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    v1.0.28
    OpenPayerBilling CodesCytogenetic StudiesCPT cpt-88289-high-resolution-chromosome-analysis-additional-study
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    CPT 88289: High-Resolution Chromosome Analysis

    CPT code 88289 describes an additional high-resolution chromosome study performed by an analyst to detect chromosomal features too small for routine analysis; this service is a specialized cytogenetic analysis typically performed as a laboratory procedure and usually provided in a hospital laboratory or specialized cytogenetics reference lab (high-complexity clinical laboratory).

    For related coverage guidance, see recent payer policy updates: RTM Testing of Homocysteine Metabolism-Related Conditions, Multimarker Serum Testing Related to Ovarian Cancer, Genomic Profiling for Selecting Targeted Cancer Therapies.

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    Table of contents

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    Clinical & Coding Specifications

    Clinical Context

    A patient is referred to a clinical cytogenetics laboratory after an abnormal prenatal screening or a postnatal evaluation for congenital anomalies, developmental delay, or multiple congenital malformations. The ordering clinician (maternal-fetal medicine specialist, neonatologist, pediatric geneticist, or clinical geneticist) requests a high-resolution chromosome study because routine karyotype at standard resolution was nondiagnostic or subtle structural abnormalities are suspected. Typical workflow: specimen collection (amniotic fluid, chorionic villus sample, peripheral blood, or bone marrow) is sent to the cytogenetics lab; cultures are established when required; a routine chromosome analysis is performed first. If routine analysis appears normal but clinical suspicion remains (for example, unexplained multiple congenital anomalies, growth restriction, intellectual disability, or abnormal first-trimester screen), the laboratory analyst performs an additional high-resolution study (88289) to detect smaller banding differences and submicroscopic structural changes not visible on routine analysis. Results are interpreted by the laboratory director or clinical cytogeneticist and reported to the ordering provider, with genetic counseling offered when clinically indicated. Typical site of service: hospital-based cytogenetics laboratory, independent reference cytogenetics laboratory, or academic medical center; specimen collection may occur in outpatient clinic, ambulatory surgery center, inpatient unit, or prenatal diagnostic center. Typical patient scenario: a 28-week fetus with ultrasound-detected cardiac and renal anomalies after normal routine karyotype, or a child with unexplained developmental delay where routine cytogenetics was nondiagnostic and high-resolution analysis is indicated.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    88240Chromosome analysis, constitutional (e.g., karyotype), lymphocyte culture, at least 20 cells - This code represents a routine chromosome analysis often performed first; 88289 is an additional high-resolution study performed when routine karyotype is nondiagnostic or higher resolution is needed.
    88241Chromosome analysis, constitutional, peripheral blood, cell culture; complete karyotype with banding - Alternative routine cytogenetic karyotype codes that may precede a high-resolution study.
    88267Chromosome analysis, prenatal, such as amniocentesis, chorionic villus sampling - Prenatal specimen-specific analysis codes often accompany or precede a high-resolution study in prenatal diagnostic workflows.
    88271Chromosome analysis, resolution study or banding for increased sensitivity - Additional high-resolution or banding enhancement procedures that are related techniques to 88289 and may be used in conjunction.
    89240Cell culture for cytogenetics (e.g., amniotic fluid, chorionic villi) - Laboratory culture services necessary to obtain metaphase spreads for both routine and high-resolution chromosome analyses.

    Related Modifiers

    7 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…
    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…
    62Modifier 62 indicates that two surgeons function as co‑surgeons, each performing distinct parts of the same primary surgical procedure. It is appended to the primary procedure code (and any…- Use modifier -62 when two surgeons act as co‑surgeons (both primary surgeons) on a single definitive primary procedure, each performing distinct parts of the same surgical procedure (append -62 to…
    78CPT modifier -78 indicates an unplanned, related return to the operating or procedure room by the same provider during the global postoperative period. It is appended when treatment for a…- Use modifier -78 when an unplanned, related complication during the original procedure’s global postoperative period requires the patient to return to a formal operating or procedure room and the…
    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…
    82Modifier 82 is appended to a surgical CPT code to indicate that an attending physician acted as an assistant because a qualified resident surgeon was unavailable. In teaching hospitals it documents…- When to use: Append modifier 82 in teaching-hospital settings to indicate a physician served as an assistant surgeon because a qualified resident surgeon was unavailable (includes situations where…
    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…

    Related Provider Taxonomies

    8 rows

    Taxonomy CodeSpecialtyNotes
    207Q00000XFamily Medicine PhysicianFamily Medicine is the medical specialty which is concerned with the total health care of the individual and the family. It is the specialty in breadt…
    208D00000XGeneral Practice PhysicianA physician who specializes in the general practice of diagnosing, treating, and managing patients with a variety of illnesses and conditions.
    207K00000XAllergy & Immunology PhysicianAn allergist-immunologist is trained in evaluation, physical and laboratory diagnosis, and management of disorders involving the immune system. Select…
    207L00000XAnesthesiology PhysicianAn anesthesiologist is trained to provide pain relief and maintenance, or restoration, of a stable condition during and immediately following an opera…
    103TM1800XIntellectual & Developmental Disabilities PsychologistBehavioral Health & Social Service Providers · Psychologist
    273Y00000XRehabilitation Hospital UnitIn general, a distinct unit of a general acute care hospital that provides care encompassing a comprehensive array of restoration services for the dis…
    225CX0006XOrientation and Mobility Training Rehabilitation CounselorOrientation and Mobility (O&M) specialists teach children and adults who have visual impairments the specific orientation skills used to find one's wa…
    275N00000XMedicare Defined Swing Bed Hospital UnitA unit of a hospital that has a Medicare provider agreement and has been granted approval from HCFA to provide post-hospital extended care services an…

    Related ICD-10-CM Codes

    25 rows

    ICD-10-CM CodeDescription
    D82.1Di George's syndrome
    E03.9Hypothyroidism, unspecified
    F80.9Developmental disorder of speech and language, unspecified
    F84.0Autistic disorder
    I82.409Acute embolism and thrombosis of unspecified deep veins of unspecified lower extremity
    N97.9Female infertility, unspecified
    O09.811Supervision of pregnancy resulting from assisted reproductive technology, first trimester
    Q45.3Other congenital malformations of pancreas and pancreatic duct
    Q87.89Other specified congenital malformation syndromes, not elsewhere classified
    Q89.3Situs inversus

    Showing 1–10 of 25

    Related Payer Policy Updates

    Specialty: Genetic & Molecular Testing1 / 3

    10 rows

    PolicyPayerEffective Date
    RTM Testing of Homocysteine Metabolism-Related ConditionsOscar Health2026-10-01
    Multimarker Serum Testing Related to Ovarian CancerBlue Cross Blue Shield - Rhode Island2026-09-01
    Genomic Profiling for Selecting Targeted Cancer TherapiesBlue Cross Blue Shield - Rhode Island2026-09-01
    Whole Exome and Whole Genome Sequencing for Diagnosis of Genetic DisordersBlue Cross Blue Shield - Rhode Island2026-09-01
    Biomarker and Genetic/Molecular Testing Coverage and Prior AuthorizationBlue Cross Blue Shield - Rhode Island2026-09-01
    Non-Invasive Prenatal Testing (NIPT)univerahealthcare2026-08-17
    Lumizyme (alglucosidase alfa) — Pompe Disease (acid alpha‑glucosidase deficiency)Cigna2026-08-15
    Molecular Oncology Testing for Solid Tumor Cancer Diagnosis, Prognosis, and Treatment DecisionsColorado Rocky Mountain Health Plans2026-08-01
    Carrier Testing Panels for Genetic DiseasesColorado Rocky Mountain Health Plans2026-08-01
    Molecular Oncology Testing for Hematologic Cancer Diagnosis, Prognosis, and Treatment DecisionsColorado Rocky Mountain Health Plans2026-08-01

    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-88249-CHROMOSOME-ANALYSIS-BREAKAGE-SYNDROME-CLASTOGEN-STRESS

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

    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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    89250Chromosome preparation, harvesting and slide preparation - Technical laboratory preparation codes that support both routine and high-resolution chromosome studies