CPT 0260U: Optical Genome Mapping for Chromosomal Structural Variant Detection - OpenPayer

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Summary & Overview

CPT 0260U: Optical Genome Mapping for Chromosomal Structural Variant Detection

CPT code 0260U designates a Proprietary Laboratory Analyses (PLA) test — the Augusta Optical Genome Mapping (OGM) assay from Georgia Esoteric and Molecular (GEM) Laboratory LLC. The test performs OGM on specimens such as blood to detect chromosomal structural variants relevant to diagnosing neurodevelopmental genetic disorders. As a PLA code, 0260U is specific to this single manufacturer's test and is used to ensure accurate identification and tracking of utilization of this proprietary assay.

This publication covers key national payers including Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise overview of clinical context for OGM testing, typical sites of service, and payer coverage patterns. Content includes benchmarking of reimbursement and utilization where available, summaries of policy positions and coverage criteria, and practical coding and billing considerations tied to this PLA code.

The analysis is intended for a national audience of health plan analysts, laboratory billing staff, and policy stakeholders interested in how a single-source genomic assay is represented in claims and coverage frameworks. Data not available in the input is noted where applicable.

AetnaBlue Cross Blue ShieldCigna HealthUnitedHealthcareMedicare0260UCPTProprietary Laboratory AnalysesOptical Genome MappingGenomic TestingMolecular DiagnosticsNeurodevelopmental Disorders

Billing Code Overview

CPT code 0260U is a Proprietary Laboratory Analyses (PLA) code that applies exclusively to the Augusta Optical Genome Mapping test performed by Georgia Esoteric and Molecular (GEM) Laboratory LLC. The assay uses optical genome mapping (OGM) on specimens such as blood to identify chromosomal structural variants that aid in the diagnosis of neurodevelopmental genetic disorders.

Service Type: Laboratory — Molecular/Genomic Diagnostic Test

Typical Site of Service: Clinical laboratory or specialized molecular diagnostics laboratory

Data not available in the input.

Clinical & Coding Specifications

Clinical Context

A pediatric patient with global developmental delay and multiple congenital anomalies is referred by a pediatric neurologist for genomic structural variant testing after prior chromosomal microarray and targeted gene panels were non-diagnostic. A peripheral blood specimen is collected in the outpatient phlebotomy suite and sent to Georgia Esoteric and Molecular (GEM) Laboratory LLC for Augusta Optical Genome Mapping. The laboratory performs optical genome mapping (OGM) to detect chromosomal structural variants (deletions, duplications, translocations, inversions, and complex rearrangements) that can explain neurodevelopmental genetic disorders. The lab returns a structured report with detected clinically significant structural variants, technical limitations, and recommendations for confirmatory testing where applicable. Results are reviewed by the ordering pediatric neurologist or geneticist, who incorporates findings into diagnostic counseling, medical management, and family cascade testing discussions.

Coding Specifications

Modifier	Description	When to Use
`00`	No modifier - standard reporting	Use when no specific modifier applies to the service.
`22`	Increased procedural services

Taxonomy Code	Specialty	Notes
2080P0200X	Clinical Molecular Genetics	Laboratories and physicians specializing in molecular and genomic testing.
208D00000X	Clinical Cytogenetics	Specialists interpreting chromosomal structural variant data.
207RG0100X	Pediatric Neurology	Ordering clinicians for neurodevelopmental disorder evaluation.
207K00000X	Medical Genetics & Genomics	Geneticists ordering and interpreting results for diagnostic evaluation.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`Q87.8`	Other specified congenital malformation syndromes affecting multiple systems	Structural variants detected by OGM can explain syndromic congenital anomalies.
`Q99.9`	Chromosomal abnormality, unspecified	OGM is used to identify specific chromosomal structural abnormalities underlying this category.
`R62.0`	Delayed milestone in childhood	OGM can identify genetic structural causes of developmental delay.
`F82`	Specific developmental disorder of motor function	Structural genomic variants may contribute to motor developmental disorders evaluated with OGM.
`F80.9`	Developmental speech or language disorder, unspecified	Structural variants are a possible genetic etiology for speech and language disorders.
`G80.9`	Cerebral palsy, unspecified	When suspected genetic contributions exist, OGM may be part of the diagnostic evaluation.
`Q93.9`	Chromosomal abnormality, unspecified (mosaicism and structural variants)	OGM can detect cryptic structural rearrangements contributing to this diagnosis.
`Z13.79`	Encounter for screening for other genetic and chromosomal anomalies	OGM may be ordered in screening or evaluation settings for patients with developmental concerns.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`0260U`	Augusta Optical Genome Mapping — optical genome mapping to identify chromosomal structural variants for neurodevelopmental disorders (Proprietary Laboratory Analyses code specific to GEM Laboratory LLC)	Primary test code for OGM performed by GEM Laboratory LLC.
`81406`	Molecular pathology procedure level 6 (sequencing of genomic regions, large gene panels)	May have been performed earlier in the diagnostic workup; complements OGM by detecting sequence-level variants not identified by OGM.
`81211`	Chromosome analysis (karyotype), constitutional; peripheral blood	Conventional cytogenetic testing used before or to confirm large structural rearrangements detected by OGM.
`88271`	Chromosome analysis, tissue culture, constitutional (per culture), prenatal/postnatal	Alternate cytogenetic technique that may be used for confirmation depending on specimen type.
`81479`	Unlisted molecular pathology procedure	Used for reporting ancillary or confirmatory molecular tests not described by a specific CPT when needed after OGM findings.