Billing and Coding: Molecular Pathology and Genetic Testing

Internet-Only Manuals (IOMs):

• CMS IOM Publication 100-02, Medicare Benefit Policy Manual,
  • Chapter 15, Section 80 Requirements for Diagnostic X-Ray, Diagnostic Laboratory, and Other Diagnostic Tests, and Section 280 Preventive and Screening Services
• CMS IOM Publication 100-04, Medicare Claims Processing Manual,
  • Chapter 16, Section 10 Background, Section 40.8 Date of Service (DOS) for Clinical Laboratory and Pathology Specimens and Section 120.1 Negotiated Rulemaking Implementation
  • Chapter 18 Preventive and Screening Services
• CMS IOM Publication 100-08, Medicare Program Integrity Manual,
  • Chapter 3 Verifying Potential Errors and Taking Corrective Actions

Social Security Act (Title XVIII) Standard References:

• Title XVIII of the Social Security Act, Section 1833(e) states that no payment shall be made to any provider of services or other person under this part unless there has been furnished such information as may be necessary in order to determine the amounts due such provider or other person under this part for the period with respect to which the amounts are being paid or for any prior period.
• Title XVIII of the Social Security Act, Section 1862 [42 U.S.C. 1395Y] (a) states notwithstanding any other provision of this title, no payment may be made under part A or part B for any expenses incurred for items or services—
  • (1)(A) which, except for items and services described in a succeeding subparagraph, are not reasonable and necessary for the diagnosis or treatment of illness or injury or to improve the functioning of a malformed body member.

Code of Federal Regulations (CFR) References:

• CFR, Title 42, Subchapter B, Part 410 Supplementary Medical Insurance (SMI) Benefits, Section 410.32 Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions
• CFR, Title 42, Section 414.502 Definitions
• CFR, Title 42, Subpart G, Section 414.507 Payment for clinical diagnostic laboratory tests and Section 414.510 Laboratory date of service for clinical laboratory and pathology specimens
• CFR, Title 42, Part 493 Laboratory Requirements
• CFR, Title 42, Section 493.1253 Standard: Establishment and verification of performance specifications
• CFR, Title 42, Section 1395y (b)(1)(F) Limitation on beneficiary liability

Medicare National Correct Coding Initiative (NCCI) Policy Manual

• Chapter 10, Section F Molecular Pathology

This Billing and Coding Article provides billing and coding guidance for molecular pathology services, genomic sequencing procedures and other multianalyte assays, multianalyte assays with algorithmic analyses, and applicable proprietary laboratory analyses codes and Tier 1 and Tier 2 molecular pathology procedures. Consistent with CFR, Title 42, Section 414.502, advanced diagnostic laboratory tests must provide new clinical diagnostic information that cannot be obtained from any other test or combination of tests.

This instruction focuses on coding and billing for molecular pathology diagnostics and genetic testing. Nothing stated in this instruction implies or infers coverage.

Molecular diagnostic testing and laboratory developed testing are rapidly evolving areas and thus present billing and coding challenges. Due to the rapid changes in this field, the CMS Clinical Laboratory Fee Schedule pricing methodology does not account for the unique characteristics of these tests. These challenges have led to services being incorrectly coded and improperly billed. It is the MAC’s responsibility to pay for services that are medically reasonable and necessary and coded correctly. The intent of this billing and coding article is to provide guidance for accurate coding and proper submission of claims.

Prior to January 1, 2013, each step of the process of a molecular diagnostic test was billed utilizing a separate CPT code to describe that process. Such billing was termed “stacking” with each step of a molecular diagnostic test utilizing a different CPT code to create a “Stack”. The updates to CPT after January 1, 2013, were to create a more granular, analyte and/or gene specific coding system for these services and to eliminate, or greatly reduce, the “stacking” of codes in billing for molecular pathology services. The current CPT and HCPCS codes include all analytic services and processes performed with the test. This approach has resulted in the following subgroups of CPT codes:

• Genomic Sequencing Procedures
• Multi-Analyte with Algorithmic Analyses (MAAAs)
• Proprietary Laboratory Analyses (PLA codes)
• Tier 1 - Analyte Specific codes; a single test or procedure corresponds to a single CPT code
• Tier 2 – Rare disease and low volume molecular pathology services

However, the updates to CPT since 2013 have NOT resulted in the elimination or reduction of stacking of codes in billing. Rather the billing of multiple CPT codes for a unique molecular pathology or genetic test has significantly increased over the last two years. Coding issues have been identified throughout all the molecular pathology coding subgroups, but these issues of billing multiple CPT codes for a specific test have been significant in the Tier 2 (81400 - 81408) and Not Otherwise Classified (81479 and 81599) codes. Per Title 42 of the United States Code (USC) Section 1320c-5(a)(3), providers are required by law to “provide economical medical services and then, only where medically necessary”. In keeping with Title 42 of the USC Section 1320c-5(a)(3), claims inappropriately billed utilizing stacking or unbundling of services will be rejected or denied.

Many applications of the molecular pathology procedures are not covered services given a 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 meet the medically 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 medically reasonable and necessary testing for the beneficiary. Certain molecular pathology procedures may be subject to medical review (medical records requested). The medical records must support the service billed.

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) are subject to automatic denials since these tests are generally not relevant to a Medicare beneficiary.

The following types of tests are examples of services that are not relevant to a Medicare beneficiary, are not considered a Medicare benefit (statutorily excluded), and therefore will be denied as Medicare Excluded Tests:

• Tests considered screening in the absence of clinical signs and symptoms of disease that are not specifically identified by the law
• Tests performed to determine carrier screening
• Tests performed for screening hereditary cancer syndromes
• Prenatal diagnostic testing
• Tests performed on patients without signs or symptoms to determine risk for developing a disease or condition
• Tests performed to measure the quality of a process
• Tests without diagnosis specific indications
• Tests identified as investigational by available literature and/or the literature supplied by the developer and are not a part of a clinical trial

Screening services such as pre-symptomatic genetic tests and services used to detect an undiagnosed disease or disease predisposition are not a Medicare benefit and are not covered.

In accordance with the Code of Federal Regulations, Title 42, Subchapter B, Part 410, Section 410.32, the referring/ordering practitioner must have an established relationship with the patient, and the test results must be used by the ordering/referring practitioner in the management of the patient’s specific medical problem.

For ease of reading, the term “gene” in this document will be used to indicate a gene, region of a gene, and/or variant(s) of a gene.

Coding Guidance

Notice: It is not appropriate to bill Medicare for services that are not covered as if they are covered. When billing for non-covered services, use the appropriate modifier.

Code selection is based on the specific gene(s) that is being analyzed. Codes that describe tests to assess for the presence of gene variants use common gene variant names. All of the listed variants would usually be tested; however, these lists are not exclusive. If additional variants, for the same gene, are also tested in the analysis they are included in the procedure and are not reported separately.

Full gene sequencing is not reported using codes that assess for the presence of gene variants unless the CPT code specifically states full gene sequence in the descriptor.

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). These codes represent rare diseases and molecular pathology procedures that are performed in lower volumes than Tier 1 procedures. These codes should rarely, if ever, be used unless instructed by other coding and billing articles.

If billing utilizing the following Tier 2 codes, additional information will be required to identify the specific analyte/gene(s) tested in the narrative of the claim or the claim will be rejected:

• 81400
• 81401
• 81402
• 81403
• 81404
• 81405
• 81406
• 81407
• 81408

Unlisted Molecular Pathology - CPT Code 81479

Providers are required to use a procedure code that most accurately describes the service being rendered. 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.

However, when reporting CPT code 81479, the specific gene being tested must be entered in block 80 (Part A for the UBO4 claim), box 19 (Part B for a paper claim) or electronic equivalent of the claim. Failure to include this information on the claim will result in Part A claims being returned to the provider and Part B claims being rejected. In addition, medical records may be requested when 81479 is billed. The medical record must clearly identify the unique molecular pathology procedure performed, its analytic validity and clinical utility, and why CPT code 81479 was billed.

When multiple procedure codes are submitted on a claim (unique and/or unlisted), the documentation supporting each code must be easily identifiable. If on review the contractor cannot link a billed code to the documentation, these services will be denied based on Title XVIII of the Social Security Act, Section 1833.

Testing for Multiple Genes and Next Generation Sequencing (NGS) testing

A panel of genes is a distinct procedural service from a series of individual genes. All services billed to Medicare must be medically reasonable and necessary. As such, if a provider or supplier submits a claim for a panel, then the patient’s medical record must reflect that the panel was medically reasonable and necessary. Alternatively, if a provider or supplier bills for individual genes, then the patient’s medical record must reflect that each individual gene is medically reasonable and necessary.

Genes can be assayed serially or in parallel. Genes assayed on the same date of service are considered to be assayed in parallel if the result of one assay does not affect the decision to complete the assay on another gene, and the two genes are being tested for the same indication.

Genes assayed on the same date of service are considered to be assayed serially when there is a reflexive decision component where the results of the analysis of one or more genes determines whether the results of additional analyses are medically reasonable and necessary.

If the laboratory method is NGS testing, and the laboratory assays two or more genes in a patient in parallel, then those two or more genes will be considered part of the same panel, consistent with the NCCI manual Chapter 10, Section F, number 8.

If the laboratory assays genes in serial, then the laboratory must submit claims for genes individually. The order by the treating clinician must reflect whether the treating clinician is ordering a panel or single genes, and additionally, the patient’s medical record must reflect that the service billed was medically reasonable and necessary.

CMS payment policy does not allow separate payment for multiple methods to test for the same analyte.

We would not expect that a provider or supplier would routinely bill for more than one distinct laboratory genetic testing procedural service on a single beneficiary on a single date of service. In the rare circumstance that more than one distinct genetic test is medically reasonable and necessary for the same beneficiary on the same date of service, the provider or supplier must attest that each additional service billed is a distinct procedural service using the 59 modifier.

-59 Modifier; Distinct Procedural Service

This modifier is allowable for radiology services and it may also be used with surgical or medical codes in appropriate circumstances.

When billing, report the first code without a modifier. On subsequent lines, report the code with the modifier. Under certain circumstances, it may be necessary to indicate that a procedure or service was distinct or independent from other non-Evaluation and Management (E/M) services performed on the same day. Modifier 59 is used to identify procedures/services, other than E/M services, that are not normally reported together, but are appropriate under the circumstances. Documentation must support a different session, different procedure or surgery, different site or organ system, separate incision/excision, separate lesion, or separate injury (or area of injury in extensive injuries) not ordinarily encountered or performed on the same day by the same individual. However, when another already established modifier is appropriate it should be used rather than modifier 59. Only if a more descriptive modifier is unavailable, and the use of modifier 59 best explains the circumstances, should modifier 59 be used.

The use of the 59 modifier will be considered an attestation that distinct procedural services are being performed rather than a panel and may result in the request for medical records.

Frequent use of the 59 modifier may be subject to medical review.

Genomic Sequencing Profiles (GSP)

When a GSP assay includes a gene or genes that are listed in more than one code descriptor, the code for the most specific test for the primary disorder sought must be reported, rather than reporting multiple codes for the same gene(s). Reporting multiple codes for the same gene will result in claim rejection or denial.

Multianalyte Assays with Algorithmic Analyses (MAAAs) and Proprietary Laboratory Analyses (PLA)

A valid PLA code takes precedence over Tier 1 and Tier 2 codes and must be reported if available. Reporting of a Tier 1 or Tier 2 code in this circumstance or in addition to a PLA code is incorrect coding and will result in claim rejection or denial.

The results of individual component procedure(s) that are inputs to the MAAAs may be provided on the associated reporting; however, these assays are not reported separately using additional codes. Claims reporting such will be rejected or denied.

All MAAAs, including those that do not have a Category I code, may be found in Appendix O of the CPT Manual. When a specific MAAA procedure is not listed in Appendix O, the service must be reported with the unlisted MAAA procedure code 81599. Additionally, when an analysis is performed that may fall within the descriptor of one of the specific MAAA CPT codes, but the proprietary name is not included, the service should be reported with 81599.

When reporting CPT code 81599, a description of the analysis (totaling less than 80 characters) must be entered in block 80 (Part A for the UBO4 claim), box 19 (Part B for a paper claim) or electronic equivalent of the claim. Failure to include this information on the claim will result in Part A claims being returned to the provider and Part B claims being rejected. In addition, medical records may be requested when 81599 is billed. The medical record must clearly identify the analysis performed, its analytic validity and clinical utility, and why CPT code 81599 was billed.

Date of Service (DOS)

As a general rule, the DOS for either a clinical laboratory test or the technical component of a physician pathology service is the date the specimen was collected. In situations where a specimen is collected over a period of two calendar days, the DOS is the date the collection ended. There are some exceptions to the DOS policy. Please refer to the CMS IOM Publication 100-04, Chapter 16, Section 40.8 for complete information related to the DOS policy.

Documentation Requirements

1. All documentation must be maintained in the patient's medical record and made available to the contractor upon request.
2. Every page of the record must be legible and include appropriate patient identification information (e.g., complete name, dates of service[s]). The documentation must include the legible signature of the physician or non-physician practitioner (NPP) responsible for and providing the care to the patient.
3. The submitted medical record must support the use of the selected ICD-10-CM code(s). The submitted CPT/HCPCS code must describe the service performed.
4. In accordance with CFR Section 410.32, the medical record must contain documentation that the testing is expected to influence treatment of the condition toward which the testing is directed and will be used in the management of the beneficiary's specific medical problem.
5. The medical record must support that the referring/ordering practitioner who ordered the test for a specific medical problem is treating the beneficiary for this specific medical problem. An example of documentation that could support the practitioner’s management of the beneficiary’s specific medical problem would be at least two E/M visits performed by the ordering/referring practitioner over the previous six months.
6. The medical record must include documentation of how the ordering/referring practitioner used the test results in the management of the beneficiary’s specific medical problem.
7. The ordering physician/NPP documentation in the medical record must include, but is not limited to, history and physical or exam findings that support the decision making, problems/diagnoses, relevant data (e.g., lab testing, imaging results).
8. The medical record from the ordering physician/NPP must clearly indicate all tests that are to be performed.
9. Documentation requirements of the performing laboratory (when requested) include, but are not limited to, lab accreditation, test requisition, test record/procedures, reports (preliminary and final), and quality control record.