The Association for Molecular Pathology is in the midst of creating a framework for current procedural terminology coding for next-generation sequencing-based assays, which it plans to complete by the end of June.
Following the completion of the proposal, the committee will release it for feedback from stakeholders and then submit a formal proposal to the American Medical Association's CPT Editorial Panel. Depending on the feedback that is received, the earliest the proposed CPT codes could be adopted is 2014, according to Jeffrey Kant, chair of AMP's Economic Affairs Committee.
Kant told Clinical Sequencing News that AMP decided to tackle the issue of CPT codes for NGS assays because "the promise of the technology has continued to rise and it [holds great] potential in various clinical applications." Additionally, "it's an expensive technology to perform, so if it's going to be useful, people are going to have to get paid for it."
He said that AMP plans to submit a code change proposal after gaining feedback from a wide variety of stakeholders and that the draft proposal will also be referred to the AMA's Molecular Pathology CPT Workgroup before being submitted to the CPT Editorial Panel.
Kant said that there would be different codes for different types of tests — including targeted panels, whole-exome tests, or whole-genome sequencing tests — and there may also be different codes depending on specific genes or disease indications.
"We're still working on the technical aspects," he said, "but I don't anticipate that you can cover all of next-gen sequencing with one or two codes."
AMP's effort parallels an ongoing AMA initiative to create new CPT codes to eliminate so-called "code-stacking" for complex molecular tests.
Early last year, AMA's CPT Editorial Panel Molecular Pathology Coding Workgroup released two types of codes for molecular pathology tests — Tier 1 codes for commonly performed analyte-specific tests and Tier 2 codes describing less common tests. These codes stopped short of high-throughput sequencing-based assays, however (See CSN sister publication PGx Reporter 3/16/2011).
Developing CPT codes for next-gen sequencing tests is particularly tricky, Kant said, because the same test can yield information on a wide range of diseases.
"If you have a technology that impacts a wide swath of medicine, it becomes harder to make those types of decisions," he said. "That's why feedback from payors is equally as important as feedback from labs."
Kant noted that the improved CPT codes will provide "a way for payors to know what they're paying for so they can make coverage decisions." Code-stacking does not provide this level of granularity, but neither would a general CPT code for whole-exome or whole-genome sequencing with no ties to a specific disease.
Payors need a "particular test or procedure to be tied to a particular patient with a particular condition," which is a "challenge with a technology that interrogates multiple targets, potentially up to the entire genome, at a single time."
Kant said the eventual proposal will not resolve this problem completely. Even if the team creates a separate CPT code for each gene, actual sequencing assays will be different combinations of genes. So for a tumor panel, for instance, one lab may offer a targeted panel of one set of genes, while another lab may offer a different set of genes. He declined to disclose specifics about how AMP would address this issue and said the details are still being worked out.
The proposed framework will also take into account the amount of interpretation and analysis that is offered, which also differs from lab to lab. Dealing with "differing levels of interpretation is an active part of our proposal," he said.
For instance, the amount of interpretation that goes into a whole-genome or exome sequencing test for a child with an unknown disorder is completely different than a targeted sequencing panel that screens for a set of known pathogenic variants.
Kant said that AMP will circulate its draft CPT guidelines to professional organizations, clinical laboratories, and payers to solicit feedback. The AMP workgroup will then incorporate that feedback into a code change proposal and submit it to the AMA.
After the proposal is submitted, it goes through a formal comment process, where the pathology coding caucus and other advisors to the AMA Editorial Panel comment on the proposal. This process lasts about three to four months from the submission deadline. If the caucus supports the proposal, it goes to the AMA Editorial Panel for a vote, and the changes are then incorporated into the following year's guidelines.
Kant said that if things go smoothly, the new codes could be in place as early as 2014.
Despite not yet having CPT codes, some groups have already reported receiving reimbursement for next-gen sequencing-based tests.
The Medical College of Wisconsin, the University of California of Los Angeles, and Ambry Genetics have all reported receiving reimbursement for sequencing tests for children with undiagnosed diseases. So far none have formal agreements with providers and reimbursement is on a case-by-case basis (CSN 8/24/2011 and CSN 3/7/2012).
Additionally, Sequenom has reported receiving reimbursement for its MaterniT21 Plus trisomy test. The company recently struck its first contract with Multiplan Incorporated and has said it has a goal of securing contracts with two national providers by the year's end (CSN 5/9/2012).