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    OpenPayerPolicy UpdatesReimbursement/Payment Policyelderplan NYS Medicaid lab coverage update | OpenP…
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    CurrentelderplanPolicy N/A

    Fee-for-service laboratory procedure codes and coverage guidelines manual (NYS Medicaid FFS) — selected excerpt

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    Governs reimbursement rules, coding and coverage criteria for clinical laboratory tests under the New York State Medicaid fee-for-service laboratory fee schedule; affects laboratories and ordering providers billing NYS Medicaid. This brief covers material in the first part of the manual.

    Policy Summary
    Payerelderplan
    PolicyFee-for-service laboratory procedure codes and coverage guidelines manual (NYS Medicaid FFS) — selected excerpt
    Policy CodePolicy N/A
    Change TypeNo material changes
    Effective DateAug 1, 2021
    Next Review DateN/A
    Key ActionOrder confirmatory quantitative testing for any positive or inconclusive presumptive drug screen and document a specific presumptive diagnosis in the medical record.
    SourceLink
    POLICY UPDATE CHANGES

    No material clinical or coverage changes in this revision.

    CPT/HCPCS 2016Coding edition
    WES codesWES coverage
    Not coveredWGS stance
    12In-home phlebotomy limit
    $675.2987903 reimbursement

    Coverage Criteria and Policy Rules

    Laboratory coverage and billing criteria

    Genetic testing coverage and billing highlights — covered with specific clinical criteria or billing requirements:

    ALL of the following

    • Clinical presentation and history suggest a genetic etiology
    • Presentation does not fit a well-defined syndrome
    • Presentation cannot be attributed to an environmental exposure, injury, infection, or other non-genetic etiology
    • Prior targeted genetic testing failed to yield a diagnosis
    • No additional genetic tests are being ordered concurrently
    Policy Summary
    Payerelderplan
    PolicyFee-for-service laboratory procedure codes and coverage guidelines manual (NYS Medicaid FFS) — selected excerpt
    Policy CodePolicy N/A
    Change TypeNo material changes
    Effective DateAug 1, 2021
    Next Review DateN/A
    Key ActionOrder confirmatory quantitative testing for any positive or inconclusive presumptive drug screen and document a specific presumptive diagnosis in the medical record.
    SourceLink
    On This Page
    Coverage Criteria and Policy RulesCodes, Groups and Reimbursement LimitsProvider Billing Actions and Documentation RequirementsTerminology and Definitions
  1. Test ordered by a physician specializing in clinical genetics or with extensive experience evaluating suspected genetic syndromes
  2. Testing is expected to inform management decisions and/or avoid additional diagnostic tests

    3. ALL of the following

    • WES is covered once in a lifetime for members ≤18 years

    • Exception considered for

      • Members 19 years and older may be considered if they meet the above criteria and would have benefited if testing were available when younger
      • WES for fetal screening or diagnosis is not covered
    Whole genome sequencing (WGS) is not covered by NYS Medicaid.

    ALL of the following

    • Applicable indications include

      • Patients with Huntington's disease requiring tetrabenazine (Xenazine®) >50 mg/day
      • Patients with Gaucher disease type 1 to determine eliglustat (Cerdelga®) eligibility
    Other pharmacogenetic testing: CYP2D6 testing for purposes other than those specified above is not reimbursable.

    ALL of the following

    • Presumptive screening (80305-80307) positives or inconclusive results require confirmatory quantitative testing (80321-80377) to be reimbursable
    • Definitive confirmation (G0480) is allowed only when no screening test exists
    • Tests must be ordered by a provider; broad panels, reflex tests initiated solely by the laboratory, and routine standing orders are not reimbursable
    • Medical record documentation supporting follow-up testing is required

    ALL of the following

    • Procedures billed 'By Report' must include documentation on the claim of need for service, test performed, results, specimen number and source, and the laboratory's usual and customary charge

    ALL of the following

    • When two or more organ/disease-oriented panel codes with overlapping tests are billed, duplicate reimbursement is not allowed and tiered maximum fees for combined chemistry tests apply

    Tumor markers

    Tumor marker and oncofetal antigen testing reimbursement rules:

    Tumor marker tests (examples include CPT 82105, 82106, 82378, 83950, 83951, 84066, 84153, 84154, 84702, 86316) are reimbursable when used as adjunctive tests in monitoring for tumor recurrence after irradiation or surgical removal.
    CPT 82105 and 82106 are reimbursable for alpha-fetoprotein when used for prenatal (non-diagnostic), gestational age–dependent screening for neural tube defects.
    CPT 86316 (immunoassay for a tumor antigen not elsewhere specified) is billable 'By Report'.
    Tumor marker tests are reimbursable for diagnostic purposes only when used in accordance with the FDA approval criteria for their intended diagnostic use.
    When CPT 84153 is billed with 84152 or 84154 in combination, the maximum fee for 84152 or 84154 is $21.35. When CPT 82378 is performed with Comprehensive Metabolic Panel (80053), the maximum reimbursable fee for 82378 is $8.00.

    Indication-based coverage

    Clinical indication requirements for select tests:

    Follow-up testing claims must be supported by a specific (presumptive) diagnosis provided by the ordering practitioner that considers initial test results, patient history, and symptoms.
    CPT 82172 is reimbursable for diagnostic purposes when the patient has documented total cholesterol >240 mg/dL and HDL <35 mg/dL and/or a documented family history of coronary artery disease; apolipoprotein tests are not reimbursable for CAD screening.
    Thyroid function tests (other than defined 'screen' tests) are reimbursable only when indicated for differential diagnosis, to resolve discordant or equivocal results, or to monitor therapy. 'Screen' tests are total thyroxine (84436) or free thyroxine index (84436 + 84479) or sensitive TSH (84443).
    Serologic markers for viral hepatitis B are reimbursable only when initial diagnostic testing determines the patient has type B hepatitis.
    CPT 86341 (islet cell antibody) is reimbursable to differentiate type I from type II diabetes in patients with equivocal presentation; it is not reimbursable as predictive screening in asymptomatic first-degree relatives.
    CPT 87536 (HIV-1 quantitation) is reimbursable when used to predict clinical outcomes, disease progression risk, or to inform antiretroviral therapy decisions; allowed up to six times per year when clinically indicated.

    Lymphocyte panels

    Lymphocyte immunophenotyping coverage and billing rules:

    Lymphocyte immunophenotyping is reimbursable for analysis of subpopulations to monitor disease activity and therapeutic response; only FDA-cleared/Department-approved antibodies/markers are reimbursable.

    Billing unit rules

    • Bill 1 unit of 86360 for an 'abbreviated lymphocyte' panel that reports absolute CD4 with CD8 counts.
    • Bill 2 units of 86360 for a 'full lymphocyte' panel reporting absolute CD4 with CD8 counts.
    • Bill 1 unit of 86361 when non-flow methods report CD4 counts (86360 and 86361 may not be billed the same date of service).
    When multiple-marker flow cytometry is performed (e.g., lymphoma/leukemia testing), bill 1 unit of codes such as 86355/86357/86359/86367/88184 and, when appropriate, 88185; bill interpretation code (88187–88189) based on total number of markers performed. When CD4/CD8 analysis is included with multi-marker testing, bill 1 unit of 86360 in addition; when CD4 only is included, bill 1 unit of 86361 in addition.

    HIV resistance testing

    HIV resistance testing coverage and payment limits:

    HIV genotypic/phenotypic drug resistance testing and phenotypic prediction using genotypic comparison to databases is covered when clinically indicated.
    Medicaid reimburses each test (87900, 87901, 87903, 87904, 87906) up to a maximum of 3 times in a 365-day period across all providers; any combination of 87901 and 87903 is reimbursable up to 4 times in 365 days across all providers.
    CPT 87903 reimburses $675.29 for resistance determinations of up to 10 antiviral drugs. CPT 87904 should be billed in addition to 87903 to claim reimbursement for each additional drug (one unit per additional drug).
    When CPT 87901, 87903 and 87906 are billed together on the same date, the maximum reimbursable fee for the combination is $100 less than the additive maximum fees for the codes.

    In-home phlebotomy travel reimbursement

    In-home phlebotomy travel reimbursement and billing examples:

    Eligibility and billing: Travel expenses for in-home phlebotomy are reimbursable using code P9604 when the recipient is homebound and participating in a Medicaid-covered home care program or receiving a Medicaid-covered home care service; eligibility must be documented by the ordering practitioner.
    Non-covered travel: Travel is NOT covered when blood draws occur in a skilled nursing facility, when another professional provides blood draws in the residence, or when specimens are picked up/transported by non-laboratory personnel.
    Reimbursement limits and prorating: The laboratory is entitled to one fee for one-way or round-trip travel to a single address regardless of specimens or recipients drawn. There is a limit of 12 claims per recipient per year. Laboratories must document number of specimens collected per trip and prorate reimbursement across recipient claims.

    Billing examples

    • One recipient round-trip: submit single-line claim for $18.70 (2 x $9.35).
    • Circuit of multiple one-way stops (six recipients): total $65.45 divided by six → $10.91 per recipient.
    • Multiple recipients at single address (six recipients): one round-trip $18.70 divided by six → $3.12 per recipient.
    • Mixed multi-stop example: total stops $46.75 divided by six → $7.79 per recipient (detailed in manual).

    Panels and therapeutic drug monitoring

    Panel definitions and therapeutic drug assay coverage:

    Organ/disease-oriented panel codes (e.g., 80047, 80048, 80051, 80053, 80061, 80069, 80076) require the specified component tests listed for reimbursement.
    Quantitative therapeutic drug monitoring is reimbursable only when performed on blood specimens as outlined; numerous specific therapeutic drug assay CPT codes are listed (examples: 80145 adalimumab; 80150 amikacin; 80156/80157 carbamazepine total/free; 80178 lithium; 80204 methotrexate; 80299 quantitation not elsewhere specified).
    Use CPT 80299 for quantitation of a therapeutic drug not otherwise specified.

    Drug testing

    Definitive and presumptive drug testing coverage:

    Presumptive drug testing codes (80305, 80306) and definitive testing code (80307) are defined and reimbursable as described; presumptive screens that are positive/inconclusive require confirmatory quantitative testing to be reimbursable.
    Enumerated definitive test family codes (80323–80367 series) specify substance family and marker counts; definitive confirmation (80321–80377) or G0480 when no screening exists must be ordered by a provider and supported by the medical record. Broad reflex panels or laboratory-initiated reflex testing are not reimbursable.

    Evocative/Suppression testing reimbursement

    Reimbursement rules for evocative/suppression testing and handling of costs for provocative agents:

    Costs of evocative or suppressive agents are not included in the test fee, except oral glucose for codes 80430 and 82950–82953.
    When multiple evocative or suppressive tests are performed in combination, reimbursement is limited to the greater fee plus 50% of the lesser fee(s).

    Single-gene analysis mappings

    Code-to-gene mappings (informational):

    ATN/ATXN single-gene analyses (examples)

    • CPT 81177 — ATN1 gene analysis (detect abnormal/expanded alleles)
    • CPT 81178 — ATXN1 gene analysis (detect abnormal/expanded alleles)
    • CPT 81179 — ATXN2 gene analysis (detect abnormal/expanded alleles)
    • CPT 81180 — ATXN3 gene analysis (detect abnormal/expanded alleles)
    • CPT 81181 — ATXN7 gene analysis (detect abnormal/expanded alleles)
    • CPT 81182 — ATXN8OS gene analysis (detect abnormal/expanded alleles)
    • CPT 81183 — ATXN10 gene analysis (detect abnormal/expanded alleles)
    CPT 81205 — BCKDHB gene analysis (common variants e.g., R183P, G278S, E422X) — example mapping present in list.

    Coding list without explicit coverage rules

    This section enumerates procedure codes paired with gene analyses; no explicit coverage criteria are provided in these excerpts:

    Document lists multiple CPT codes (e.g., 81178–81183, 81205–81209, and others) paired with gene/test descriptors; these entries are informational code mappings without explicit medical necessity criteria in the excerpt.

    Coding listing (no coverage rules in excerpt)

    Billable CPT codes and brief test descriptors — informational only (no coverage rules in this excerpt):

    Section lists CPT codes with brief descriptors (e.g., ATXN3/ATXN7/ATXN8OS/ATXN10, BCKDHB, BCR/ABL1) for billing reference; no prior authorization or explicit medical necessity criteria appear in this fragment.

    Genetic test code list (partial)

    Genetic test code list (partial) — informational mapping of codes to gene targets:

    Examples in the list include CPT 81205 (BCKDHB), 81206–81208 (BCR/ABL1 breakpoints), 81209 (BLM), 81210 (BRAF V600), and CPT 81162 (BRCA1/BRCA2) — descriptors present but coverage/medical necessity not specified in these chunks.

    Codes, Groups and Reimbursement Limits

    By Report billingmixed
    By Report (BR)Procedures billed By Report require documentation of need, test type, results, specimen number/source and lab usual charge on claim
    Genetic testing codesCPT
    81415, 81417Whole exome sequencing (WES)
    81400-81408, 81479Molecular pathology / DNA-based genetic testing (general guidance)
    81162, 81163, 81164, 81165, 81166, 81167, 81212, 81215-81217BRCA testing codes
    Selected tumor marker and related codesCPTCovered
    82105Oncofetal antigen (tumor marker) procedure; reimbursable as adjunctive test and for AFP prenatal screening
    82106Oncofetal antigen (tumor marker); AFP prenatal screening
    82378CEA carcinoembryonic antigen; when combined with comprehensive metabolic panel max fee $8.00
    84153Pregnancy or tumor marker related code (paired fee rules with 84152/84154)
    84154Pregnancy or tumor marker related code (paired fee rules with 84152/84153)
    86316Immunoassay for tumor antigen not elsewhere specified; billable By Report
    Lymphocyte immunophenotyping codes and billing rulesCPTCovered
    86360Flow cytometry lymphocyte analysis (billing units differ for abbreviated vs full panel)
    86361Lymphocyte subpopulation counts by non-flow methods (CD4 counts)
    86355Flow cytometric testing using multiple markers (example code for marker billing)
    88184Unlisted marker testing / markers used to gate/set cursors
    88185Unlisted marker testing, when appropriate
    88187Interpretation code; bill 1 unit based on total number of markers performed
    HIV resistance testing codes and limitsCPTCovered
    87900HIV resistance/genotypic testing (covered when clinically indicated; reimbursement limits apply)
    87901HIV resistance/genotypic testing (combined reimbursement limits described)
    87903Resistance determinations up to 10 antiviral drugs; reimburses $675.29
    87904Additional drug resistance determinations billed in addition to 87903, one unit per additional drug
    87906HIV resistance testing code; combination billing reimbursement adjustments apply
    Drug testing codes (presumptive and definitive)CPTCovered
    80305Presumptive drug test(s), any number of classes, direct optical observation immunoassay; includes sample validation
    80306Presumptive drug test(s) read by instrument-assisted direct optical observation; includes sample validation
    80307Definitive drug testing by instrument chemistry analyzers, chromatography, mass spectrometry; includes sample validation
    Common laboratory panels and component requirementsCPT
    80053Comprehensive metabolic panel (listed panel components)
    80047Organ or disease oriented panels
    80076Hepatic function panel (listed components)
    80051Electrolyte panel (listed components)
    80061Lipid panel (listed components)
    Definitive drug testing codesCPTCovered
    80305Drug test(s), presumptive, any number of drug classes; direct optical observation; includes sample validation when performed
    80306Read by instrument assisted direct optical observation; includes sample validation when performed
    80307By instrument chemistry analyzers, chromatography, mass spectrometry; includes sample validation when performed
    80320Alcohols
    Urinalysis codesCPTCovered
    81000Urinalysis by dip stick or tablet reagent with microscopy
    81001Automated urinalysis with microscopy
    81002Non-automated urinalysis without microscopy
    81003Automated urinalysis without microscopy
    81007Bacteriuria screen, except by culture or dipstick
    81015Microscopic only
    81025Urine pregnancy test, by visual color comparison
    Molecular pathology codes (excerpt)CPTCovered
    0211UOncology (pan-tumor), DNA and RNA by next-generation sequencing, FFPE tissue, interpretative report including SNVs, CNAs, TMB, MSI, with therapy association
    81170ABL1 gene analysis, variants in kinase domain
    81171AFF2 (FRAXE) gene analysis, evaluation to detect abnormal/expanded alleles
    81201APC gene analysis; full gene sequence
    ATN/ATXN single-gene analysis codesCPTCovered
    81177ATN1 (atrophin 1) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81178ATXN1 (ataxin 1) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81179ATXN2 (ataxin 2) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81180ATXN3 (ataxin 3) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81181ATXN7 (ataxin 7) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81182ATXN8OS (ATXN8 opposite strand [non-protein coding]) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81183ATXN10 (ataxin 10) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    Listed genetic test procedure codesCPTCovered
    81178ATXN1 (ataxin 1) detect abnormal (e.g., expanded) alleles
    81179ATXN2 (ataxin 2) detect abnormal (e.g., expanded) alleles
    81180ATXN3 (ataxin 3) detect abnormal (e.g., expanded) alleles
    81181ATXN7 (ataxin 7) detect abnormal (e.g., expanded) alleles
    81182ATXN8OS (ATXN8 opposite strand [non-protein coding]) detect abnormal (e.g., expanded) alleles
    81183ATXN10 (ataxin 10) detect abnormal (e.g., expanded) alleles
    81205BCKDHB gene analysis, common variants (e.g., R183P, G278S, E422X)
    81206BCR/ABL1 (t(9;22)) translocation analysis; major
    Genetic test CPT codes listedCPTCovered
    81179ATXN2 (ataxin 2) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81180ATXN3 (ataxin 3) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81181ATXN7 (ataxin 7) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81182ATXN8OS (ATXN8 opposite strand [non-protein coding]) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81183ATXN10 (ataxin 10) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81205BCKDHB gene analysis, common variants (e.g., R183P, G278S, E422X)
    81206BCR/ABL1 translocation analysis; major breakpoint, qualitative or quantitative
    81207BCR/ABL1 translocation analysis; minor breakpoint, qualitative or quantitative
    Genetic test CPT codesCPTCovered
    81180ATXN3 gene analysis — evaluation to detect abnormal (expanded) alleles
    81181ATXN7 gene analysis — evaluation to detect abnormal (expanded) alleles
    81182ATXN8OS gene analysis — evaluation to detect abnormal (expanded) alleles
    81183ATXN10 gene analysis — evaluation to detect abnormal (expanded) alleles
    81205BCKDHB gene analysis — common variants (e.g., R183P, G278S, E422X)
    81206BCR/ABL1 translocation analysis; major breakpoint, qualitative or quantitative
    81207BCR/ABL1 translocation analysis; minor breakpoint, qualitative or quantitative
    81208BCR/ABL1 translocation analysis; other breakpoint, qualitative or quantitative
    81209BLM gene analysis (Bloom syndrome) — gene analysis descriptor present
    Genetic/molecular procedure codesCPT
    81180ATXN3 gene analysis; expanded alleles (spinocerebellar ataxia, Machado-Joseph disease)
    81181ATXN7 gene analysis; expanded alleles (spinocerebellar ataxia)
    81182ATXN8OS gene analysis; expanded alleles (ATXN8 opposite strand)
    81183ATXN10 gene analysis; expanded alleles (spinocerebellar ataxia)
    81205BCKDHB gene analysis; common variants (e.g., R183P, G278S, E422X)
    81206BCR/ABL1 translocation analysis; major breakpoint
    81207BCR/ABL1 translocation analysis; minor breakpoint
    81208BCR/ABL1 translocation analysis; other breakpoint
    81209BLM gene analysis; Bloom syndrome; specific variant 2281del6ins7 referenced
    Genetic/molecular CPT codes in sectionCPTCovered
    81181ATXN7 gene analysis, evaluation to detect abnormal (expanded) alleles
    81182ATXN8OS gene analysis, evaluation to detect abnormal (expanded) alleles
    81183ATXN10 gene analysis, evaluation to detect abnormal (expanded) alleles
    81205BCKDHB gene analysis, common variants (e.g., R183P, G278S, E422X)
    81206BCR/ABL1 (t(9;22)) translocation analysis; major breakpoint, qualitative or quantitative
    81207BCR/ABL1 minor breakpoint, qualitative or quantitative
    81208BCR/ABL1 other breakpoint, qualitative or quantitative
    81209BLM gene analysis, 2281del6ins7 variant
    81210BRAF gene analysis, V600 variant(s)
    Molecular/genetic CPT codes in excerptCPTCovered
    81181ATXN7 gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81182ATXN8OS gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81183ATXN10 gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81162BRCA1/BRCA2 gene analysis (BRCA1, BRCA2), detect abnormal alleles
    81205BCKDHB gene analysis, common variants (e.g., R183P, G278S, E422X)
    81206BCR/ABL1 translocation analysis (t(9;22)); major/minor/other breakpoints
    81207BCR/ABL1 minor breakpoint analysis
    81208BCR/ABL1 other breakpoint analysis
    81209BCR/ABL1 other translocation analysis
    81210BLM gene analysis 2281del6ins7 variant / BRAF gene analysis V600 variant(s) referenced
    Genetic procedure codesCPT
    81205BCKDHB gene analysis, common variants (e.g., R183P, G278S, E422X)
    81206BCR/ABL1 (t(9;22)) translocation analysis; major breakpoint, qualitative or quantitative
    81207BCR/ABL1 minor breakpoint, qualitative or quantitative
    81208BCR/ABL1 other breakpoint, qualitative or quantitative
    81209BLM gene analysis, 2281del6ins7 variant
    81210BRAF gene analysis, V600 variant(s)
    81182ATXN8OS gene analysis, evaluation to detect abnormal (expanded) alleles
    81183ATXN10 gene analysis, evaluation to detect abnormal (expanded) alleles
    81162BRCA1, BRCA2 (DNA repair associated)
    listed_genetic_CPT_codesCPT
    81162BRCA1/BRCA2 (BRCA1, BRCA2) gene analysis; referenced in list
    81182ATXN8OS gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81183ATXN10 (ataxin 10) gene analysis, evaluation to detect abnormal (e.g., expanded) alleles
    81205BCKDHB gene analysis, common variants
    81206BCR/ABL1 translocation analysis; major breakpoint
    81207BCR/ABL1 translocation analysis; minor breakpoint
    81208BCR/ABL1 translocation analysis; other breakpoint
    81209BLM gene analysis, 2281del6ins7 variant
    81210BRAF gene analysis, V600 variant(s)
    Genetic/molecular test CPT codes in excerptCPTCovered
    81162BRCA1/BRCA2 gene analysis; full sequence analysis and/or duplication/deletion analysis (large rearrangements) referenced throughout chunks
    81182ATXN8OS gene analysis, evaluation to detect abnormal (expanded) alleles
    81183ATXN10 gene analysis, evaluation to detect abnormal (expanded) alleles
    81205BCKDHB gene analysis, common variants (e.g., R183P, G278S, E422X)
    81206BCR/ABL1 translocation analysis; major breakpoint, qualitative or quantitative
    81207BCR/ABL1 translocation analysis; minor breakpoint, qualitative or quantitative
    81208BCR/ABL1 translocation analysis; other breakpoint, qualitative or quantitative
    81209BLM gene analysis, 2281del6ins7 variant
    81210BRAF gene analysis, V600 variant(s)
    molecular_genetic_codesCPTCovered
    81162BRAF V600 variant(s) gene analysis
    81163BRCA1/BRCA2 full sequence analysis / full duplication-deletion analysis
    81183Evaluation to detect abnormal (expanded) alleles (e.g., trinucleotide repeat)
    81205ATXN10 gene analysis, evaluation to detect expanded alleles
    81206BCKDHB gene analysis, common variants
    81207BCR/ABL1 translocation analysis; major breakpoint
    81208BCR/ABL1 translocation analysis; minor breakpoint
    81209BCR/ABL1 translocation analysis; other breakpoint
    81210BLM gene analysis, 2281del6ins7 variant
    Genetic/molecular pathology CPT codes (examples)CPTCovered
    81162BRAF V600 variant(s) gene analysis
    81163BRCA1/BRCA2 full sequence analysis
    81164BRCA1/BRCA2 full duplication/deletion analysis
    81183ATXN10 evaluation for expanded alleles
    81205ATXN10 / BCKDHB common variants (appears repeated)
    81206BCR/ABL1 translocation analysis (major breakpoint)
    81207BCR/ABL1 translocation analysis (minor breakpoint)
    81208BCR/ABL1 translocation analysis (other breakpoint)
    81209BLM 2281del6ins7 variant analysis
    81210BRAF gene analysis V600 variant(s)
    Maximum reimbursable fee tiers for overlapping chemistry tests
    Maximum reimbursable fee tiers for overlapping chemistry testsUp to 2 = $5.03; 3–6 = $6.04; 7–9 = $7.25; 10–12 = $9.09; 13–16 = $10.00; 17–18 = $11.00; 19+ = $12.00
    Applies when panel codes with overlapping component tests are billedRule triggered when 2 or more panel codes (e.g., 80047, 80048, 80051, 80053, 80076) with overlapping chemistry tests are billed together
    Effective linkage to panel billingLimits apply to combined chemistry test payments regardless of whether tests were ordered individually or as panels
    HIV resistance testing frequency per 365 days
    Maximum reimbursable frequency (365 days)Each HIV resistance test (87900, 87901, 87903, 87904, 87906) reimbursable up to 3 times in a 365-day period across all providers
    Combination exceptionAny combination of codes 87901 and 87903 reimbursable up to 4 times in a 365-day period across all providers
    Fee note for 87903Code 87903 reimburses for resistance determinations of up to 10 antiviral drugs (see separate fee amount)
    HIV-1 quantitation (87536) annual maximum
    Annual maximum usesHIV-1 quantitation (CPT 87536) reimbursable up to 6 times per year when clinically indicated
    Clinical purposeAllowed when used to predict clinical outcomes, disease progression risk, or to inform antiretroviral therapy decisions
    ConditionReimbursement contingent on clinical indication and appropriate documentation

    Provider Billing Actions and Documentation Requirements

    Prior Authorization

    Two-step drug testing: order screening then confirm positives for confirmation

    NYS Medicaid requires a two-step drug testing workflow: presumptive screening using CPT codes 80305–80307 followed by confirmatory quantitative testing (CPT 80321–80377) only for specimens with positive, inconclusive, or clinically inconsistent screening results; definitive direct confirmation (G0480) is reimbursable only when no screening method exists. All tests must be ordered by the provider; broad panels, reflex tests initiated by the laboratory, and routine standing orders are not reimbursable. Medical record documentation must support the medical necessity for each drug or drug class tested and be retained for audit purposes.

    • Presumptive screening: CPT 80305, 80306, 80307.
    • Confirmatory quantitative testing: CPT 80321–80377 (only for positive/inconclusive screens or inconsistent clinical presentation).
    • Direct confirmation: G0480 only when no screening exists.
    • Provider must order tests; lab-initiated reflex/broad panels/standing orders not reimbursable.
    • Maintain supporting medical record documentation for each tested drug/class.
    Documentation Required

    Provide a presumptive diagnosis to support follow-up testing

    For follow-up or confirmatory testing claims the ordering practitioner must provide a specific (presumptive) diagnosis or reason for the encounter that takes into account initial test results, patient history and symptoms; this diagnosis must be supplied to the laboratory and documented in the medical record to support reimbursement.

    • Ordering practitioner must report a presumptive diagnosis or reason for encounter to the laboratory.
    • Documentation should reflect initial test results, history and symptoms to justify follow-up testing.
    Billing Rule

    Bill in‑home phlebotomy travel via P9604 and follow pro‑rating and limits

    Travel expenses for in-home phlebotomy are billable using code P9604 when the recipient is homebound and participating in or receiving a Medicaid-covered home care program; labs may bill one travel fee per one-way or round-trip to a single address and must document specimens collected, prorate payment across recipients when applicable, and observe the annual claim limit.

    • Eligibility: recipient must be homebound and participating in a Medicaid-covered home care program (chunk 23).
    • One travel fee per one-way or round-trip to a single address regardless of number of specimens; pro-rate reimbursement across recipient claims and document number of specimens per trip (chunk 24).
    • Limit of 12 claims per recipient per year; billing examples and pro-ration methods provided (chunk 25).
    • Bill travel using code P9604.
    Billing Rule

    Combined evocative/suppression tests: limited reimbursement and agent cost exclusion

    When multiple evocative or suppressive tests are performed in combination, reimbursement is limited to the greater fee plus 50% of the lesser fee(s); the cost of evocative/suppressive agents is not included in the test fee except for oral glucose with codes 80430 and 82950–82953.

    • Reimbursement for combined evocative/suppression tests = greater fee + 50% of lesser fee(s).
    • Costs of provocative agents are excluded from the fee except oral glucose for codes 80430 and 82950–82953.
    Documentation Required

    Map CPT 81177–81183 to ATN/ATXN single‑gene expanded‑allele analyses

    CPT codes 81177–81183 correspond to single‑gene analyses in the ATN/ATXN series (ATN1, ATXN1, ATXN2, ATXN3, ATXN7, ATXN8OS, ATXN10) for evaluation to detect abnormal (expanded) alleles; providers should map ordered CPTs to the specific gene analysis when submitting claims.

    • 81177–81183 mapped to ATN/ATXN gene analyses for expanded‑allele detection (ATN1, ATXN1–ATXN10).
    • Purpose: evaluation to detect abnormal (e.g., expanded) alleles (trinucleotide repeat/expanded allele testing).
    Billing Rule

    Use listed CPT codes with their gene/test descriptors when billing genetic procedures

    The policy lists CPT procedure codes paired with gene/test descriptors for billing (examples include ATXN series codes 81178–81183 and gene tests such as 81205 BCKDHB and 81206–81209 BCR/ABL1 breakpoints); providers must use the appropriate CPT for the specific gene/test ordered.

    • Examples: 81178–81183 (ATXN1–ATXN10 expanded allele testing); 81205 (BCKDHB common variants); 81206–81208 (BCR/ABL1 translocation analyses); 81209 (BLM).
    • Providers should select the CPT that matches the gene/test performed when billing.
    Note

    Refer to the enumerated CPT code list for molecular/genetic tests (no prior‑auth instructions in excerpt)

    The document enumerates numerous CPT codes and brief test descriptors for molecular/genetic analyses (for example, ranges including 81179–81207); this excerpt provides code names and descriptors but does not impose additional prior authorization or step‑therapy instructions—providers should bill using the listed CPTs for the specific tests ordered.

    • Code examples present across the section include 81179–81207 and many others for specific gene analyses.
    • No explicit prior authorization or utilization management instructions appear in these code‑listing excerpts; follow standard ordering/documentation rules elsewhere in the policy.
    Billing Rule

    Bill using the CPT that matches the molecular/genetic assay performed (examples listed)

    The policy lists CPT procedure codes for gene analysis including expanded‑allele detection and translocation/breakpoint analyses (examples: 81180–81183 for ATXN3–ATXN10 expanded‑allele testing; 81205 BCKDHB common variant analysis; 81206–81208 BCR/ABL1 breakpoint analyses). Use the exact CPT corresponding to the performed molecular/genetic assay when submitting claims.

    • 81180–81183: ATXN3, ATXN7, ATXN8OS, ATXN10 — expanded allele detection.
    • 81205: BCKDHB common variant analysis (examples R183P, G278S, E422X).
    • 81206–81208: BCR/ABL1 translocation analyses (major, minor, other breakpoints).
    • 81209: BLM gene analysis (Bloom syndrome) with variant references (e.g., 2281del6ins7).
    Billing Rule

    Use the CPT/PLA procedure codes shown in the policy when reporting genetic tests

    The policy repeatedly provides CPT/PLA code listings and short descriptors for molecular/genetic procedures (e.g., 81180–81183, 81205–81210). Providers must reference and use these precise procedure codes and descriptors when reporting genetic testing services.

    • Repeated listing examples: 81180–81183 (ATXN series), 81205–81210 (BCKDHB, BCR/ABL1, BLM, BRAF, etc.).
    • Ensure claims reflect the specific CPT/PLA code that corresponds to the performed test.
    Billing Rule

    Align procedure code and descriptor when billing molecular/genetic tests

    Procedure code listings in the policy include CPT/PLA codes and short descriptors for molecular/genetic tests (for example, 81181–81183 and 81205–81210); providers should ensure test descriptors and CPTs align on the claim to avoid billing errors.

    • Examples shown: ATXN7–ATXN10 (81181–81183), BCKDHB (81205), BCR/ABL1 breakpoints (81206–81208), BLM (81209), BRAF V600 (81210).
    • Align test performed with CPT descriptor on the claim.
    Billing Rule

    Refer to the policy code list for genetic tests and bill the exact CPT for the gene analysis

    The policy provides a comprehensive code list for genetic tests (e.g., 81181–81210 and related entries) including gene/test descriptors used for billing; providers must select and bill the specific CPT that corresponds to the gene analysis performed.

    • Code list examples: ATXN series, BCKDHB, BCR/ABL1, BLM, BRAF, BRCA1/BRCA2 entries across chunks.
    • No special prior authorization instructions appear in these excerpts—follow clinical documentation and billing rules elsewhere in the policy.
    Billing Rule

    Use the excerpted CPT/HCPCS genetic codes (e.g., BCKDHB, BCR/ABL1, BRAF, BRCA) when billing

    Excerpted genetic test codes include CPT/HCPCS entries and brief descriptors such as 81205 (BCKDHB), 81206 (BCR/ABL1 major breakpoint), 81210 (BRAF V600), and BRCA testing codes (81162/81163); providers should use the specific CPT listed for each gene/test when submitting claims.

    • Examples in excerpt: 81205 BCKDHB; 81206–81208 BCR/ABL1 breakpoints; 81210 BRAF V600; 81162/81163 BRCA1/BRCA2 full sequence/duplication analysis.
    • Select the CPT code that matches the exact genetic assay performed.
    Billing Rule

    Confirm and bill the specific CPT for each genetic test listed (multiple examples provided)

    Multiple sections list genetic test CPT codes (e.g., 81206–81209, 81210, 81162, 81182, 81183, 81205); providers must ensure claims reference the proper CPT code for the specified gene/test and include required clinical documentation per policy rules.

    • Code examples: 81206–81209 (BCR/ABL1 series), 81210 (BRAF), 81162/81163 (BRCA1/BRCA2), 81182/81183 (ATXN8OS/ATXN10).
    • Include supporting clinical documentation per policy when applicable.
    Note
    Note
    Note

    Terminology and Definitions

    CBC — Complete Blood Count (CBC)
    DefinitionComplete Blood Count (CBC) includes hematocrit, hemoglobin, RBC count, RBC indices, WBC count and platelet count (see code 85027)
    CBC with automated differentialUse code 85025 for CBC with automated differential WBC count
    Component billing restrictionIndividual component codes (85013, 85014, 85018, 85048, 85049) may NOT be billed in conjunction with panel CBC codes 85025 or 85027
    Therapeutic drug monitoring — definition and references
    DefinitionTherapeutic drug monitoring: quantitative blood concentration determinations to maintain therapeutic effect within a defined range; reimbursable when specific criteria met and performed on blood specimens
    CodesUse drug-specific CPT codes 80150–80203; code 80299 By Report when applicable
    Peak/troughPeak and trough (or predose/postdose) analyses, when clinically indicated, are reimbursable as two procedures
    screening by automated system — code 88174 definition
    Code 88174 definitionScreening by automated system (88174): primary exam by a slide profiling system without human review or human review of fields selected by a location-guidance system, with or without QA re-screening
    Use contextApplies to instrumented screening of PAP smears using automated slide profiling or location-guidance selection
    QA noteMay include quality assurance manual or automated re-screening
    screening by automated systems and manual rescreening — code 88175 definition
    Code 88175 definitionScreening by automated systems and manual rescreening (88175): primary human review of fields selected by a location-guidance system plus full slide review (AutoScan mode), with or without QA re-screening
    Use contextEngaged when human review with full slide review is performed following automated selection
    QA noteMay include quality assurance manual or automated re-screening
    homebound — definition for in-home phlebotomy eligibility
    DefinitionHomebound: condition due to illness or injury that precludes access to routine medical services outside the residence without special transportation or makes leaving medically contraindicated
    Eligibility linkageRecipient must also be participating in a Medicaid-covered home care program or receiving a Medicaid-covered home care service to qualify for in‑home phlebotomy reimbursement
    Billing codeTravel expenses for in-home phlebotomy reimbursable using code P9604 when eligibility documented
    Evocative/Suppression testing — definition
    DefinitionEvocative/Suppression testing: administration of evocative or suppressive agents with baseline and subsequent measurements of their effects on chemical constituents
    Fee exclusionCosts of evocative or suppressive agents are not included in the test fee except oral glucose for codes 80430 and 82950–82953
    Combination reimbursement ruleWhen multiple evocative/suppressive tests are performed in combination, reimbursement limited to the greater fee plus 50% of the lesser fee(s)
    ATN/ATXN gene analysis — definition for expanded allele detection
    DefinitionATN/ATXN gene analysis: single-gene analysis to evaluate and detect abnormal (expanded) alleles associated with disorders such as spinocerebellar ataxias and related conditions
    Codes mappedCPT codes 81177–81183 correspond to ATN/ATXN family analyses (ATN1, ATXN1–ATXN10)
    Clinical examplesUsed for detection of trinucleotide repeat expansions in conditions like spinocerebellar ataxia and Machado–Joseph disease
    Expansion detection / abnormal allele detection — definition
    DefinitionExpansion detection / abnormal allele detection: molecular/genetic testing to detect abnormal (e.g., expanded) nucleotide repeat alleles
    Use caseApplied in repeat expansion disorders (e.g., spinocerebellar ataxias) and reported under CPT codes such as 81180–81183
    DescriptorOften described as 'evaluation to detect abnormal (e.g., expanded) alleles' in code listings
    BCKDHB common variant analysis — example variants (R183P, G278S, E422X)
    Example variantsBCKDHB common variant analysis includes examples such as R183P, G278S, E422X
    Associated conditionBCKDHB analysis relates to branched-chain keto acid dehydrogenase E1, beta polypeptide (maple syrup urine disease)
    Code mappingCPT 81205 used for BCKDHB common variant analysis
    repeat expansion testing / gene analysis — definition
    DefinitionRepeat expansion testing / gene analysis: testing to evaluate and detect abnormal (expanded) nucleotide repeat alleles in single genes associated with repeat-expansion disorders
    Typical targetsIncludes ATXN series genes (ATXN1–ATXN10) and related loci reported under CPT codes 81177–81183
    Diagnostic contextUsed in diagnosis of spinocerebellar ataxias and similar inherited neurologic disorders
    BCR/ABL1 translocation analysis — qualitative/quantitative and breakpoint notes
    ScopeBCR/ABL1 translocation analysis encompasses qualitative or quantitative testing for t(9;22) (BCR/ABL1) with reporting by breakpoint (major, minor, other)
    Breakpoints notedCodes distinguish major, minor, and other breakpoints (e.g., CPT 81206, 81207, 81208)
    Clinical examplesUsed in evaluation of chronic myelogenous leukemia and other BCR/ABL1-associated disorders
    expanded-allele analysis — definition for diagnostic context (e.g., spinocerebellar ataxia)
    DefinitionExpanded-allele analysis: molecular testing to detect nucleotide repeat expansions associated with disorders such as spinocerebellar ataxias
    Clinical contextCommonly applied when clinical suspicion for repeat-expansion disorders (e.g., spinocerebellar ataxia) exists
    Code examplesSee CPT codes 81177–81183 for single-gene expanded-allele analyses
    translocation/breakpoint analysis — definition and examples
    DefinitionTranslocation/breakpoint analysis: qualitative or quantitative methods to detect chromosomal translocations and specify breakpoints (e.g., BCR/ABL1 t(9;22) major/minor/other)
    Code examplesCPT codes 81206–81208 map to major, minor and other BCR/ABL1 breakpoints respectively; 81209 and related codes cover other translocation analyses
    Clinical usageEmployed in hematologic malignancy diagnosis and monitoring (e.g., CML)
    gene analysis (expanded alleles) — definition
    DefinitionGene analysis (expanded alleles): testing focused on detecting abnormal (expanded) repeat alleles in specific genes implicated in neurologic disorders
    Common gene targetsATXN family (ATXN1–ATXN10), ATN1 and related loci for spinocerebellar ataxias
    ReportingOften reported as 'evaluation to detect abnormal (e.g., expanded) alleles' alongside the CPT procedure code
    translocation analysis (BCR/ABL1) — specific note on t(9;22) breakpoint testing
    BCR/ABL1 t(9;22) breakpoint noteTranslocation analysis for t(9;22) (BCR/ABL1) specifies testing for major, minor, or other breakpoints and may be reported qualitatively or quantitatively
    CodesUse CPT 81206 for major breakpoint, 81207 for minor, and 81208 for other breakpoint analyses
    Clinical exampleApplied in chronic myelogenous leukemia evaluation and monitoring
    expanded allele detection — definition
    DefinitionExpanded allele detection: laboratory evaluation to detect abnormal (expanded) nucleotide repeat alleles in single-gene analyses
    Associated codesOften represented by CPT codes 81177–81183 and related entries for ATXN/ATN genes
    Disorder examplesUsed for conditions such as spinocerebellar ataxias and dentatorubral–pallidoluysian atrophy
    translocation analysis — definition
    DefinitionTranslocation analysis: qualitative or quantitative assessment of chromosomal translocations and breakpoints
    ScopeIncludes BCR/ABL1 breakpoint testing (major/minor/other) and other translocation analyses under CPT codes 81206–81209
    Clinical relevanceImportant for hematologic malignancy diagnosis and therapeutic monitoring
    BRAF V600 — variant definition and clinical context
    Variant definitionBRAF V600: oncogenic V600 variants of the BRAF gene commonly tested in oncology (e.g., colon cancer, melanoma)
    Code mappingBRAF V600 referenced in code listings (e.g., CPT 81210) as V600 variant testing
    Clinical contextUsed to inform targeted therapy decisions in relevant malignancies
    BLM 2281del6ins7 — specific variant reference
    Variant referenceBLM 2281del6ins7: specific variant in the BLM gene cited in the code listing for Bloom syndrome-related testing
    Associated conditionBLM gene analysis relates to Bloom syndrome (RecQ helicase-like) testing
    Code linkageReferenced alongside CPT entries for BLM gene analysis in the policy code lists
    Genetic test codes (CPT) — general note about CPT/HCPCS codes used for gene analyses
    General noteGenetic test codes (CPT/HCPCS) are used to report single-gene analyses, expanded-allele detection, translocation/breakpoint analysis, and variant testing
    ExamplesCodes listed across the policy include 81162–81183 and 81205–81210 among others for gene/variant/translocation testing
    Billing implicationThese procedure codes appear in listings without explicit additional coverage rules in portions of the document; refer to specific sections for clinical criteria
    BRCA1/BRCA2 full sequence analysis — definition and clinical context
    Definition & contextBRCA1/BRCA2 full sequence analysis: gene analysis for hereditary breast and ovarian cancer, referenced as full sequence and duplication/deletion analysis
    Code examplesBRCA testing appears in code listings (e.g., CPT 81162, 81163) for full sequence and duplication/deletion analysis
    Clinical implicationUsed for hereditary breast/ovarian cancer evaluation; listed as full sequence analysis in the policy code entries
    BRCA1/BRCA2 (81162) — code-specific definition
    Code-specificBRCA1/BRCA2 (CPT 81162): gene analysis referenced for hereditary breast and ovarian cancer, including full sequence and duplication/deletion analysis
    PurposeUsed to detect pathogenic variants associated with hereditary breast and ovarian cancer syndromes
    Listing note81162 appears repeatedly in policy code lists as BRCA1/BRCA2 gene analysis
    BRAF (81210) — code-specific definition
    Code-specificBRAF (CPT 81210): gene analysis referencing V600 variant(s) commonly tested in oncology (e.g., colon cancer, melanoma)
    VariantPolicy specifically notes V600 variants for BRAF testing
    Clinical useUsed to inform targeted therapy in cancers with BRAF V600 alterations
    full duplication/deletion analysis — definition
    DefinitionFull duplication/deletion analysis: testing to detect large gene rearrangements (duplications or deletions) across a gene
    ApplicationReported for genes where large rearrangements are clinically relevant (e.g., BRCA1/BRCA2 full duplication/deletion analysis)
    Coding noteAppears in code listings alongside full sequence analysis (e.g., CPT 81163/81164 entries)
    expanded allele testing / trinucleotide repeat analysis — definition
    DefinitionExpanded allele testing / trinucleotide repeat analysis: evaluation to detect abnormal (expanded) nucleotide repeat alleles in single genes
    Typical targetsATXN/ATN family genes and other loci associated with repeat-expansion disorders
    Code examplesLinked to CPT codes 81177–81183 and related entries for expanded-allele detection
    full duplication/deletion analysis — duplicate listing
    Definition (duplicate)Full duplication/deletion analysis: detection of large gene rearrangements (duplications/deletions)
    ExampleBRCA1/BRCA2 full duplication/deletion analysis listed in policy code entries
    Billing implicationMay be reported separately or alongside full sequence testing depending on code descriptors
    expanded allele testing — duplicate listing/definition
    Definition (duplicate)Expanded allele testing: evaluation to detect abnormal (expanded) nucleotide repeat alleles
    Associated CPTsCPTs 81177–81183 frequently used for these analyses
    Diagnostic examplesSpinocerebellar ataxias and related repeat-expansion disorders