Association for Molecular Pathology


June 2011, Volume 17, Number 2


Economic Affairs Committee Report

Jeffrey A. Kant, MD, PhD

By Jeffrey A. Kant, MD, PhD
Chair, Economic Affairs Committee


The Economic Affairs Committee (EAC) continues to focus on CPT code reform for molecular testing in the genetics and oncology arenas. In a departure from normal confidentiality practices, the AMA CPT Editorial Panel released a draft of the new system in March for public comment which ended mid-April.

The new system, modeled off the 2009 AMP EAC whitepaper (, is organized in two groups of CPT codes to replace the ‘stacking codes’ (83890-83914) over approximately two years. The first group (tier 1) provides individual codes for specific procedures performed in high volume or desired by payers. For example, CFTR screening and full sequencing assays would have unique codes, so too KRAS mutation testing. The second group (tier 2) is a series of 9 codes encompassing the large number of less commonly performed tests, divided according to increasing amounts of technical and professional resources. This is similar to the six CPT levels (88300-88309) used for Surgical Pathology services. For example, level 2 includes trinucleotide repeat disorders; level 4, sequencing of a single target/exon; level 9 covers full sequencing of genes>50 exons. New technologies (e.g. next generation sequencing) may fit within existing tiers as medical utility is established. There will be a ‘not otherwise specified’ code (ending in 99) for new or unlisted assays. An expert group with process and technical expertise will advise the CPT Editorial Panel on whether new assays should receive tier 1 codes or be placed with others of similar complexity in a tier 2 ‘level’ code.

Many thanks to all who have submitted data and completed surveys associated with parallel activities this Winter and Spring revolving around practice expense and professional work that go into the valuation of these codes for reimbursement. CMS will decide, probably in June, whether (and which) CPT codes go on the Physician Fee Schedule (PFS) or Clinical Laboratory Fee Schedule (CLFS). Professional component interpretive work is not recognized typically on the CLFS (83912 is an anomaly).

Representatives of EAC continue to participate in multi-stakeholder discussions seeking legislative recognition for PhD laboratory scientists with appropriate molecular training as ‘qualified healthcare practitioners.’ Qualified healthcare practitioners could bill for professional component reimbursement for relevant molecular CPT codes on the PFS. A revised group of ‘principles’ is being discussed from which statutory language will be derived, as Congressional authorization is required. Valuation of new CPT codes and ‘scoring’ of this proposal will be an important aspect of this process given the current fiscally conservative mood in Washington.

EAC coordinated with the Clinical Practice Committee to submit this past March a code change proposal for multiplex viral testing, an emerging assay format for which unambiguous CPT codes are not currently available. This proposal will be discussed within the Pathology Coding Caucus and with other interested parties. Hopefully it will become recognized as a set of CPT codes in 2013.

This Committee will be conducting discussions around more controversial concepts (e.g. value-based reimbursement, recoupment of developmental costs) with the hope of producing a whitepaper outlining a balanced perspective of issues in these areas.