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    v1.0.30
    OpenPayerBilling CodesCytogenetic StudiesCPT cpt-88249-chromosome-analysis-breakage-syndrome-clastogen-stress
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    CPT 88249: Chromosome Analysis for Breakage Syndrome, 100-Cell Clastogen Test

    CPT code 88249 describes a laboratory cytogenetic service performing a chromosome analysis for suspected breakage syndromes, in which the analyst exposes cells to a clastogen (such as diepoxybutane, mitomycin C, ionizing or UV radiation) and scores 100 cells to detect chromosomal breakage; service type: specialized cytogenetic testing; typical site of service: hospital or reference laboratory clinical cytogenetics laboratory.

    For related coverage guidance, see recent payer policy updates: Oral Cancer Screening and Testing, RTM Testing for Alpha-1 Antitrypsin Deficiency, Cytochrome P450 Genotype-Guided Treatment Strategy Corporate Medical Policy.

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    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.

    Related CPT Codes

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

    Related Modifiers

    8 rows

    ModifierDescriptionWhen to Use
    26Modifier 26 (Professional Component) identifies and bills only the professional portion of a split service — the physician’s interpretation, report, and medical judgment — when the technical…- Use CPT Modifier -26 when you are billing only the professional component (PC) of a split‑bill eligible service—i.e., you performed the physician interpretation, medical judgment and prepared a…
    90Modifier ‑90 (Reference/Outside Laboratory) indicates that a laboratory test was performed by an entity other than the treating or reporting provider. The American Medical Association defines…- Use CPT modifier -90 when a laboratory test is performed by an outside/reference laboratory (an entity other than the treating or reporting physician or qualified professional) and the claim needs…
    91Modifier 91 — “Repeat Clinical Diagnostic Laboratory Test” — is appended when the exact same CPT laboratory test is performed more than once for the same patient on the same day because serial,…- Use modifier 91 when the exact same CPT laboratory test is performed more than once on the same patient on the same date because serial or repeated testing is medically necessary to monitor…
    52Modifier ‑52 (Reduced Services) indicates that a service or procedure was partially reduced or omitted at the provider’s discretion, allowing reporting of the basic procedure number with a qualifier…- Use modifier -52 when a physician or qualified health professional electively reduces or omits part of a procedure or service (for example, performing fewer required views or omitting a portion of…
    53Modifier 53 (Discontinued Procedure) signals that a surgical or diagnostic service was begun by the physician but terminated because of extenuating circumstances that threatened the patient’s…- Use modifier -53 when a physician/qualified healthcare professional has started a surgical or diagnostic procedure (e.g., anesthesia administered, incision or scope insertion) and then discontinues…
    22Modifier –22 (Increased Procedural Services) is used when a reported procedure is substantially more extensive than normally required. The CPT Manual and CMS state it may be appended only when the…- When to use: Append modifier -22 to a procedural CPT code when the service performed is substantially more extensive than the usual service described by that code — i.e., the procedure required…
    59Modifier 59 indicates a distinct procedural service when two procedures that are not normally billed together are clinically and procedurally separate. The CPT definition (as reiterated by CMS)…- Use modifier -59 to report a distinct procedural service when documentation supports that the procedure reported is not normally billed together with another service on the same day because of a…
    80CPT® Modifier 80 (Assistant Surgeon) is appended to a surgical CPT code when a physician (MD or DO) provides full, continuous assistance throughout the operative procedure. It is intended only for…- Use CPT Modifier -80 when a physician (MD or DO) serves as an assistant surgeon and provides full, continuous assistance throughout the entire operative procedure; append -80 to the surgical CPT…

    Related Provider Taxonomies

    8 rows

    Taxonomy Code
    207RC0000X
    207L00000X
    207Q00000X
    207ZP0104X
    1223X0008X
    163WU0100X
    133VN1006X
    204E00000X

    Related Payer Policy Updates

    Specialty: Genetic & Molecular Testing1 / 3

    10 rows

    PolicyPayerEffective Date
    Oral Cancer Screening and TestingOscar Health2027-01-01
    RTM Testing for Alpha-1 Antitrypsin DeficiencyOscar Health2027-01-01
    Cytochrome P450 Genotype-Guided Treatment Strategy Corporate Medical Policybcbsvermont2027-01-01
    Carrier Testing Panels for Genetic Diseases (for Kentucky Only)UnitedHealthcare2026-10-01
    Genetic Testing for Neurological Disorders (for Kansas Only)UnitedHealthcare2026-10-01
    Genetic and Molecular TestingProvidence Health Plan2026-10-01
    Cell-Free Fetal DNA Testing (for Idaho Only)UnitedHealthcare2026-10-01
    Next Generation Sequencing for Minimal Residual Disease DetectionProvidence Health Plan2026-10-01
    Pharmacogenetic Panel Testing (for Kansas Only)UnitedHealthcare2026-10-01
    Non-Covered Genetic Panel TestsProvidence Health Plan2026-10-01

    Related Codes

    CPT-88230-LYMPHOCYTE-TISSUE-CULTURE-NONNEOPLASTIC-DISORDER

    CPT 88230: Lymphocyte Culture for Nonneoplastic Disorder

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

    CPT 88233: Tissue Culture for Nonneoplastic Disorders

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

    CPT 88235: Tissue Culture Preparation from Amniotic Fluid or Chorionic Villi

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

    CPT 88237: Cell Culture for Neoplastic Disorders

    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, Karyotype with Banding

    Showing 1–10 of 26

    Frequently Asked Questions

    References

    1. 1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
    2. 2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
    3. 3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.
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