Summary & Overview
CPT 81297: MSH2 Large Deletion/Duplication Analysis
CPT code 81297 represents technical laboratory testing to detect long-sequence deletions or duplications in the MSH2 gene, a key gene linked to Lynch syndrome and hereditary colorectal cancer risk. This molecular diagnostic procedure identifies large-scale copy number changes that standard sequencing may miss and therefore plays a critical role in comprehensive genetic evaluation for cancer predisposition. Nationally, such testing influences diagnostic pathways, cascade testing decisions, and access to targeted surveillance and management.
Key payers covered in this overview include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise briefing on clinical context and the laboratory setting for this service, along with national payer coverage themes and typical billing considerations. The publication summarizes benchmarks for utilization and payment where available, highlights recent policy or coding clarifications affecting molecular diagnostics, and outlines how CPT code 81297 fits within broader genetic testing workflows. Data not available in the input is noted where applicable.
Billing Code Overview
CPT code 81297 describes a laboratory procedure to detect long-sequence deletions or duplications in the MSH2 gene (mutS homolog 2), a gene associated with hereditary nonpolyposis colorectal cancer (Lynch syndrome). The service involves technical laboratory analysis to identify large-scale genetic rearrangements in the MSH2 locus.
-
Service type: Diagnostic molecular genetic testing (technical component)
-
Typical site of service: Clinical or reference laboratory performing molecular diagnostics
Clinical & Coding Specifications
Clinical Context
A 42-year-old patient with a personal history of early-onset colorectal cancer and a strong family history of Lynch syndrome–associated cancers is referred to a molecular diagnostics laboratory for targeted genetic testing of the MSH2 gene. The clinician orders deletion/duplication analysis to detect large exon-level or multi-exon deletions and duplications not identified by sequence-based testing. A blood sample is collected at an outpatient phlebotomy site and sent under chain-of-custody to the reference laboratory. The molecular lab performs the technical assay, commonly by MLPA (multiplex ligation-dependent probe amplification) or quantitative PCR/CNV detection using next-generation sequencing read-depth analysis, and generates a technical report. The laboratory documents specimen receipt, assay controls, quality metrics, and technical interpretation; the ordering clinician receives the test result, integrates it with family history and clinical findings, and discusses implications with the patient.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
26 | Professional component | Use when billing only the professional interpretation component separate from the technical component if split billing applies. |
TC | Technical component |