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AMA Makes Progress on Final CPT Codes for Molecular Diagnostics, But Job Far from Done


By Turna Ray

At a meeting held last week in Los Angeles, the American Medical Association's CPT Editorial Panel appeared to agree upon a handful of codes describing the most commonly used molecular diagnostics, PGx Reporter has learned. However, a second tier of codes, which would be based on the complexity of the technology and the level of effort involved in performing the test, still needs more work, according to sources knowledgeable of the procedures.

The AMA maintains Current Procedural Terminology, or CPT, codes through its CPT Editorial Panel. In order for healthcare providers to bill insurers for medical, diagnostic, or surgical procedures, they must use CPT codes published by the AMA to describe the work performed. With a new coding structure for molecular diagnostics, the AMA is attempting to develop a system for more accurately describing these tests so that payors have a better sense of what procedures are being performed and what they are paying for.

The CPT Editorial Panel is developing a two-tier coding system for genetic testing and molecular diagnostics. The first tier of codes is for commonly used tests, as well as those for uncommon genetic diseases. Recognizing the need for flexibility in the face of a rapidly advancing molecular diagnostics industry, the CPT Editorial Panel is also developing a second tier of codes, which will classify newer tests according to their technological complexity (PGx Reporter 6/16/2010).

The first coding tier may include pharmacogenetic tests for warfarin sensitivity, KRAS testing in colorectal cancer, tests for cystic fibrosis, and others. The second tier will likely include more complex tests such as Myriad Genetics' BRACAnalysis test for predicting hereditary risk of breast and ovarian cancer. BRACAnalysis is a Sanger sequencing-based test that Myriad performs at its CLIA-certified lab in Salt Lake City.

The Tier 1 workgroup has so far submitted 28 codes and is planning to submit more than 60 additional codes at the upcoming meeting of the CPT Editorial Panel in February.

In discussing Tier 1 tests, the Centers for Medicare and Medicaid Services raised a concern that many genetic tests may not identify abnormalities that require a physician's interpretation. This point was raised since "the most common major genetic disease, cystic fibrosis, is only abnormal in one individual in 30," a source who wished to remain anonymous told PGx Reporter last week.

Although meetings of AMA's CPT Editorial Panel are open to the public, the AMA requires participants to sign confidentiality agreements restricting them from discussing what went on outside the meeting. As such, PGx Reporter has gathered this update from a number of sources knowledgeable of what went on at the most recent meeting, but who have chosen to remain anonymous.

According to one source, the Tier 2 workgroup also made progress in its effort to develop codes for newer tests, but this category of tests will require additional work.

Tier 2 codes developed so far describe as many as 1,000 tests spanning nine coding levels. The first level describes tests that analyze single SNPs through "simple techniques." Level 9 is for the analysis of more than 50 exons in a single gene, and might comprise, for example, whole-genome sequencing tests, fibrillin 1 gene mutation testing for Marfan syndrome, and sequencing of the von Willebrand factor gene to identify disease-causing mutations in von Willebrand disease.

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Although progress has been made, the Tier 2 panel's "work will extend well into 2011," the source said.

For tests that don't fit into the second tier, healthcare providers can stack codes for non-specific technologies, such as DNA extraction and DNA amplification. However, the work group wants to retire the practice of stacking codes, and eventually plans to develop coding methods for all tests so that stacking will not be necessary.

Code stacking has presented difficulties for test providers as well as insurers. For example, at a conference this week, Lee Newcomer, senior vice president of oncology at United Healthcare, suggested that the company currently doesn't have a good sense of which specific genetic tests it is reimbursing for since providers choose from 19 or 20 CPT codes to describe different genetic processes via CPT stacking.

According to sources familiar with AMA's plans, the association might develop a new website that will list how hundreds of less-common and newer tests are assigned to the second tier of codes in order to speed up the assignment of Tier 2 codes to such tests. Meanwhile, tests that fall in the first tier of gene-specific codes will continue to go through the regular CPT coding cycle, which takes around two years.

Since the flow of new, increasingly complex molecular diagnostics will continuously funnel into Tier 2, the CPT Editorial Panel also discussed plans to develop a new molecular pathology expert panel to decide which tests will fall into this coding category going forward. The panel could include nine members, each serving staggered three-year terms. Panel members will come from the CPT Editorial panel, various stakeholder groups, the diagnostic industry, as well as commercial and academic labs.

Finally, the CPT Editorial Panel at last week's meeting did not come to any agreement on how to code for so-called boutique tests, such as Genomic Health's Oncotype DX and Agendia's MammaPrint, according to meeting attendees PGx Reporter spoke to. Genomic Health and Agendia did not comment for this article.

Jeffrey Kant, the Association of Molecular Pathology's economic affairs committee chair, previously told PGx Reporter that any new CPT coding structure would have to account for single-lab, multi-gene tests such as Oncotype DX and MammaPrint. However, Kant refused to comment for this article.

One industry insider who attended the meeting last week said that with regard to boutique tests, it is likely that such diagnostics will receive a unique CPT code. However, the issue that hasn't yet been resolved is whether that code assigned to a singular company's test can be used by other labs that wish to run the test.

"They still haven't agreed on whether another lab can use this unique CPT code, or whether they would need some special certification in order to run a [boutique] test and use this unique CPT code," the source said.

The AMA first developed and published CPT codes in 1966. The group owns the copyright for CPT and collects royalties from their use. Although CPT is the most widely used coding system in the medical field for reimbursement, other coding structures include the Systematized Nomenclature of Medicine, owned and maintained by CAP, as well as International Classification of Diseases codes.

The new CPT coding structure for molecular diagnostics is expected take hold in 2012, but before then the CPT editorial panel can make significant changes to the structure proposed currently.