Summary & Overview
CPT 81229: Chromosomal Microarray (CGH/CMA) Molecular Karyotype
CPT code 81229 represents high-resolution chromosomal microarray testing (comparative genomic hybridization/molecular karyotype) that evaluates the entire genome for copy‑number variants (CNVs) and examines single‑nucleotide polymorphisms (SNPs) indicative of long runs of homozygosity. This molecular diagnostic test is a key tool in evaluating unexplained developmental delays, congenital anomalies, and intellectual disability, and its use affects clinical genetics workflows and laboratory reimbursement nationally. Key payers in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find an overview of clinical and coding context for CPT code 81229, comparisons of payer coverage patterns, common billing and service considerations, and benchmarks for utilization and payment where available. The publication also outlines relevant policy updates affecting genomic testing coverage, typical sites of service, and expected documentation and claim elements for laboratory processing. Data not available in the input is noted explicitly where applicable.
Billing Code Overview
CPT code 81229 describes a comparative genomic hybridization (CGH) microarray test, also known as chromosomal microarray (CMA) or molecular karyotype performed by microarray. The procedure is a high-resolution, genome-wide laboratory analysis that detects copy-number variants (CNVs) and evaluates single-nucleotide polymorphisms (SNPs) to identify long stretches of homozygosity or other structural genomic abnormalities. This testing is commonly used to investigate genetic causes of developmental delays, congenital anomalies, and intellectual disabilities.
Service type: Clinical laboratory molecular diagnostic test (genomic microarray analysis)
Typical site of service: Clinical diagnostic laboratory or reference molecular laboratory; specimens are typically collected in outpatient clinics, hospitals, or specialty genetics centers and sent to the laboratory for processing.
Clinical & Coding Specifications
Clinical Context
A child aged 18 months presents to a pediatric genetics clinic for evaluation of global developmental delay, hypotonia, and dysmorphic features. The pediatrician orders a high-resolution chromosomal microarray (comparative genomic hybridization / CMA) to detect copy-number variants (CNVs) or regions of homozygosity that could explain the phenotype. A genetics nurse obtains informed consent and collects a blood sample in an EDTA tube at an outpatient laboratory collection site. The sample is sent to the molecular diagnostics laboratory where a medical technologist extracts DNA and runs the CGH/SNP microarray platform. The lab analyst performs the technical test corresponding to 81229 and generates raw and analyzed data; a board-certified molecular geneticist reviews and signs the interpretive report. Results identifying a pathogenic CNV prompt genetic counseling and coordination of confirmatory testing or targeted family testing. Typical sites of service include outpatient hospital laboratories, independent reference laboratories, and hospital-based molecular diagnostics laboratories.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
26 | Professional component | Use when billing only the professional interpretation component separate from the technical test (rare for 81229 when split billing applies). |