In 2013, payment coding for molecular diagnostics tests focused on the purpose of the test performed rather than the method used. Specific information is available for molecular cytogenomic testing and cystic fibrosis carrier screening and diagnostic testing.

For more information on MoPath codes, especially those relevant to cystic fibrosis and cytogenomics testing, see the Laboratory Coding and Payment resources.

Molecular pathology (MoPath) codes provide a consistent framework for laboratories to label molecular diagnostics tests, enabling payers (i.e., Medicare, private insurance companies) to properly identify and bill for services. Until recently, these codes were based on the type of test being performed and not the analyte being analyzed. This made it difficult for payers to identify and properly reimburse molecular diagnostics tests. The new MoPath codes set out by the American Medical Association (AMA) Current Procedural Terminology (CPT) replace the previous methodology-based "stacking" MoPath codes with analyte-specific codes.

On January 1, 2013, the “stacking” codes (CPT 83890-83914; 88384-88386) were retired and are no longer available for provider billing. Therefore, laboratories are now required to use the new MoPath codes when billing for molecular diagnostic services.

MoPath codes are categorized into Tier 1 and Tier 2 codes:

  • Tier 1 codes represent the majority of commonly performed single-analyte molecular tests.
  • Tier 2 codes represent procedures that are generally performed in lower volumes than Tier 1 procedures (e.g., when the incidence of the disease being tested is rare), and correspond to nine ascending levels of technical resources and interpretive work performed by the physician or other qualified healthcare professional.

Gapfilling is one of two methodologies that the Centers for Medicare and Medicaid Services (CMS) can employ to set the Medicare payment rate for a new CPT code that is reimbursed under the Clinical Laboratory Fee Schedule (CLFS). The second is crosswalking, which involves benchmarking payment for the new code to the same rate for comparable, existing test(s) or code(s).

When CMS decides to gapfill payment for a new code, the local Medicare Administrative Contractors (MACs) are responsible for determining the appropriate fee schedule amounts in the first year. The map below shows a breakdown of MACs by jurisdication (as of December 2012). In the second year, CMS calculates a national payment rate based on the median of these local fee schedule amounts. This median payment rate is referred to as the National Limitation Amount (NLA).

MAC Jurisdiction Map

It is up to the discretion of each MAC to identify and use the most appropriate methodologies to set a gapfill payment amount. However, the following information should be considered in the rate setting process, if available:

  • Charges for the test and routine discounts to charges
  • Cost of resources required to perform the test
  • Payment amounts determined by other payers
  • Charges, payment amounts, and resources required for other tests that may be comparable or otherwise relevant.2
Gapfilling timelines (2012-2014)
What are the timelines for the gapfilling process?

The key milestones in the Medicare gapfilling process for the MoPath codes are shown in the timeline above.

Because Medicaid and commercial payers often use Medicare as a benchmark when developing their own payment policies, the outcome of gapfilling initiatives at the MAC level could influence payment rates set by other payers as well. Some private payers may also undertake activities similar to gapfilling to develop 2013 fee schedules for the MoPath codes.

Reimbursement for molecular diagnostic testing will be uncertain during the period when MACs are developing gapfill payment rates. Laboratories may experience delayed claims processing timelines before payment rates are established. While each MAC will operate on their own timelines, under Medicare guidelines they are required to either reimburse or deny a submitted claim within 30 calendar days of receipt, with interest to be paid on claims that are not reimbursed within this time window3. This may result in a series of "evolving" payment rates for molecular diagnostic claims in the first three months of 2013, as the MACs seek to comply with their claims processing responsibilities until gapfill amounts are finalized for submission to CMS by April 1, 2013.

In some cases, it may be medically necessary for physicians to provide interpretation and a written report for a molecular diagnostic test, beyond the technical reporting of test results. To allow physician billing and reimbursement for these services when performed, CMS created new Healthcare Common Procedure Coding System (HCPCS) code G0452 (Molecular pathology procedure; physician interpretation and report), which will go into effect in 2013. G0452 is not billable by non-physician geneticists and other lab personnel; any interpretation and reporting services performed by these individuals would be included in the payment rate for the associated MoPath CPT code.

Interested in receiving newsletters, case studies, and information on new applications? Enter your email address.
  1. Wisconsin Physician Services (WPS) is the Medicare Part B carrier for J6 and therefore processes provider claims for all services covered under Medicare Part B, which include outpatient laboratory services.
  2. Code of Federal Regulations (CFR) Title 42 - Public Health, Part 414 - Payment for Part B Medical and Other Health Services, Section 414.508 - Payment for a new clinical diagnostic laboratory test.
  3. Centers for Medicare and Medicaid Services. Medicare Claims Processing Manual; Chapter 1 - General Billing Requirements. Revised Oct 26, 2012. Available at:

Illumina is providing this review of the molecular pathology reimbursement landscape in collaboration with Quorum Consulting for educational purposes only. The content should not be considered legal advice. For official ruling on the MoPath codes readers should consult CMS, the AMA, and other sources as appropriate.