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CPT 88249: Chromosome Analysis for Breakage Syndrome, 100-Cell Clastogen Stress

CPT code 88249 denotes a specialized cytogenetic service: chromosome analysis for breakage syndromes with scoring of 100 cells under clastogen-induced stress. This assay is used to detect increased chromosomal fragility and to aid diagnosis of inherited or acquired conditions characterized by chromosomal breakage. Nationally, the test matters for precise genetic diagnosis, informing care decisions for affected patients, and for laboratory billing and coverage policy given its specialized nature.

Key payers in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find an explanation of the clinical context for 88249, typical settings where the service is performed, and the relevance for payer coverage and claim adjudication. The publication outlines common modifiers and operational considerations associated with billing this laboratory procedure, and provides benchmarks and policy-oriented summaries where available.

The piece offers a concise resource for clinicians, laboratory billing staff, and policy analysts seeking to understand the role of this cytogenetic assay in diagnosis workflows, how it is documented and billed, and which payers commonly encounter claims for this service. Data not available in the input will be noted where applicable.

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Billing Code Overview

CPT code 88249 describes a chromosome analysis for breakage syndromes in which a laboratory analyst scores 100 cells under clastogen stress. The test uses agents such as diepoxybutane, mitomycin C, ionizing radiation, UV radiation, or other methods to induce chromosomal breaks or disorder and reveal underlying genetic instability.

Service Type: Specialized cytogenetic laboratory testing for chromosomal breakage assessment

Typical Site of Service: Clinical laboratory or hospital laboratory setting, including genetics laboratories and reference labs

Data not available in the input.

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CPT 88249: Chromosome Analysis for Breakage Syndrome, 100-Cell Clastogen Stress

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Get alerted when payer policies referencing 88249 are released or updated.

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Billing Code Overview

Service Type: Specialized cytogenetic laboratory testing for chromosomal breakage assessment

Typical Site of Service: Clinical laboratory or hospital laboratory setting, including genetics laboratories and reference labs

Data not available in the input.

Clinical & Coding Specifications

Clinical Context

A pediatric or adult patient with a personal or family history suggestive of a constitutional chromosome breakage syndrome (for example, Fanconi anemia or Bloom syndrome) is referred for specialized cytogenetic testing. The ordering clinician (typically a geneticist, hematologist, or pediatrician) documents signs such as unexplained aplastic anemia, congenital anomalies, growth failure, recurrent infections, or early-onset malignancy, and requests a clastogen-induced chromosome breakage assay. The laboratory receives a whole-blood sample or cultured peripheral blood lymphocytes. A cytogenetics technologist or lab analyst exposes cultured cells to a clastogen agent (for example, diepoxybutane or mitomycin C) or to ionizing/UV radiation under standardized conditions, harvests metaphase cells, prepares slides, and performs G-banding or other staining. The analyst scores 100 cells for chromosomal breaks, radial configurations, and other aberrations under microscopy, documents breakage rates, and generates a report comparing findings to established control ranges. Results are transmitted to the ordering clinician via the laboratory information system; positive or indeterminate results often prompt confirmatory testing, genetic counseling, and family cascade testing. Typical site of service is an outpatient clinical cytogenetics laboratory within a hospital, academic medical center, or independent reference laboratory; specimen collection usually occurs in an outpatient clinic or hospital phlebotomy area.

Coding Specifications

Modifier	Description	When to Use
`26`	Professional component	Use when reporting the professional interpretation/reporting portion separately from the technical laboratory work (if applicable and payer allows split billing).
`TC`	Technical component	Use when reporting only the technical component (laboratory processing, cell culture, scoring) when the performing facility bills separately from the interpreting professional.
`90`	Reference (outside) laboratory	Use when the service was performed by a qualified outside laboratory and billing must indicate an outside reference lab performed the work.
`91`	Data not in provided list	Data not available in the input.
`52`	Reduced services	Use when fewer than the full 100 cells are scored due to inadequate specimen or early termination, and the lab documents the reduction.
`53`	Discontinued procedure	Use when testing is started but discontinued for documented medical or specimen issues before completion of scoring.
`22`	Increased procedural services	Use when work required is substantially greater than typical (extensive troubleshooting, prolonged culture failures) and documentation supports increased effort.
`90`	Duplicate entry to maintain required order	Data not available in the input.
`59`	Distinct procedural service	Use when a separate distinct cytogenetic service is performed the same day that is not bundled (verify payer bundling rules).
`80`	Assistant surgeon (not typically applicable)	Data not applicable for this laboratory procedure.

Taxonomy Code	Specialty	Notes
2080P0200X	Clinical Cytogenetics Laboratory	Laboratory specialists and cytogenetic technologists who perform chromosome analyses.
207RC0000X	Clinical Molecular Genetics	Medical geneticists who may order and interpret cytogenetic breakage assays.
207L00000X	Hematology	Hematologists who evaluate patients with aplastic anemia or marrow failure syndromes and order testing.
2080S0002X	Pediatric Laboratory Medicine	Pediatric specialists and labs performing testing in children with congenital anomalies.
207Q00000X	Medical Genetics	Genetic counselors and medical geneticists involved in result interpretation and family counseling.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`D61.9`	Aplastic anemia, unspecified	Aplastic anemia can be a presenting feature of Fanconi anemia and prompts clastogen breakage testing.
`D61.2`	Constitutional aplastic anemia	Directly associated with inherited bone marrow failure syndromes evaluated by clastogen assays.
`Q87.8`	Other specified congenital malformation syndromes affecting multiple systems	Syndromic congenital anomalies may raise suspicion for chromosomal instability disorders.
`C80.1`	Malignant neoplasm without specification of site, in remission	Early-onset malignancy or unusual cancer history may prompt evaluation for underlying chromosomal breakage syndromes.
`R62.50`	Unspecified lack of expected normal physiological development in childhood	Growth failure can be a feature of inherited breakage syndromes leading to testing.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`88249`	Chromosome analysis for breakage syndrome; lab analyst scores 100 cells for clastogen stress	Primary procedure: scoring 100 cells after clastogen exposure to detect chromosomal breakage syndromes.
`88235`	Chromosome analysis; culture, harvest, and banding (per culture)	Often performed before or alongside breakage testing to provide baseline karyotype and detect constitutional chromosomal abnormalities.
`88240`	Chromosome analysis; at least 20 cells, metaphase	May be used for routine karyotyping when fewer cells are evaluated; not specific for clastogen testing but complements the diagnostic workup.
`88262`	Chromosome analysis, postnatal; fluorescence in situ hybridization (FISH) per probe	May be used after abnormal breakage results to target specific chromosomal rearrangements or confirm findings.
`88293`	Microarray analysis, genomic; CNA detection by microarray	Often used in parallel or subsequent to cytogenetic assays to identify submicroscopic copy-number changes not detected by standard karyotype.

CPT 88230: Lymphocyte Tissue Culture for Nonneoplastic Disorders

CPT-88233-TISSUE-CULTURE-SKIN-SOLID-TISSUE-NONNEOPLASTIC

CPT 88233: Tissue Culture from Skin or Solid Tissue Biopsy for Nonneoplastic Disorder

CPT-88235-AMNIOTIC-FLUID-CHORIONIC-VILLUS-TISSUE-CULTURE

CPT 88235: Amniotic Fluid or Chorionic Villus Tissue Culture for Chromosome Analysis

CPT-88237-BONE-MARROW-BLOOD-CELL-CULTURE-NEOPLASTIC-DISORDER

CPT 88237: Cell Culture for Bone Marrow or Blood in Neoplastic Disorder

CPT-88239-SOLID-TUMOR-CELL-CULTURE-NEOPLASTIC-DISORDER

CPT 88239: Cell Culture From Solid Tumor for Neoplastic Disorder

CPT-88240-CELL-LINE-CRYOPRESERVATION-STORAGE

CPT 88240: Cryopreservation and Storage of Cell Line

CPT-88241-THAW-AND-EXPAND-FROZEN-CELLS-SINGLE-ALIQUOT

CPT 88241: Thaw and Expand Previously Frozen Cells, Single Aliquot

CPT-88245-CHROMOSOME-ANALYSIS-SISTER-CHROMATID-EXCHANGE-SCE

CPT 88245: Chromosome Analysis for Sister Chromatid Exchange

CPT-88248-CHROMOSOME-ANALYSIS-BREAKAGE-SYNDROME

CPT 88248: Chromosome Analysis for Breakage Syndromes

CPT-88261-CHROMOSOME-ANALYSIS-KARYOTYPE-BANDING

CPT 88261: Chromosome Analysis with Banded Karyotype

Showing 1–10 of 26

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Jul 29, 2026.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.

Published by

Trek Health powers OpenPayer with a leading commercial payer intelligence platform, seamlessly converting fragmented payer data into actionable insights for provider organizations.

Trek Health ingests and normalizes Transparency in Coverage data and payer policy updates to give provider organizations a clear view of how commercial reimbursement behaves across markets, payers, and services. Our platform transforms raw payer disclosures into structured intelligence that supports contract evaluation, payer negotiations, and service line strategy. By combining market benchmarks with ongoing policy visibility, Trek helps teams identify variability, risk, and opportunity in commercial reimbursement. The result is faster insight, stronger negotiating positions, and more informed financial decisions.

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Modifier	Description	When to Use
`26`	Professional component	Use when reporting the professional interpretation/reporting portion separately from the technical laboratory work (if applicable and payer allows split billing).
`TC`	Technical component	Use when reporting only the technical component (laboratory processing, cell culture, scoring) when the performing facility bills separately from the interpreting professional.
`90`	Reference (outside) laboratory	Use when the service was performed by a qualified outside laboratory and billing must indicate an outside reference lab performed the work.
`91`	Data not in provided list	Data not available in the input.
`52`	Reduced services	Use when fewer than the full 100 cells are scored due to inadequate specimen or early termination, and the lab documents the reduction.
`53`	Discontinued procedure	Use when testing is started but discontinued for documented medical or specimen issues before completion of scoring.
`22`	Increased procedural services	Use when work required is substantially greater than typical (extensive troubleshooting, prolonged culture failures) and documentation supports increased effort.
`90`	Duplicate entry to maintain required order	Data not available in the input.
`59`	Distinct procedural service	Use when a separate distinct cytogenetic service is performed the same day that is not bundled (verify payer bundling rules).
`80`	Assistant surgeon (not typically applicable)	Data not applicable for this laboratory procedure.

Taxonomy Code	Specialty	Notes
2080P0200X	Clinical Cytogenetics Laboratory	Laboratory specialists and cytogenetic technologists who perform chromosome analyses.
207RC0000X	Clinical Molecular Genetics	Medical geneticists who may order and interpret cytogenetic breakage assays.
207L00000X	Hematology	Hematologists who evaluate patients with aplastic anemia or marrow failure syndromes and order testing.
2080S0002X	Pediatric Laboratory Medicine	Pediatric specialists and labs performing testing in children with congenital anomalies.
207Q00000X	Medical Genetics	Genetic counselors and medical geneticists involved in result interpretation and family counseling.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`D61.9`	Aplastic anemia, unspecified	Aplastic anemia can be a presenting feature of Fanconi anemia and prompts clastogen breakage testing.
`D61.2`	Constitutional aplastic anemia	Directly associated with inherited bone marrow failure syndromes evaluated by clastogen assays.
`Q87.8`	Other specified congenital malformation syndromes affecting multiple systems	Syndromic congenital anomalies may raise suspicion for chromosomal instability disorders.
`C80.1`	Malignant neoplasm without specification of site, in remission	Early-onset malignancy or unusual cancer history may prompt evaluation for underlying chromosomal breakage syndromes.
`R62.50`	Unspecified lack of expected normal physiological development in childhood	Growth failure can be a feature of inherited breakage syndromes leading to testing.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`88249`	Chromosome analysis for breakage syndrome; lab analyst scores 100 cells for clastogen stress	Primary procedure: scoring 100 cells after clastogen exposure to detect chromosomal breakage syndromes.
`88235`	Chromosome analysis; culture, harvest, and banding (per culture)	Often performed before or alongside breakage testing to provide baseline karyotype and detect constitutional chromosomal abnormalities.
`88240`	Chromosome analysis; at least 20 cells, metaphase	May be used for routine karyotyping when fewer cells are evaluated; not specific for clastogen testing but complements the diagnostic workup.
`88262`	Chromosome analysis, postnatal; fluorescence in situ hybridization (FISH) per probe	May be used after abnormal breakage results to target specific chromosomal rearrangements or confirm findings.
`88293`	Microarray analysis, genomic; CNA detection by microarray	Often used in parallel or subsequent to cytogenetic assays to identify submicroscopic copy-number changes not detected by standard karyotype.

CPT 88230: Lymphocyte Tissue Culture for Nonneoplastic Disorders

CPT-88233-TISSUE-CULTURE-SKIN-SOLID-TISSUE-NONNEOPLASTIC

CPT 88233: Tissue Culture from Skin or Solid Tissue Biopsy for Nonneoplastic Disorder

CPT-88235-AMNIOTIC-FLUID-CHORIONIC-VILLUS-TISSUE-CULTURE

CPT 88235: Amniotic Fluid or Chorionic Villus Tissue Culture for Chromosome Analysis

CPT-88237-BONE-MARROW-BLOOD-CELL-CULTURE-NEOPLASTIC-DISORDER

CPT 88237: Cell Culture for Bone Marrow or Blood in Neoplastic Disorder

CPT-88239-SOLID-TUMOR-CELL-CULTURE-NEOPLASTIC-DISORDER

CPT 88239: Cell Culture From Solid Tumor for Neoplastic Disorder

CPT-88240-CELL-LINE-CRYOPRESERVATION-STORAGE

CPT 88240: Cryopreservation and Storage of Cell Line

CPT-88241-THAW-AND-EXPAND-FROZEN-CELLS-SINGLE-ALIQUOT

CPT 88241: Thaw and Expand Previously Frozen Cells, Single Aliquot

CPT-88245-CHROMOSOME-ANALYSIS-SISTER-CHROMATID-EXCHANGE-SCE

CPT 88245: Chromosome Analysis for Sister Chromatid Exchange

CPT-88248-CHROMOSOME-ANALYSIS-BREAKAGE-SYNDROME

CPT 88248: Chromosome Analysis for Breakage Syndromes

CPT-88261-CHROMOSOME-ANALYSIS-KARYOTYPE-BANDING

CPT 88261: Chromosome Analysis with Banded Karyotype

Showing 1–10 of 26

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Jul 29, 2026.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.

Published by

Trek Health powers OpenPayer with a leading commercial payer intelligence platform, seamlessly converting fragmented payer data into actionable insights for provider organizations.

OpenPayer

CPT 88249: Chromosome Analysis for Breakage Syndrome, 100-Cell Clastogen Stress

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Billing Code Overview

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CPT 88249: Chromosome Analysis for Breakage Syndrome, 100-Cell Clastogen Stress

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Billing Code Overview

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

References

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

References

CPT 88249: Chromosome Analysis for Breakage Syndrome, 100-Cell Clastogen Stress

Sign up for cpt 88249 policy alerts

Billing Code Overview

CPT 88249: Chromosome Analysis for Breakage Syndrome, 100-Cell Clastogen Stress

Sign up for cpt 88249 policy alerts

Billing Code Overview

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

What does CPT 88249 cover and where is the test typically performed?

Which billing modifiers are relevant for reporting CPT 88249?

Who typically orders and performs the clastogen breakage assay and which specialties are listed?

What other cytogenetic or genomic tests are commonly related to or used with 88249?

Which payers are highlighted and does the page provide reimbursement rates or coverage details?

References

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

What does CPT 88249 cover and where is the test typically performed?

Which billing modifiers are relevant for reporting CPT 88249?

Who typically orders and performs the clastogen breakage assay and which specialties are listed?

What other cytogenetic or genomic tests are commonly related to or used with 88249?

Which payers are highlighted and does the page provide reimbursement rates or coverage details?

References