LCD - Molecular Pathology Procedures (L35000) (2023)

Document Information

LCD ID
L35000

LCD Title
Molecular Pathology Procedures

Proposed LCD in Comment Period
N/A

Source Proposed LCD
DL35000

Original Effective Date
For services performed on or after 10/01/2015

Revision Effective Date
For services performed on or after 07/01/2020

Revision Ending Date
N/A

Retirement Date
N/A

Notice Period Start Date
07/17/2018

Notice Period End Date
08/31/2018

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CMS National Coverage Policy

N/A

Coverage Guidance

Coverage Indications, Limitations, and/or Medical Necessity

Molecular pathology procedures have broad clinical and research applications. The following examples of applications may not be relevant to a Medicare beneficiary or may not meet a Medicare benefit category and/or reasonable and necessary threshold for coverage. Such examples include Genetic Testing and Genetic Counseling (when applicable) for:

• Disease Risk,
• Carrier Screening,
• Hereditary Cancer Syndromes,
• Gene Expression Profiling for certain cancers,
• Prenatal Diagnostic testing,
• Diagnosis and Monitoring Non-Cancer Indications, and
• Several Pharmacogenomic applications.

This Local Coverage Determination (LCD) addresses the circumstances under which the item or service may be reasonable and necessary. For laboratory services, a service may be reasonable and necessary if the service is safe and effective; and appropriate, including the duration and frequency that is considered appropriate for the item or service, in terms of whether it is furnished in accordance with accepted standards of medical practice for the diagnosis of the patient's condition; furnished in a setting appropriate to the patient's medical needs and condition; ordered and furnished by qualified personnel; one that meets, but does not exceed, the patient's medical need; and is at least as beneficial as an existing and available medically appropriate alternative.

Many applications of the molecular pathology procedures are not covered services given lack of benefit category (e.g., preventive service or screening for a genetic abnormality in the absence of a suspicion of disease) and/or failure to the reasonable and necessary threshold for coverage (e.g., based on quality of clinical evidence and strength of recommendation or when the results would not reasonably be used in the management of a beneficiary). Furthermore, payment of claims in the past (based on stacking codes) or in the future (based on the new code series) is not a statement of coverage since the service may not have been audited for compliance with program requirements and documentation supporting the reasonable and necessary testing for the beneficiary. Certain molecular pathology procedures may be subject to prepayment medical review (records requested) and paid claims must be supportable, if selected, for post payment audit by the MAC or other contractors. Molecular pathology tests for diseases or conditions that manifest severe signs or symptoms in newborns and in early childhood or that result in early death (e.g., Canavan disease) could be subject to automatic denials since these tests are not usually relevant to a Medicare beneficiary.

This LCD gives general guidance to the medically reasonable and necessary applications of the Molecular Pathology Procedures and Genomic Sequencing Procedures, described in Current Procedural Terminology (CPT). Coding guidance is provided in Molecular Pathology Procedures Article A56199, attached below.

Indications:
Molecular pathology procedures (Tier1 and Tier 2) may be eligible for coverage when ALL of the following criteria are met:

  • Alternative laboratory or clinical tests to definitively diagnose the disorder/identify the condition are unavailable or results are clearly equivocal; AND
  • Availability of a clinically valid test, based on published peer reviewed medical literature; AND
  • Testing assay(s) are Food and Drug Administration (FDA) approved/cleared or if LDT (lab developed test) or LDT protocol or FDA modified test(s) the laboratory documentation should support assay(s) of analytical validity and clinical utility; AND
  • Results of the testing must directly impact treatment or management of the Medicare beneficiary; AND
  • For testing panels, including but not limited to, multiple genes or multiple conditions, and in cases where a tiered approach/method is clinically available, testing would be covered ONLY for the number of genes or test that are reasonable and necessary to obtain necessary information for therapeutic decision making; AND
  • Individual has not previously received genetic testing for the disease/condition. (In general, diagnostic genetic testing for a disease should be performed once in a lifetime.) Exceptions include clinical scenarios whereby repeat testing of somatically-acquired mutations (for example, pre- and post- therapy) may be required to inform appropriate therapeutic decision-making.

Limitations:

  • Any procedures required prior to cell lysisshould be reported separately and utilization must be clearly supported based on the application and clinical utility. Such claims may be subject to prepayment medical review.
  • The medically necessary interpretation and report of a molecular pathology test, written by a pathologist, which is above and beyond the report of standard laboratory results may not be reported by Non- physician practitioners (e.g., PhD, scientists etc.); only physicians are eligible to reportthis service.
  • Testing for quality assurance component of the service is not separately billable.

Indications and Limitations of Coverage

ABL1 (ABL proto-oncogene 1, non-receptor tyrosine kinase) (eg, acquired imatinib tyrosine kinase inhibitor resistance), gene analysis, variants in the kinase domain is considered medically necessary in patients with acute lymphoblasic leukemia (ALL) and chronic myeloid leukemia (CML) to guide therapeutic decision making.

ATP7B is considered medically necessary in patients with symptoms of Wilson’s disease to guide therapeutic decision making.

BCR/ABL is indicated in patients with suspected CML with either persistent, unexplained leukocytosis or thrombocytosis. BCR/ABL is considered medically necessary in the evaluation of individuals with chronic myelogenous leukemia or BCR-ABL positive acute lymphoblastic leukemia to evaluate treated individuals who manifest suboptimal response to initial tyrosine kinase inhibitor therapy or loss of response to tyrosine kinase inhibitor therapy.

BLM (Bloom syndrome, RecQ helicase-like)(e.g. Bloom syndrome) gene analysis, 2281 del6ins7 variant is considered medically necessary for a beneficiary who may have Bloom syndrome to confirm diagnosis and guide medical decision-making.

BRAF gene analysis is considered medically necessary for patients who have malignant melanoma, non-small cell lung cancer, hairy cell leukemia, or metastatic colorectal cancer when needed to determine if a Medicare covered therapy is a reasonable option given the individual's specific clinical presentation.

BRCA1 and BRCA2 genetic testing is considered medically necessary for a beneficiary with a current diagnosis or a personal history of a cancer associated with the BRCA mutation who meets one or more of the criteria found in the most recent version of the NCCN guidelines for Genetic/Familial High-Risk Assessment: Breast and Ovarian or other evidence based guideline addressing genetic testing, and the results will be used to benefit the individual tested in terms of potential to guide therapeutic decision making.

Cardiology (heart transplant), mRNA, gene expression profiling by real-time quantitative PCR of 20 genes (11 content and 9 housekeeping), utilizing subtraction of peripheral blood, algorithm reported as rejection risk score is considered medically necessary for heart transplant patients to guide therapeutic decision-making.

CEBPA (CCAAT/enhancer binding protein [C/EBP], alpha) (eg, acute myeloid leukemia), full gene sequence is considered medically necessary in patients with acute myelogenous leukemia (AML) to guide therapeutic decision making.

CALR (calreticulin) (eg, myeloproliferative disorders), gene analysis, common variants in exon 9 is considered medically necessary in the initial diagnostic work-up of BCR-ABL negative, JAK2-negative adults with clinical, laboratory, or pathological findings suggesting polycythemia vera (PV), essential thrombocythemia (ET) or primary myelofibrosis (PMF).

CCND1/IGH (BCL1/IgH, t)(eg, mantle cell lymphoma) translocation analysis, major breakpoint, qualitative and quantitative, if performed is considered medical necessary for patients who have non- Hodgkin’s lymphoma to guide therapeutic decision-making.

CFTR (cystic fibrosis transmembrane conductance regulator) (e.g.cystic fibrosis) gene analysis, common variants (e.g. ACMG/ACOG guidelines) is considered medically necessary for a beneficiary who has or may have cystic fibrosis to guide therapeutic decision-making.

Chimerism analysis to identify appropriate donors and monitor engraftment success or disease reoccurrence is considered medically necessary.

CYP2C6 19-cytochrome P450 CYP2C6 19-cytochrome P450 Based on the FDA’s Black Box warning for clopidogrel, the effectiveness of clopidogrel is dependent on its activation to an active metabolite by the cytochrome P450 (CYP) system, principally CYP2C19. CYP2C619 genotyping may be medically necessary once per lifetime to identify individuals:

  • Who are poor metabolizers of clopidogrel, so that alternative treatment or treatment strategies can be considered
  • Who are poor metabolizers of clopidogrel with acute coronary syndrome or who are undergoing percutaneous coronary intervention

CYP2C9 (cytochrome P450, family 2, subfamily D polypeptide 9) (e.g., drug metabolism), gene analysis, is only considered medically necessary for individuals who have relapsing forms of multiple sclerosis, and require CYP2C9 genotyping for dosing in accordance with the FDA prescribing information for Mayzent. CYP2C9 testing must include the *1, *2, and *3 alleles that are necessary to safely dose the FDA-approved drug Mayzent.

CYP2D6 (cytochrome P450, family 2, subfamily D polypeptide 6) (e.g., drug metabolism), gene analysis, is only considered medically necessary for individuals with Huntington’s disease for whom doses of tetrabenazine greater than 50 mg per day are being considered, and for testing prior to the initiation of CerdelgaTM (eliglustat) for Gaucher’s disease.

EGFR (epidermal growth factor receptor) (eg, non-small cell lung cancer) gene analysis, common variants (eg, exon 19 LREA deletion, L858R, T790M, G719A, G719S, L861Q) [when specified as EGFR mutation analysis testing] EGFR testing is considered medically necessary as a technique to predict treatment response for individuals with non-small cell lung cancer undergoing treatment with EGFR tyrosine kinase inhibitor (TKI) therapy (for example, erlotinib [Tarceva® ], gefitinib [Iressa® ], or afatinib [Gilotrif® ]).

F2 gene (prothrombin coagulation factor II) and F5 gene (coagulation factor V) The F2 and F5 genetic tests are not considered to be clinically efficacious; therefore, testing is not medically necessary.

FLT3 is considered medically necessary in patients with acute myeloid leukemia (AML) to guide therapeutic decision making.

Gene Testing for Warfarin Response Pharmacogenomic Testing for Warfarin Response, gene testing on CYP2C9 and/or VKORC1 see NCD 90.1 for coverage information.

HFE (hemochromatosis)(hereditary hemochrosis) gene analysis, common variants (e.g. C282Y, H63D) is considered medically necessary in patients with iron overload of uncertain etiology (e.g. when the test is used to avoid liver biopsy in someone when the ferritin and the transferrin saturation are elevated greater than 45%). The genotyping of patients with iron overload of uncertain etiology is allowed only once per lifetime.

HLA Class I or II typing is considered medically necessary when one of the following indications is met:

  • Transplantation:
    • Standard of care determination of HLA matching for solid organ transplant (donor/recipient). – Solid organ transplant registries include both serological HLA testing (e.g., crossmatch) and genomic molecular DNA typing. Family members, or unrelated living donors or cadaveric donors who donate bone marrow or a solid organ are HLA tested pre-transplant to determine compatibility with the potential recipients.
    • Standard of care determination of HLA matching for solid organ transplant (donor/recipient). – Solid organ transplant registries include both serological HLA testing (e.g., crossmatch) and genomic molecular DNA typing. Family members, or unrelated living donors or cadaveric donors who donate bone marrow or a solid organ are HLA tested pre-transplant to determine compatibility with the potential recipients.
    • Standard of care identification of determination of HLA matching for hematopoietic stem cell/bone marrow transplantation -allele-level typing will provide clinical guidance for the HLA-A,B,C Class I and DRB1, DQB1,DPB1, and DQA1 Class II loci in the average transplant program because it is well established that mismatches at certain HLA loci between donor-recipients are closely linked to the risk of graft versus host disease. Potential marrow donors may enroll with a national registry such as the United States National Marrow Donor Program or the Canadian Blood Services registry.
  • Disease Association:
    • Standard of care testing to diagnose certain HLA related diseases/conditions when the testing is supported by the clinical literature and is informative for the direct management of a patient bearing a certain allele(s). It is not expected that more than one test would be required in a given beneficiary’s lifetime. Possible covered indications when standard laboratory testing (tissue typing) not adequate:
      • HLA-B*27 for the diagnosis of certain cases of symptomatic patients with presumed ankylosing spondylitis or related inflammatory disease. HLA-B*27 is covered for ankylosing spondylitis in cases where other methods of diagnosis would not be appropriate or have yielded inconclusive results (NCD 190.1).
      • In the work-up of certain patients with an unclear diagnosis of celiac disease and gluten hypersensitivity usually related to ambiguous standard laboratory results and/or inconsistent biopsy results (e.g., HLA-DQ2 by HLA-DQB1*02 and of DQ8 by HLA-DQB1*0302).
  • Pharmacogenetics:
    • Standard of care testing to diagnose certain HLA related drug hypersensitivity reactions when the testing is supported by the clinical literature and is informative for the direct management of a patient bearing a certain allele(s) associated to fatal skin drug reactions (Stevens-Johnson syndrome and toxic epidermal necrolysis). It is not expected that more than one test would be required in a given beneficiary’s lifetime. Possible covered indications:
      • HLA –B*5701 when testing performed prior to the initiation of an abacavir-containing regime in the treatment of HIV Infection.
      • HLA-B*1502 when genotyping may be useful for risk stratification when the testing is performed prior to the initiation of carbamazepine therapy in the treatment of patients at high risk of having this allele. HLA-B*1502 occurs almost exclusively in patients with ancestry across broad areas of Asia, including South Asian Indians.
      • Identification of HLA compatible platelets for transfusion when standard typing is not adequate.

HUMAN PLATELET ANTIGEN 1-15 as genotyping for human platelet antigens is important for identifying woman at risk for neonatal alloimmune thrombocytopenia (NAIT). Post-transfusion purpura is an immune reaction against human platelet antigens, often occurring when a woman is sensitized during pregnancy, then subsequently receives a transfusion. There are few Medicare beneficiaries for whom this testing will be clinically actionable.

IGH@ (Immunoglobulin heavy chain locus) is considered medically necessary for acute lymphoblastic leukemia (ALL) and lymphoma, B-cell to guide therapeutic decision making.

JAK2 V617F genotyping is considered medically necessary in the initial diagnostic work-up of BCR-ABL negative, JAK2-negative adults with clinical, laboratory, or pathological findings suggesting myeloproliferative neoplasm (MPN) (polycythemia vera (PV), essential thrombocythemia (ET) or primary myelofibrosis (PMF)) or a myelodysplastic syndrome (MDS). Note: JAK2 (exons 12 and 13) (reported with 81403) is medically necessary in individuals for whom PV is a strong consideration.

JAK2 (Janus kinase 2) (eg, myeloproliferative disorder), exon 12 sequence and exon 13 sequence is considered medically necessary in the initial work-up of BCR-ABL and JAK2 (V617F variant) negative adults with clinical, laboratory, or pathological findings suggesting polycythemia vera.

KIT (v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog) (eg, gastrointestinal stromal tumor [GIST], acute myeloid leukemia, melanoma), gene analysis, targeted sequence analysis (eg, exons 8, 11, 13, 17, 18) is considered medically necessary in patients who have GIST, acute myeloid leukemia (AML) or melanoma to guide therapeutic decision making.

KIT (v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog) (eg, mastocytosis), gene analysis, D816 variant(s) is considered medically necessary in patients who have mastocytosis to guide therapeutic decision making.

KRAS gene analysis, variants in codons 12 and 13, is considered medically necessary in patients with colorectal cancer or non-small cell lung cancer when needed to determine if a Medicare covered therapy is a reasonable option given the individual's specific clinical presentation.

KRAS (Kirsten rat sarcoma viral oncogene homolog) (e.g., carcinoma) gene analysis; additional variant(s) (e.g., codon 61, codon 146) is considered medically necessary in patients with colorectal cancer or non-small cell lung cancer when needed to determine if a Medicare covered therapy is a reasonable option given the individual's specific clinical presentation.

MEN1 (multiple endocrine neoplasia 1) (eg, multiple endocrine neoplasia type 1, Wermer syndrome), duplication/deletion and CPT code 81405 MEN1 (multiple endocrine neoplasia 1) e.g. multiple endocrine neoplasia type 1, Wermer syndrome), duplication/deletion analysis) are considered medically necessary in patients with multiple endocrine neoplasia to guide therapeutic decision-making.

MET proto-oncogene, receptor tyrosine kinase, is considered medically necessary in patients with non-small cell lung cancer when needed to determine if a Medicare covered therapy is a reasonable option given the individuals specific clinical presentation.

MGMT (O-6-methylguanine-DNA methyltransferase) (e.g., glioblastoma multiforme), methylation analysis) is considered medically necessary in patients with malignant brain neoplasm to guide therapeutic decision making.

MPL (myeloproliferative leukemia virus oncogene, thrombopoietin receptor, TPOR) (eg, myeloproliferative disorder), common variants (eg, W515A, W515K, W515L, W515R) is considered medically necessary in the initial work-up of BCR-ABL negative, JAK2 negative, and CALR negative adults with clinical, laboratory, or pathological findings suggesting thrombocytosis, essential thrombocythemia (ET), or primary myelofibrosis (PMF).

MPL (myeloproliferative leukemia virus oncogene, thrombopoietin receptor, TPOR) (eg, myeloproliferative disorder), exon 10 sequence is considered medically necessary in the initial work-up of BCR-ABL negative, JAK2 negative, and CALR negative adults with clinical, laboratory, or pathological findings suggesting thrombocytosis, essential thrombocythemia (ET), or primary myelofibrosis (PMF).

MTHFR (5,10-methyenetetrahydrofolate reductase) (e.g. hereditary hypercoaguability), gene analysis, common variants(e.g., EG, 677T, 1298C) is not considered to be clinically efficacious; therefore, testing is not medically necessary.

Microsatellite instability analysis (e.g., hereditary non-polyposis colorectal cancer, Lynch syndrome) of markers for mismatch repair deficiency (e.g. BAT25, BAT26), includes comparison of neoplastic and normal tissue and is considered medically necessary in individuals who have colorectal cancer (CRC) diagnosed at less than or equal to 70 years of age, and those greater than 70 years who meet the revised Bethesda Lynch Syndrome (LS) guidelines to guide therapeutic decision-making. Despite the high penetrance of CRC and endometrial cancer and recommendations of consideration for screening unaffected first-degree relatives following diagnosis of an LS proband, testing of genetic carriers who are unaffected with a Lynch- related cancer is not a Medicare benefit, and is statutorily excluded from coverage.

MSI testing is also required by FDA for the clinical use of Keytruda (pembrolizumab) in a restricted population of patients. These are patients who have unresectable or metastatic solid tumors who have progressed following prior treatment and have no satisfactory alternative options. When Keytruda (pembrolizumab) is a potential clinically appropriate therapeutic choice, MSI testing is medically necessary in these patients. Because this is a wide-ranging population of advanced cancer patients, ICD-10 specificity is impractical, therefore use an ICD-10 appropriate for the tumor type and location.

MYD88 genetic test is considered medically necessary in patients with Marginal Zone Lymphoma (MZL), Waldenstrom’s Macroglobulinemia (WM) and Lymphoplasmacytic Lymphoma (LPL) to guide therapeutic decision-making.

NPM1 (nucleophosmin) is considered medically necessary in patients with acute myeloid leukemia (AML) to guide therapeutic decision making.

NRAS (neuroblastoma RAS viral [v-ras] oncogene homolog) (e.g., colorectal carcinoma), gene analysis, variants in exon 2 (e.g., codons 12 and 13) and exon 3 (e.g., codon 61) is considered medically necessary in patients with colorectal cancer when needed to determine if a Medicare covered therapy is a reasonable option given the individual's specific clinical presentation.

Oncology (breast), mRNA, gene expression profiling by real-time RT-PCR of 21 genes, utilizing formalin-fixed paraffin embedded tissue, algorithm reported as recurrence score is considered medically necessary to guide therapeutic decision-making in patients with the following findings:

  • estrogen-receptor positive, node-negative carcinoma of the breast
  • estrogen-receptor positive micrometastases of carcinoma of the breast, and
  • estrogen-receptor positive breast carcinoma with 1-3 positive nodes.

PCA3 testing is considered medically necessary in patients ONLY when all biopsies in previous encounter(s) are negative for prostatic cancer, the subsequent prostate specific antigen (PSA) is rising, and when the patient or physician wants to avoid repeat biopsy (“watchful waiting”). When the physician plans to biopsy the prostate, NGS will consider a PCA3 test as not medically necessary, and thus, not a covered Medicare benefit. NGS considers all other indications for PCA3 not reasonable and necessary. Medical record documentation must indicate the rationale to perform a PCA3 assay.

PDGFRA (platelet-derived growth factor receptor, alpha polypeptide) (e.g., gastrointestinal stromal tumor [GIST]), gene analysis, targeted sequence analysis (eg, exons 12, 18) is considered medically necessary in patients with PDGFRA-associated chronic eosinophilic leukemia or GIST caused by mutations in the PDGFRA gene to guide therapeutic decision making.

PML/RARALPHA, (T(15;17)), (PROMYELOCYTIC LEUKEMIA/RETINOIC ACID RECEPTOR ALPHA) (EG, PROMYELOCYTIC LEUKEMIA) TRANSLOCATION ANALYSIS; COMMON BREAKPOINTS (EG, INTRON 3 AND INTRON 6), QUALITATIVE OR QUANTITATIVE is considered medically necessary in patients with promyelocytic leukemia.

Prosigna® Breast Cancer Prognostic Gene Signature Assay is considered medically necessary in patients who have undergone surgery in conjunction with locoregional treatment consistent with standard of care, either as:

  • A prognostic indicator for distant recurrence-free survival at 10 years in post- menopausal women with Hormone Receptor-Positive (HR+), lymph node-negative, Stage I or II breast cancer to be treated with adjuvant endocrine therapy alone, when used in conjunction with other clinicopathological factors.
  • A prognostic indicator for distant recurrence-free survival at 10 years in post- menopausal women with Hormone Receptor-Positive (HR+), lymph node-positive (1-3 positive nodes}, Stage II breast cancer to be treated with adjuvant endocrine therapy alone, when used in conjunction with other clinicopathological factors. The device is not intended for patients with 4 or more positive nodes

RARS (SF3B1 mutation) is considered medically necessary in patients with Myelodysplastic Syndrome to guide therapeutic decision-making.

RET (ret-proto-oncogene) is considered medically necessary in patients with medullary CA of thyroid, multiple endocrine neoplasia, pheochromocytoma, and parathyroid tumors) to guide therapeutic decision making.

ROS proto-oncogene 1, receptor tyrosine kinase, is considered medically necessary in patients with non-small cell lung cancer when needed to determine if a Medicare covered therapy is a reasonable option given the individuals specific clinical presentation.

SERPINA1 (serpin peptidase inhibitor, clade A, alpha-1- antiproteinase, antitrypsin, member 1) (e.g., antitrypsin deficiency), gene analysis, common variants (e.g. *S and *Z) is considered medically necessary for patients who have antitrypsin deficiency to guide therapeutic decision-making.

Targeted genomic sequence analysis panel, solid organ neoplasm, DNA analysis, and RNA analysis when performed, 5-50 genes (EG, ALK, BRAF, CDKN2A, EGFR, ERBB2, KIT, KRAS, NRAS, MET, PDGFRA, PDGFRB, PGR, PIK3CA, PTEN, RET), interrogation for sequence variants and copy number variants or rearrangements, if performed is considered not medically necessary except when used to guide treatment decision making in individuals with non-small cell lung cancer (please refer to LCD L36376).

TP53 (tumor protein 53) (e.g. tumor samples), targeted sequence analysis of 2-5 exons, and CPT code 81405 TP53 (tumor protein 53) (e.g. Li-Fraumeni syndrome, tumor samples), full gene sequence or targeted sequence analysis of >5 exons are considered medically necessary in individuals who have Acute Myelogenous Leukemia or Myeloplastic Disease to guide therapeutic decision-making.

TRB@ (T CELL antigen receptor, BETA) (e.g., leukemia and lymphoma), gene rearrangement analysis to detect abnormal cloning population(s); using amplification methodology is considered necessary to guide therapeutic decision-making for individuals with acute lymphoid leukemia, aplastic anemia, and T cell prolymphocytic leukemia.

TRG@ (T CELL antigen receptor, GAMMA ) (e.g., leukemia and lymphoma), gene rearrangement analysis , evaluation to detect abnormal cloning population(s) are considered medically necessary to guide therapeutic decision-making for individuals with acute lymphoid leukemia, aplastic anemia, and T cell prolymphocytic leukemia and mastocytosis.

Tier 2 Covered Gene/Gene Combinations

Limited coverage may be provided for specific genes reported below:

ACE
ATP7B (ATPase, Cu++ transporting, beta polypeptide)
CCND1/IGH
CBFB-MYH11
CDKN2A (cyclin-dependent kinase inhibitor 2A)
E2A/PBX1
EML4-ALK
ETV6-RUNX1
EWSR1/ERG
EWSR1/FLI1
EWSR1/WT1
F11coagulation factor XI
F13B
F5
F7
F8 (coagulation factor VIII)
FGB
FIP1L1-PDGFR
FOXO1/PAX3
FOXO1/PAX7
MEN1 (multiple endocrine neoplasia 1) (eg, multiple endocrine neoplasia type 1, Wermer syndrome), duplication/deletion
MEN1 (multiple endocrine neoplasia 1) (eg, multiple endocrine neoplasia type 1, Wermer syndrome), full gene sequence
MUTYH (mutY homolog [E.coli])
NPM/ALK
PAX8/PPARG
PRSS1 (protease, serine, 1 [trypsin 1])
RARS (SF3B1
RUNX1/RUNX1T1
TP53 (tumor protein 53) (e.g. tumor samples), targeted sequence analysis of 2-5 exons
TP53 (tumor protein 53) (e.g. Li-Fraumeni syndrome, tumor samples), full gene sequence or targeted sequence analysis of >5 exons
VHL (von Hippel-Lindau tumor suppressor)

Tier 2 Individual Review Codes/Gene Combinations

Any genetic test reported with a Tier 2 CPT code, not listed above or below, is subject to individual review.

Tier 2 Non-covered Codes/Gene Combinations

The following individual Tier 2 genetic tests are unlikely to impact therapeutic decision-making, directly impact treatment, outcome and/or clinical management in the care of the beneficiary and will be denied as not medically necessary (Please note that this list of non-covered genes is not exhaustive, and the fact that a specific gene is not mentioned does not mean it is covered. In addition, many genes have several names that are used. The most common names have been used in this policy):

ABCC8
ACADM
ACADS (acyl-CoA dehydrogenase)
ACADVL (acyl-CoA dehydrogenase, very long chain)
ADRB2
AGTR1
AIRE (APSI)
AKT1
ANG (angiogenin, ribonuclease, RNase A family, 5)
APOE
AQP2 (aquaporin 2 [collecting duct])
AR (androgen receptor)
ARX (aristaless related homeobox)
ATN1
BTD (biotinidase)
C9orf72
CASR (CAR, EIG8, extracellular calcium-sensing receptor, FHH, FIH, GPRC2A, HHC, HHC1, NSHPT, PCAR1)
CAV3 (caveolin 3) (eg, CAV3-related distal myopathy, limb-girdle muscular dystrophy type 1C), full gene sequence
CBS (cystathionine-beta-synthase)
CCR5
CDKL5 (cyclin-dependent kinase-like 5)
CFH/ARMS2
Chromosome 18q-
CLRN1
CLRN1 (clarin 1)
CYP1B1 (cytochrome P450, family 1, subfamily B, polypeptide 1)
CYP21A2 (cytochrome P450, family 21, subfamily A, polypeptide2)
CYP21A2
DEK/NUP214
DLAT (dihydrolipoamide S-acetyltransferase)
DLD (dihydrolipoamide dehydrogenase)
DMPK (dystrophia myotonica-protein kinase (DM gene and DM1)
DMPK (dystrophia myotonica-protein kinase)
DYT1 (TOR1A)
EGR2 (early growth response 2) (eg, Charcot-Marie-Tooth)
F8 (coagulation factor VIII)
F8 (coagulation factor VIII)
FGFR2 (fibroblast growth factor receptor 2) (2 EXONS)
FGFR3
FGFR3
FGFR3 (fibroblast growth factor receptor 3) (4 EXONS)
FGFR3 (fibroblast growth factor receptor 3) one exon
FKRP (Fukutin related protein)
FOXG1 (forkhead box G1)
FSHMD1A (facioscapulohumeral muscular dystrophy 1A)
FSHMD1A (facioscapulohumeral muscular dystrophy 1A)
FXN (frataxin)
GALT (galactose-1-phosphate uridylyltransferase)
GALT (galactose-1-phosphate uridylyltransferase)
GJB1 (gap junction protein, beta 1) (eg, Charcot-Marie-Tooth X-linked), full gene sequence
H19
HADHA (hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase [trifunctional protein] alpha subunit)
HAX1 (HAX1_HUMAN, HCLS1- associated protein X-1, HCLSBP1, HS1-associating protein X-1, HS1 binding protein, HS1-binding protein 1, HS1BP1, HSP1BP-1)
HEXA (hexosaminidase A, alpha polypeptide)
HNF1B (HNF1 homeobox B)
HRAS (v-Ha-ras Harvey rat sarcoma viral oncogene homolog Costello syndrome)
HRAS (v-Ha-ras Harvey rat sarcoma viral oncogene homolog)
HTT (huntingtin)
IL28B
IVD
KCNJ10 (potassium inwardly-rectifying channel, subfamily J, member 10)
KCNQ10T1 (KCNQ1 overlapping transcript 1)
KIF6
Level 8 Molecular Pathology Procedures
Level 9 Molecular Pathology Procedures
LMNA (lamin A/C)
LPA intron 25 genotype
MEFV (Mediterranean fever) (eg, familial Mediterranean fever)
MEG3/DLK1
MEK1
MLH1
MLL/AFF
MPZ (myelin protein zero)
MT-ATP6
MT-ND4, MT-ND6
MT-ND5 mitochondrially encoded tRNA leucine 1 [UUA/G] mitochondrially encoded NADH dehydrogenase 5)
MT-RNR1 (mitochondrially encoded 12S RNA)
MT-RNR1 (mitochondrially encoded 12S RNA)
MT-TK (mitochondrially encoded tRNA lysine)
MT-TL1
MT-TS1
MT-TS1 (mitochondrially encoded tRNA serine 1)
MUTYH (mutY homolog [E. coli])
NF2 (neurofibromin 2 [merlin])
NSD1 (nuclear receptor binding SET domain protein 1)
PAH (phenylalanine hydroxylase)
PAX2 (paired box 2)
PDHA1 (pyruvate dehydrogenase [lipoamide] alpha1)
PIK3C, PI3Ks, PI(3)Ks, PI-3Ks
POLG (polymerase [DNA directed], gamma)
PRKAG2 (protein kinase, AMP-activated, gamma 2 non-catalytic subunit)
PRSS1 (protease, serine, 1 [trypsin 1])
PTPN11 (protein tyrosine phosphatase, non-receptor type 11)
RET (ret-proto-oncogene) (eg, Hirschsprung disease), full gene sequence
SCA1
SDA2
SLC25A4 (solute carrier family 25 [mitochondrial carrier; adenine nucleotide translocation]
SLC9A6 (solute carrier family 9 [sodium/hydrogen exchanger] member 6)
SMN1
SMN1 (survival of motor neuron 1, telomeric)
SMN1/SMN2 (survival of motor neuron 1, telomeric/survival of motor neuron 2, centromeric)
SOS1 (son of sevenless homolog 1)
SPG4
TAZ (tafazzin)
TOR1A
TRD
TSC1 (tuberous sclerosis 1)
TSC2 (tuberous sclerosis 2)
UBE3A (ubiquitin protein ligase)
UPD (Uniparental disomy)
VEGFR2 (CD309, FLK1, VEGFR)
VWF (von Willebrand factor)

Summary of Evidence

HUMAN PLATELET ANTIGEN 1-15

Coverage of(HUMAN PLATELET ANTIGEN 1-15) as genotyping for human platelet antigens is important for identifying woman at risk for neonatal alloimmune thrombocytopenia (NAIT). Post-transfusion purpura is an immune reaction against human platelet antigens, often occurring when a woman is sensitized during pregnancy, then subsequently receives a transfusion. There are few Medicare beneficiaries for whom this testing will be clinically actionable.

IFNL3 (IL28B)

Newer treatment regimens are replacing PEG-interferon therapies. Per UpToDate: “Several clinical features that were predictors of response to interferon-based regimens are no longer relevant to combination direct-acting antiviral (DAA) regimens…Polymorphisms in the IL28B gene, which encodes interferon lambda 3, effectively predicted responses to treatment with interferon-based therapies and accounted for a significant proportion of the differential response observed in patients of certain races, such as patients of African descent. In contrast, neither non-CC IL28 genotype nor race has consistently been associated with lower sustained virologic response (SVR) rates in multiple trials and cohort studies of contemporary DAA combination regimens. Although some studies have suggested a limited impact of IL28 genotype or race on SVR rates with DAA regimens, the magnitude of the impact is small when appropriate regimens are used and not sufficient enough to recommend IL28B genotype testing in routine clinical practice."

G6PD

The WHO recommends testing of drugs to predict for risk of hemolysis in G6PD deficient individuals if the drugs are to be prescribed in areas of high prevalence of G6PD deficiency.

Analysis of Evidence (Rationale for Determination)

HUMAN PLATELET ANTIGEN 1-15

There aretoo few Medicare beneficiaries that would both be pregnant and at risk for neonatal alloimmune thrombocytopenia to warrant coverage outside of appeal.

IFNL3 (IL28B)

Given that PEG interferon treatment of HCV is becoming obsolete, so is related companion genetic testing. In addition, when used and IL28 testing is negative, there is little evidencethat clinicians still do notuse the PEG-interferon-alpha-containing regimens despite the unfavorable response genotype.The testing is, therefore, considered not medically necessary.

G6PD

While initial and even confirmatory testing for G6PD deficiency when certain high-risk drugs are used is appropriate, the use of molecular/genetic/DNA methods is not established. General screening, not to be confused with testing immediately before prescription of high-risk drugs, is not a Medicare benefit.

FAQs

What is a molecular pathology procedure? ›

According to The American Medical Association (AMA) Current Procedural Terminology (CPT) manual, molecular pathology procedures are medical laboratory procedures involving the analyses of nucleic acid to detect variants in genes that may be indicative of germline (e.g., constitutional disorders) or somatic (e.g., ...

What are the molecular pathology procedure codes? ›

Correct coding requires that when a panel code is ordered, it should be billed, rather than the individual gene codes. CPT code 81445, 81449, 81450, or 81451 should be billed when 5 to 50 genes are ordered. CPT code 81455, or 81456 should be billed when 51 or greater genes are ordered for molecular biomarkers.

What is the CPT code for molecular pathology 2023? ›

Molecular pathology procedures (e.g., CPT codes 81161-81408) include all aspects of sample preparation, cell lysis, internal measures to assure adequate quantity of DNA or RNA, and performance of the assay. These procedures include DNA analysis and/or RNA analysis.

What is the CPT code range for molecular pathology? ›

The Current Procedural Terminology (CPT) code range for Molecular Pathology Procedures 81105-81479 is a medical code set maintained by the American Medical Association.

What is an example of molecular pathology? ›

Molecular pathology can be used to diagnose disease and/or to guide the prevention and treatment of disease. As an example of the former, infections by certain viruses (e.g. cytomegalovirus and Epstein-Barr virus) can be diagnosed by molecular testing for the presence of their specific RNAs in blood.

What is the purpose of the molecular testing procedure? ›

A laboratory method that uses a sample of tissue, blood, or other body fluid to check for certain genes, proteins, or other molecules that may be a sign of a disease or condition, such as cancer.

What are the different types of molecular pathology tests? ›

Techniques are numerous but include quantitative polymerase chain reaction (qPCR), multiplex PCR, DNA microarray, in situ hybridization, in situ RNA sequencing, DNA sequencing, antibody based immunofluorescence tissue assays, molecular profiling of pathogens, and analysis of bacterial genes for antimicrobial resistance ...

What is a Tier 1 and Tier 2 molecular pathology code? ›

Tier 1 codes generally describe testing for a specific gene or Human Leukocyte Antigen (HLA) locus. Tier 2 molecular pathology procedure codes (81400-81408) are used to report procedures not listed in the Tier 1 molecular pathology codes (81161, 81200-81383).

What is the CPT code for Level 3 molecular pathology procedure? ›

81402 MOLECULAR PATHOLOGY PROCEDURE LEVEL 3-- These tests are used to analyze nucleic acid for abnormalities that may be indicative of a variety of disorders. Cell lysis, nucleic acid stabilization, extraction, digestion, amplification, and detection are included in the molecular pathology procedure codes.

What major is molecular diagnostic? ›

To become a diagnostic molecular scientist, most positions require at least a bachelor's degree in subjects such as microbiology, molecular biology, biochemistry, chemistry, medical technology, biology, and related fields. Some of these professionals hold master's degrees, while others may also have completed PhDs.

What CPT code was deleted in 2023? ›

CPT® Code Changes 2023

All changes took effect January 1, 2023. Deleted codes will no longer be covered and deny as of January 1, 2023. These changes apply to these CPT Codes: Additions - 96202, 96203, 99418, G0316, G0317, G0318.

What are the new CPT changes for 2023? ›

CPT 2023 includes multiple new codes for COVID-19 vaccines and their administration. CPT also revised several codes to accommodate changes in patient ages as vaccine guidelines were updated.

What is the CPT code for Tier 1 molecular pathology? ›

Tier 1 Molecular Pathology Procedures CPT® Code range 81105- 81383.

What is the CPT code for unlisted molecular pathology procedure? ›

Unlisted Molecular Pathology - CPT Code 81479

If the analyte being tested is not represented by a Tier 1 code or is not accurately described by a Tier 2 code, the unlisted molecular pathology procedure code 81479 should be reported.

What is the CPT code for molecular pathology procedure physician interpretation and report? ›

Physician (M.D. or D.O.) interpretation of a molecular pathology procedure (e.g., CPT codes 81161-81408) may be reported with HCPCS code G0452 when medically reasonable and necessary.

What are the three types of molecular diagnostic techniques? ›

These technologies generally can be grouped into three approaches: polymerase chain reaction (PCR), hybridization, and next-generation sequencing (NGS). Currently, a lot of PCR and hybridization assays have been approved by FDA as in vitro diagnostics.

What are the three molecular diagnostic techniques for diagnosis of a disease? ›

A range of methods such as culture, electron microscopy, and pathogen genome detection by polymerase chain reaction (PCR) are used.

What are some molecular diseases? ›

Genetic Disorders
  • Genetic Disorders. Sickle Cell Disease.
  • Cystic fibrosis. Cystic Fibrosis Liver Disease.
  • Brain, Nerves and Spine. Huntington's Disease.
  • Cleft lip and palate. Cleft Lip and Palate.

What are the disadvantages of molecular testing? ›

These can include: Cost: Molecular methodologies are usually more expensive than standard traditional methodologies. Equipment and reagent costs could be prohibitive to some laboratories. As molecular methods become more standard, the costs could potentially decrease.

What are the benefits of molecular testing? ›

Specificity: Molecular methods minimize false positive test results by targeting the specific molecule of interest. Turn Around Time: In comparison with standard traditional culture methods, molecular methodologies usually offer better turn around times from receipt to result reporting.

What is an example of a molecular diagnosis? ›

Doctors can perform a molecular test of a common inherited hereditary cancer. For example, in breast cancer, they can investigate for specific inherited mutations in the BRCA1 and BRCA2 genes, which may increase the patient's risk of breast and ovarian cancer.

What tests are done in molecular lab? ›

  • Apheresis/Transfusion Service.
  • Blood Bank.
  • Chemistry.
  • Flow Cytometry.
  • Hematology.
  • Immunology.
  • Informatics.
  • Microbiology.

Is molecular testing the same as genetic testing? ›

Molecular testing is a type of genetic testing that offers significant insight into a person's genome. It can also detect signs of certain infections and diseases based on those conditions' unique genetics.

Why is molecular diagnostics important? ›

What is the role of protein analysis in molecular diagnostics? Molecular diagnostics evaluates proteins in a cell, tissue, or organism, including the shape, function, and patterns of expression. Research seeks to identify proteins involved when normal cellular pathways support malignant growth.

What is a Tier 2 code for molecular pathology? ›

The administrative handling of Tier 2 Molecular Pathology CPT codes 81400-81408 is addressed by this guideline.

What is the difference between Level 2 and Level 3 CPT? ›

The only difference between the history requirements for a level-II and a level-III visit is the review of systems (ROS). A level-II visit does not require an ROS, while a level-III visit requires a problem-pertinent ROS, which is a description of one system that is directly associated with the problem.

What is a Tier 1 disease? ›

Three conditions are designated by the Centers for Disease Control and Prevention (CDC) as Tier 1 genomic applications having the most evidence to support their early detection and intervention: hereditary breast and ovarian cancer syndrome (HBOC), Lynch syndrome (LS), and familial hypercholesterolemia (FH) [3].

What are CPT codes Level 3? ›

CPT Category III codes are a set of temporary (T) codes assigned to emerging technologies, services, and procedures. These codes are intended to be used for data collection to substantiate more widespread usage or to provide documentation for the Food and Drug Administration (FDA) approval process.

What is the CPT code for Level 3 follow up? ›

CPT code 99233 is assigned to a level 3 hospital subsequent care (follow up) note. 99233 is the highest level of non-critical care daily progress note.

At what level do CPT Category 3 codes reimburse? ›

When a Category III code is covered, it may be assigned reimbursement on a case-by-case basis or given an Ambulatory Payment Classification level by Medicare, which will pay for the facility/technical component of the procedure but will not pay a surgeon fee.

What areas are in molecular pathology? ›

Put simply, molecular pathology is the study of disease at the molecular level. This includes molecules found in tissues, organs, and even bodily fluids. The term “molecular diagnostics” is often used to describe the medical diagnosis aspect of the field.

What is a molecular diagnosis of human diseases? ›

Molecular diagnosis of human disorders is referred to as the detection of the various pathogenic mutations in DNA and /or RNA samples in order to facilitate detection, diagnosis, sub-classification, prognosis, and monitoring response to therapy.

Is molecular diagnostics the future? ›

In the near future, physicians will use molecular tests to diagnose and monitor diseases and predict genetic conditions as routinely as they use chemistry and hematology today. 4) The role of diagnostics will expand to include individual responses to customized drug therapies (eg, pharmacogenetics).

What is the release date for Category 3 CPT codes? ›

However, due to Category III code's early release policy, these codes are effective on January 1, 2020, following the six-month implementation period, which begins July 1, 2019.

Where can I get a list of CPT codes? ›

Visit the AMA Store for coding resources from the authoritative source on the CPT code set. You'll find print and digital versions of the codebook, online coding subscriptions, data files and coding packages.

How many new Category III codes are scheduled to take effect January 1 2023? ›

The American Medical Association (AMA) CPT Editorial Panel announced 13 add-on codes for digital pathology that will go into effect on Jan. 1, 2023.

What ICD-10 guidelines changed in 2023? ›

The April 2023 updates include 42 ICD-10-CM additions, seven deletions, and one revision. For ICD-10-PCS, there are 34 additions, no deletions, and no revisions. The updates are effective beginning April 1, 2023.

What does the triangle symbol next to a CPT code indicates? ›

The following symbols are used in CPT: ¯ A solid dot ( ) preceding a code number identifies a new CPT code. ¯ A solid triangle (▲ ) preceding a code number indicates a revised description for the specified code number.

How many levels of procedural coding are there? ›

There are three types of CPT codes: Category 1, Category 2 and Category 3. CPT is a registered trademark of the American Medical Association.

What is the difference between Level 1 and Level 2 CPT? ›

Note: Level I of HCPCS (CPT-4 codes) does not include codes for medical items/services that are regularly billed by suppliers other than physicians. Level II of the HCPCS is used primarily to identify products, supplies and services that are not identified by CPT-4codes.

Does Medicare pay for molecular testing? ›

Medicare covers certain types of genetic testing to help with diagnosis or with the treatment of particular conditions. Examples include: molecular diagnostic genetic tests (MDT) Next Generation Sequencing (NGS) genetic testing, also called multigene panel testing.

What is the CPT code range for pathology? ›

Pathology and Laboratory Procedures CPT® Code range 80047- 89398.

What is unlisted molecular pathology? ›

Unlisted codes provide the means of reporting and tracking services until a more specific code is established. If no such specific code exists, reporting the service using the appropriate unlisted service code would be appropriate. The service should be adequately documented in the medical record.

What are the CPT codes for pathology and Laboratory? ›

Pathology and Laboratory Procedures CPT® Code range 80047- 89398.

What do molecular pathologists do? ›

A molecular genetic pathologist provides information about gene structure, function, and alteration and applies laboratory techniques for diagnosis, treatment, and prognosis for individuals with related disorders.

What is a molecular pathology procedure level 1? ›

81400 MOLECULAR PATHOLOGY PROCEDURE LEVEL 1--These tests are used to analyze nucleic acid for abnormalities that may be indicative of a variety of disorders. Cell lysis, nucleic acid stabilization, extraction, digestion, amplification, and detection are included in the molecular pathology procedure codes.

What diseases are molecular diagnostics? ›

Molecular diagnostics are used to identify infectious diseases such as chlamydia, influenza virus and tuberculosis; or specific strains such as H1N1 virus or SARS-CoV-2.

How is molecular testing done? ›

Molecular testing and COVID-19

Polymerase chain reaction (PCR) tests are a type of molecular test that can detect COVID-19. They work by searching for the diagnostic genetic material unique to the virus and then multiplying that tiny segment of viral DNA for laboratory confirmation.

How molecular pathology helps in controlling various diseases? ›

The goal of molecular diagnostic assays in infectious diseases is to improve the detection of the underlying disease. Amplification of the target is often used followed by detection of the organism using a nucleic acid probe. These methods work well for viral, fungal, and parasitic diseases.

What does a molecular diagnostics laboratory do? ›

The Molecular Diagnostics Laboratory is responsible for the development and performance of molecular diagnostic tests for nucleic acid targets found in a variety of settings in medicine.

What is molecular pathology laboratory? ›

Molecular pathology performs testing of DNA and RNA specimens to provide diagnostic and predictive information to laboratory physician and clinicians, in order to help guide optimal care for patients with cancer and other diseases.

What do you mean by diagnosis at molecular level? ›

Listen to pronunciation. (muh-LEH-kyoo-ler dy-ug-NOH-sis) The process of identifying a disease by studying molecules, such as proteins, DNA, and RNA, in a tissue or fluid.

What does molecular pathology mean in medical terms? ›

Put simply, molecular pathology is the study of disease at the molecular level. This includes molecules found in tissues, organs, and even bodily fluids. The term “molecular diagnostics” is often used to describe the medical diagnosis aspect of the field.

What are the most common molecular diagnostic tests? ›

Polymerase chain reaction (PCR): The various forms of PCR are the most frequently used molecular diagnostic techniques in the diagnosis of infectious pathogens.

Is molecular diagnosis expensive? ›

As molecular testing plays a bigger role in diagnosing disease, supply chain professionals “need to understand that it is expensive, no matter how you do it,” Vanatta says.

How long does molecular testing take? ›

PCR and Molecular COVID-19 Test Results

If your test sample is sent to a laboratory to be analyzed, results are usually available in one to three business days. Turnaround time can depend on the demand for testing and available laboratory resources.

What is an example of a molecular test? ›

Molecular testing for cancer

Molecular testing can identify genes with links to certain cancers. For example, mutations in the BRCA1 or BRCA2 genes have links to hereditary breast and ovarian cancer syndrome. Molecular tests can also help identify biomarkers that suggest that certain treatments might be more effective.

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