease in fetus, not applicable or unspecified.
O35.8XX0	Maternal care for other (suspected) fetal abnormality and damage, not applicable or unspecified.

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Removed Applicable ICD-10 CodesICD-10

ICD-10 codes removed: P02.9, R62.0, R62.50, R62.51

These diagnosis codes were removed from the Applicable Codes section.

NoteNone specified.

Provider Actions — Authorization, Documentation, and Counseling

Prior Authorization

Prior Authorization and Plan/Code Reference

Prior authorization requirements vary by benefit plan and state. This policy applies to Idaho (including Idaho Medicaid Plus); verify the member's benefit plan and submit prior authorization requests and supporting medical documentation when required by the member's contract or state program.

Check the member's federal/state/contractual benefit plan for prior authorization requirements before ordering testing.
When prior authorization is required, include relevant medical records demonstrating the clinical indication for chromosome microarray testing.

Billing Rule

Prior Authorization Code Mapping

Claims and prior authorization reviews may be mapped to specific diagnosis codes associated with maternal/fetal conditions, congenital anomalies, and related indications. Use appropriate ICD-10 codes when submitting requests; inclusion of these codes does not guarantee coverage and claims may be reviewed for clinical appropriateness.

Not Covered / Limitations

Preimplantation genetic testing (PGT) is explicitly not covered under this policy. PGT and related services are addressed in a separate UnitedHealthcare policy specific to preimplantation genetic testing.

Balanced chromosomal rearrangements (e.g., reciprocal translocations without net gain/loss of material) will not be detected by CMA because the technique identifies copy number changes rather than chromosomal position or structure.

Detection of balanced rearrangements requires cytogenetic methods that assess chromosome structure (for example, karyotype); therefore, testing intended to identify balanced rearrangements is not feasible with CMA alone and would be inappropriate as the sole diagnostic test.

As part of the August 1, 2025 revision, indications for CMA that previously included evaluation for intrauterine fetal demise, stillbirth, and routine testing of products of conception following pregnancy loss were removed from the medically necessary list and are no longer covered indications in this policy.

Eligibility Requirements

No top-level eligibility requirement nodes are specified in this policy excerpt. Refer to the policy criteria and the Idaho Medicaid Provider Handbook, Laboratory Services, Chapter 4.8 for any state-specific eligibility or plan-specific requirements.

This policy does not specify additional family history or other top-level eligibility prerequisites in the provided excerpt. Coverage decisions should follow the listed clinical indications and any applicable state or plan rules.

No explicit prior-testing or step-therapy eligibility requirements are included in the policy excerpt. Clinical guidance cited in the full policy describes situations where CMA is first-line or used after other testing, but no mandatory prior-test sequence is mandated here.

The policy excerpt contains no additional top-level eligibility criteria for ordering providers; follow the covered indications, documentation guidance, and any plan-specific prior authorization rules.

Background and Definitions

Chromosome microarray analysis (CMA), using array comparative genomic hybridization (aCGH) and/or single-nucleotide polymorphism (SNP) array, detects genome-wide copy number variants (CNVs) — deletions and duplications of genomic segments — and areas of homozygosity. CMA provides higher resolution than conventional karyotype for identifying submicroscopic chromosomal imbalances and is used in prenatal diagnostics (requiring invasive sampling) and in postnatal evaluation of individuals with developmental delay, intellectual disability, autism spectrum disorder, congenital anomalies, and other neurodevelopmental disorders. Limitations include detection of variants of unknown significance, potential false positives that require follow-up, and inability to detect balanced rearrangements.

Developmental Delay (children <5 years)

DefinitionDevelopmental Delay: children younger than 5 years who present with delays in attainment of developmental milestones at the expected age (Moeschler and Shevell, 2014, reaffirmed 2019).

Intellectual Disability

DefinitionIntellectual Disability: condition diagnosed before age 18 including below-average intellectual function and lack of skills necessary for daily living (MedlinePlus, 2020).

Revision History and Policy Changes

2025-08-01revisionLatest

Added instruction to refer providers to the Idaho Medicaid Provider Handbook, Laboratory Services, Chapter 4.8 for state-specific medical necessity clinical coverage criteria for genetic testing; removed language that pre-test genetic counseling is 'strongly recommended' as applied to a unique person; revised the list of medically necessary evaluations by removing indications for intrauterine fetal demise/stillbirth and testing products of conception, and removal of evaluation of a biological parent or sibling for abnormal/equivocal CMA results; added medical records documentation guidance and removed specific ICD-10 codes (P02.9, R62.0, R62.50, R62.51); updated Clinical Evidence and References.

Policy Summary

PayerUnitedHealthcare

PolicyChromosome Microarray Testing (Non-Oncology Conditions) (for Idaho Only)

Policy CodePolicy CS017ID.B

Change TypeRevisions to covered indications, counseling language, and state-specific guidance

Effective DateAug 1, 2025

Next Review DateN/A

Key ActionCheck Idaho Medicaid Provider Handbook Chapter 4.8 and submit required medical documentation when requesting covered chromosome microarray testing.

SourceLink

On This Page

Prior Authorization

Prior Authorization Requirement

Prior authorization requirement: not all requests for CMA require prior approval under every plan; confirm with the member's benefit plan. If the plan requires authorization, it must be obtained prior to performing invasive diagnostic testing when specified by the plan.

If authorization is required by the applicable benefit plan, obtain approval before performing testing that would not be reimbursed without authorization.
For Idaho Medicaid Plus, follow state-specific authorization processes.

Note

Verify Plan and State-Specific Authorization Requirements

Verify plan and state-specific authorization and coverage rules prior to ordering genetic testing. Federal, state, or contractual requirements govern in the event of conflict with this Medical Policy.

Refer to the Idaho Medicaid Provider Handbook, Laboratory Services, Chapter 4.8: Genetic Testing for state-specific medical necessity criteria and authorization procedures.
When in doubt, contact UnitedHealthcare provider services or the member's plan administrator to confirm requirements.

Denial Risk

Denial Risk for Non‑Indicated Uses

Requests for chromosomal microarray testing for indications not listed as proven/medically necessary in this policy may be considered unproven or not medically necessary and may be denied. Ensure the submitted clinical documentation supports one of the listed indications.

CMA is proven/medically necessary for specific prenatal and postnatal indications described in the policy (e.g., invasive prenatal testing for embryo/fetus, ASD, isolated severe congenital heart disease, multiple anomalies not specific to a well-delineated syndrome, developmental delay/ID when no specific syndrome suspected).
Requests outside these indications lack sufficient evidence and are at risk for denial.

Documentation Required

Genetic Counseling Strongly Recommended; Document Counseling

Genetic counseling is strongly recommended prior to ordering chromosome microarray analysis (CMA). Counseling should inform patients about the benefits, limitations, potential findings (including variants of uncertain significance, non-paternity, consanguinity, and adult-onset conditions), and alternatives to testing.

Offer comprehensive pretest genetic counseling from a professional with genetics expertise for prenatal and diagnostic contexts.
Document the counseling discussion in the medical record; failure to document that counseling was offered or performed may affect coverage determinations.

Documentation Required

Documentation of Pre‑Test Genetic Counseling and Clinical Rationale

Document pre-test genetic counseling and all supporting clinical information in the medical record when seeking coverage for CMA. Medical records may be requested to verify that clinical criteria are met and to support medical necessity determinations.

Include documentation of the clinical indication, imaging or laboratory findings (e.g., ultrasound-detected structural anomalies), and the counseling session content.
Maintain records that support the rationale for CMA and any prior authorization submissions; lack of documentation may result in denial or administrative action.

Note

Guideline‑Based Sequencing and Test Selection

Guideline-based sequencing: follow specialty society recommendations for test selection and sequencing. CMA is recommended as a first‑tier test in the evaluation of individuals with neurodevelopmental disabilities and congenital anomalies and is recommended for prenatal diagnosis in certain circumstances (e.g., fetus with one or more major structural abnormalities).

Use CMA as first‑tier testing for neurodevelopmental disability and congenital anomalies per ACMG guidance.
In prenatal diagnosis, perform CMA on samples obtained by invasive procedures when indicated (e.g., abnormal ultrasound, abnormal NIPS requiring confirmation).
Consider reflex or follow-up testing (karyotype, targeted testing) when CMA findings indicate need for clarification per laboratory and clinical guidelines.