CMS accepted comments on the proposed Physician Fee Schedule rules for 2027 until September 14, 2026.
Comments are posted and searchable here:
https://www.regulations.gov/docket/CMS-2026-2377/comments
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CAP Example Search
For example, the comments by CAP are here (38pp). After its highlights, CAP's #1 topic was revaluation of 88305 88307 (common biopsy codes) and #2 was Software as a Medical Service (SaMS). #4 was an RFI on the AMA CPT
https://www.regulations.gov/comment/CMS-2026-2377-40551
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See my prior summary of OPPS comments here. Below is a direct AI summary of six comment letters by Chat GPT.
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CY 2027 PFS Comments:
SaMS, AMA CPT, and the Parallel CLIA RFI
Across six CY 2027 PFS comment letters, the laboratory community speaks with striking unity on SaMS: CMS should not remove algorithmic laboratory analyses from the CLFS while the agency is still deciding, through its CLIA RFI, whether data-only and software-intensive testing remains laboratory activity. All six support continued use of AMA CPT, although several seek greater transparency, laboratory representation, applicant participation, and scrutiny of licensing fees. The groups differ mainly in fallback strategy: preserve CLFS pricing, permit direct laboratory billing, avoid local contractor pricing, establish national rates, and defer implementation until CMS resolves CLIA jurisdiction, enrollment, coinsurance, and operational consequences.
1. American Clinical Laboratory Association
ACLA offers the most comprehensive—and in places the most aggressive—response.
SaMS. ACLA rejects CMS’s premise that algorithmic analysis of previously generated laboratory data ceases to be laboratory testing. A genomic data file or digital pathology image remains information derived from a human specimen, and the algorithm may be the essential step that turns it into a clinically actionable result. ACLA asks CMS to withdraw the proposal and retain the ten codes on the CLFS.
ACLA also finds CMS’s code list technically unreliable. For example, 0511U requires intensive wet-lab tumor culture, 81416 requires collection and sequencing of another person’s specimen, and 0208U has been deleted. This illustrates the danger of classifying tests merely by scanning CPT descriptors for the absence of an explicitly stated laboratory method.
Additional arguments include:
Contractor pricing under the PFS would be less transparent and less predictable than CLFS crosswalk and gapfill.
Moving the services to the PFS would impose 20% coinsurance, potentially discouraging clinically necessary testing.
Laboratories could lose the ability to bill directly and instead become vendors to physician practices or hospitals that did not perform the analysis.
If CMS is worried about unregulated software vendors, it could retain CLFS payment but require performance by an accredited, CLIA-certified laboratory.
As a fallback, if CMS nevertheless proceeds, ACLA asks for direct laboratory billing and national PFS rates based on existing CLFS rates rather than unstructured MAC contractor pricing.
AMA CPT RFI. ACLA takes a deliberately mixed position. It does not support simultaneous competing code systems, which would defeat standardization and interoperability. Nor does it think ICD-10-PCS is presently capable of replacing CPT for laboratory services. Any transition would probably require a decade or more, and ACLA recommends a formal multistakeholder study before CMS considers replacing CPT.
But ACLA is far more critical of AMA than CAP or AMP. It highlights:
Insufficient laboratory representation in CPT governance.
Confidential processes and limited public scrutiny.
Lack of structure and standardized terminology within the code set.
AMA’s proposed “per reportable laboratory test result” royalty model, which reportedly would have raised licensing costs by more than 2,400% for some laboratories—even charging royalties for results not reported with CPT codes.
Thus, ACLA’s position is essentially: retain one national coding standard for now, but scrutinize both AMA governance and its licensing economics.
CLIA RFI. ACLA attaches a complete response to the separate CMS/CDC CLIA RFI. Its central distinction is between two kinds of data-only facilities:
A facility that examines patient-specific digital laboratory information and generates the patient-facing result should be a laboratory under CLIA—even if its work is entirely algorithmic or “dry.”
A facility that merely provides analytical or interpretive support to a CLIA laboratory, without issuing the result, could receive a limited CLIA exception, provided the reporting laboratory retains responsibility.
ACLA also recommends clearer requirements for algorithm validation, personnel qualifications, laboratory-director oversight, data quality, documentation, traceability, and exchanges of specimen-derived data between laboratories and software vendors.
Most importantly, ACLA says CMS should answer these CLIA questions before changing payment classification. Payment policy should follow the regulatory definition of laboratory testing, not preempt it.
2. AdvaMed
SaMS. AdvaMed agrees that software-heavy technologies require a more coherent payment framework, but it opposes removing laboratory SaMS from the CLFS now. When an algorithm is validated, performed, and reported under a CLIA laboratory’s quality system, it remains a CDLT. The apparent separation between data generation and subsequent analysis is often artificial because the two processes remain operationally and clinically integrated.
AdvaMed argues that CMS’s concern about opaque algorithm costs is a correctable weakness in the existing pricing process—not a reason to change benefit categories. It also rejects beneficiary coinsurance as a program-integrity mechanism.
AdvaMed asks CMS to:
Retain the services on the CLFS.
Develop a standardized SaMS definition coordinated with FDA and other agencies.
Permit separate payment when a subsequent algorithm produces distinct, medically necessary, actionable information from an existing specimen.
If CMS proceeds, AdvaMed recommends national PFS rates approximating existing CLFS rates, direct billing by the performing laboratory, and greater transparency and manufacturer engagement in contractor pricing.
AMA CPT RFI. AdvaMed favors improving CPT, not replacing it. Its principal complaints are slow timelines, inconsistent decisions, inadequate applicant engagement, uncertain evidentiary expectations, and insufficient transparency around policy changes and conflicts of interest.
It emphasizes a “circular barrier” for first-in-class technology: Category I codes require utilization and evidence that are difficult to generate without a code, while Category III codes often receive uncertain contractor pricing and may take years to reach Category I.
AdvaMed sees useful procedural lessons in ICD-10-PCS—public discussion, visible timelines, and direct applicant interaction—but does not consider ICD-10-PCS a substitute for CPT, particularly because it lacks a logical home for laboratory procedures.
CLIA RFI. AdvaMed does not provide a separate detailed CLIA blueprint. Its point is sequencing: because the active CLIA RFI could produce conclusions that contradict or invalidate the PFS proposal, CMS should defer SaMS reclassification until the CLIA inquiry is resolved.
3. Association for Molecular Pathology
SaMS. AMP supports distinguishing “Software as a Medical Service” from generic “Software as a Service,” but strongly opposes moving laboratory SaMS codes from the CLFS.
AMP describes data analysis as an inseparable professional component of the diagnostic-testing continuum. When software generates a reportable result, is necessary to produce or interpret that result, and contributes to patient care, a CLIA-certified laboratory should remain responsible for its validity. AMP therefore asks CMS to clarify that the CLIA definition of laboratory includes facilities examining information obtained from materials derived from the human body.
AMP also invokes PAMA: applicable laboratories have just completed private-payer data reporting for CY 2027 rates. Moving selected codes now would bypass rather than improve the market-based transparency Congress designed.
AMA CPT RFI. AMP presents the most straightforward defense of CPT. It corrects what it views as misconceptions in the RFI: applications may come from individuals and organizations, the CPT Advisory Committee does not itself create codes, and the Editorial Panel is an independent volunteer body receiving broad clinical input.
AMP stresses that:
CPT describes services.
CPT does not determine coverage, medical necessity, or Medicare payment.
Additional systems such as MolDx DEX Z-codes demonstrate the expense and confusion created by layering competing identifiers onto CPT.
AMP supports continued CPT use, coupled with collaborative improvements involving AMA, CMS, and the specialty societies.
CLIA RFI. AMP uses the CLIA RFI to support delay. CMS is simultaneously questioning how data-only facilities should be regulated while the PFS proposal assumes their work is not laboratory testing. AMP considers that internally premature and potentially inconsistent. Unlike ACLA, however, this PFS letter does not develop a detailed regulatory structure for different types of data-only entities.
4. Coalition for 21st Century Medicine
C21 provides the most operationally detailed response after ACLA.
SaMS. C21 argues that many kinds of raw laboratory data have little clinical value before computational processing. A FASTQ file is not analogous to an already interpretable radiology image; bioinformatic analysis may be the step that creates the clinically meaningful result.
C21 points to CMS precedent supporting its position:
CMS has issued CLIA certificates to dry-lab facilities.
CMS guidance recognizes that facilities interpreting digital laboratory data may operate under another laboratory’s certificate or obtain their own.
Some affected codes already carry CLIA payment edits.
C21 also identifies a potential inconsistency: the same laboratory analysis could remain on the CLFS when performed with the wet-lab component but move to the PFS when applied to data received from another laboratory, even though the reporting entity and clinical output are identical.
C21 considers the CLFS superior because it has crosswalk, gapfill, statutory pricing factors, and eventually PAMA private-payer data. The PFS RVU structure does not naturally capture software development, computing, storage, cloud services, or laboratory-scientist work. Unbounded contractor pricing would create geographic variation and investment uncertainty.
C21 also highlights unresolved coding problems: AMA no longer permits algorithm-only tests to receive PLA codes; the proposed CMAA category is not yet available; and Category III codes lack a predictable path to national payment.
If CMS proceeds, C21 requests:
Direct PFS billing by the performing laboratory.
National rates crosswalked from the proposed OPPS New Technology APC rates, rather than local contractor pricing.
Stakeholder development of a permanent, predictable rate-setting process.
AMA CPT RFI. C21 strongly opposes eliminating AMA CPT but offers the most specific CPT reforms:
Expand laboratory, diagnostic-manufacturer, patient, and Medicare representation on the PLA TAG, MPAG, and Pathology Coding Caucus.
Make those advisory meetings accessible to applicants and interested parties subject to confidentiality rules.
Require an advisory body contemplating a negative recommendation to explain its concerns and allow the applicant to respond.
Provide 30–60 days for comment on consequential coding-policy changes.
Publish more informative decision rationales and apply precedents and subjective standards such as “widespread use” consistently.
C21 specifically criticizes recent changes involving algorithm-only PLA eligibility, the possible CMAA category, and distributive-testing guidance as insufficiently transparent.
CLIA RFI. C21 argues that the PFS proposal is ahead of CMS’s own regulatory work. If the CLIA process ultimately concludes that dry-lab analyses must be performed under CLIA, the rationale for classifying them as non-laboratory “other diagnostic tests” could collapse. Payment reclassification should therefore wait.
5. College of American Pathologists
SaMS. CAP urges CMS not to move the ten identified SaMS laboratory analyses from the CLFS to the PFS. These technologies may be ordered by physicians, but they are not physician services and do not share the physician-work and practice-expense basis of the PFS.
CAP emphasizes a somewhat different concern from the laboratory trade associations: placing SaMS on the PFS would force software technologies to compete with physician services within a budget-neutral payment system. This could simultaneously reduce physician payments and fail to provide stable reimbursement for the development, maintenance, and updating of beneficial technologies.
CAP also observes that CMS lacks transparent information about proprietary algorithm costs. Contractor pricing rather than assignment of RVUs only demonstrates how poorly SaMS fits within the resource-based PFS methodology. Moving the services would also introduce beneficiary coinsurance without solving the underlying cost-transparency problem.
CAP’s long-term answer is not simply permanent CLFS placement. It argues that neither the CLFS nor the PFS provides an ideal permanent framework. CMS should work with stakeholders to develop a dedicated SaMS payment system that:
- Remains budgetarily separate from the PFS.
- Reflects the distinctive costs of software technologies.
- Promotes cost transparency.
- Avoids shifting costs to physicians, practitioners, or beneficiaries.
- Supports continuing investment and adoption.
Until that framework exists, the affected services should remain on the CLFS.
CAP also asks for a clinically informed expert process to determine which individual services actually satisfy CMS’s SaMS definition. CPT 81416 illustrates the danger of relying on descriptors alone: the service includes sequencing a patient specimen as well as subsequent analysis and therefore cannot accurately be characterized as purely stand-alone software.
AMA CPT RFI. CAP provides a strong institutional defense of CPT. It rejects the characterization of CPT as a monopoly and instead describes it as a uniform, clinically grounded, continuously maintained national standard. A single nomenclature permits consistent claims submission, processing, auditing, and comparison across payers and settings.
CAP cites MolDx DEX Z-codes as a practical warning about competing systems. Requiring molecular pathology claims to carry both CPT codes and separate Z-codes has increased administrative burden, expense, and billing uncertainty and may delay access to testing.
CAP also stresses distinctions that it believes the CMS RFI risks blurring:
- CPT codes describe services.
- The RUC recommends relative resource values.
- CMS determines Medicare coverage, medical necessity, and payment.
ICD-10-PCS is not a realistic substitute because it was designed for inpatient hospital procedures and cannot describe the full range of physician and laboratory services across settings. CAP therefore supports continued use of CPT while encouraging CMS, AMA, and the specialty societies to identify improvements within the existing framework.
CLIA RFI. Unlike ACLA, AMP, AdvaMed, C21, and the PFS Coalition, CAP does not make the parallel CLIA RFI a central reason to postpone the PFS proposal. Nor does its PFS letter offer a detailed position on how CLIA should regulate data-only facilities.
Instead, CAP approaches the boundary problem through service-specific clinical review. It asks CMS to establish an expert process for determining whether a code truly represents stand-alone SaMS rather than a combined laboratory and computational service.
Thus, CAP reaches the same immediate conclusion—do not remove the services from the CLFS—but by a somewhat different route. Its central concern is that SaMS does not belong in a budget-neutral physician payment system, while the other organizations place greater weight on CMS deciding the antecedent CLIA jurisdiction question before altering Medicare payment classification.
6. Physician Fee Schedule Pathology Payment Coalition
SaMS. The PFS Coalition distinguishes algorithm-only LDTs and laboratory SaMD from generic stand-alone software. An analysis based on the output of an underlying wet-lab process remains inseparably connected to the specimen, whether performed immediately or months later.
The Coalition favors the CLFS because it already prices algorithmic tests through crosswalk and gapfill and, under PAMA, ultimately reflects private-market rates. By contrast, PFS resource valuation does not adequately recognize R&D, bioinformatics, cloud hosting, system updates, and laboratory personnel.
Its fallback recommendations are unusually practical:
Allow laboratories to bill the PFS directly.
Do not force laboratories to enroll as IDTFs merely to bill SaMS.
If IDTF enrollment is required, delay implementation at least one year.
Reject local contractor pricing and establish national rates by crosswalking to the proposed New Technology APC bands.
AMA CPT RFI. The Coalition supports retaining AMA CPT. Rebuilding the coding infrastructure would be highly disruptive, while ICD-10-PCS lacks both a laboratory section and the test-level granularity required for coverage and payment.
It nonetheless calls for a more transparent and objective process, centered on helping applicants obtain an appropriate code rather than navigate procedural barriers. Its recommendations are less granular than C21’s but point in the same direction: preserve CPT while improving predictability, applicant engagement, and transparency.
CLIA RFI. The Coalition’s CLIA argument is concise: because CMS is actively asking whether data-only facilities require CLIA certification, it is premature for CMS to conclude in the PFS rule that their services are not laboratory services. The letter does not offer a separate detailed response to the CLIA RFI.
Bottom Line Across the Six Letters
There is near-unanimity on the immediate SaMS question: all six organizations—CAP, ACLA, AdvaMed, AMP, C21, and the PFS Pathology Payment Coalition—oppose CMS’s proposal to remove the identified laboratory analyses from the CLFS for 2027.
They converge on a central conceptual point. Specimen-derived information does not cease to be laboratory material merely because it has been converted into a genomic data file, digital pathology image, or other electronic form. In many modern tests, the algorithm is not an optional accessory; it is the step that transforms raw laboratory data into a clinically meaningful result.
Five organizations emphasize that CMS is moving prematurely because the parallel CLIA RFI is still asking whether data-only facilities and algorithmic analysis fall within laboratory regulation. CAP reaches the same immediate conclusion by a somewhat different route: SaMS technologies are not physician services, do not fit the resource-based PFS methodology, and should not compete with physicians for budget-neutral PFS dollars. CAP ultimately favors a dedicated payment framework separate from the PFS; until one exists, the affected services should remain on the CLFS.
The six letters also share several practical concerns:
PFS contractor pricing would be less transparent and predictable than national CLFS pricing.
Performing laboratories must retain a direct path to Medicare billing.
CMS should not impose beneficiary coinsurance as a surrogate program-integrity tool.
Code descriptors alone cannot reliably distinguish stand-alone software from integrated laboratory services.
CLIA jurisdiction, enrollment, billing, and rate-setting questions should be resolved before implementation.
On the AMA CPT RFI, none of the six supports replacing CPT now. But their support ranges from enthusiastic to decidedly conditional. CAP and AMP offer the strongest defense of CPT as a uniform clinical vocabulary and cite MolDx Z-codes as a warning about competing systems. AdvaMed, C21, and the PFS Coalition favor retaining CPT while improving transparency, applicant participation, consistency, and responsiveness to new technology. ACLA goes furthest, challenging AMA’s licensing economics and private governance while still warning that competing national code sets would create enormous disruption.
The collective message is therefore not simply “leave everything unchanged.” It is more nuanced:
Keep laboratory SaMS on the CLFS for now; finish the CLIA analysis before redefining laboratory testing; develop a coherent long-term payment framework; and retain one national CPT system while making its governance, licensing, and decision-making more transparent and accountable.
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Deep Dive on CAP
CAP Weighs In on 88305, Software Services, and the AMA CPT System
In its September 14 comments on the CY 2027 Medicare Physician Fee Schedule proposed rule, the College of American Pathologists takes firm positions on three unusually consequential issues.
1. Don’t Revalue 88305 and 88307 From Questionable Claims Data
CAP strongly opposes changing physician time or work RVUs for 88305, 88307, or the broader 88305 family in 2027.
The Maryland Health Care Commission had nominated these codes as potentially misvalued after finding provider-days on which accumulated CPT time exceeded eight—and occasionally 24—hours. CAP argues that these apparent anomalies do not establish that the typical service is overvalued:
The codes are exceptionally heterogeneous: 88305 covers 63 specimen types and 88307 covers 39.
The supposed outliers represent only a small fraction of observations: 2.9% of 88305 provider-days and 0.4% of 88307 provider-days exceeded eight hours.
Claims may identify the billing organization or reassignee rather than the pathologist who actually performed the work, potentially combining several physicians’ services into one artificial “provider-day.”
The claim date may reflect the specimen or billing date rather than when the pathologist performed and signed out the professional work.
The analysis considers accumulated time but not service intensity, although work RVUs incorporate both.
CAP also attacks the frequently cited Urban Institute estimate of two minutes for 88305. That number came from just 23 direct observations at three health systems, without documented pathologist review, and the study itself cautioned that the sample was not representative.
The bottom line: the data may justify asking questions, but not cutting RVUs. If CMS wants further review, CAP says it must use the formal potentially misvalued-code process, allow meaningful public comment, and, if necessary, send the codes through the clinically informed RUC process.
2. SaMS Doesn’t Belong on the Physician Fee Schedule
CMS proposes moving ten “Software as a Medical Service” laboratory analyses from the CLFS to the PFS. CAP says no—but its position is more nuanced than simply defending CLFS jurisdiction.
CAP agrees that stand-alone algorithmic analyses have distinctive characteristics. However, software ordered by physicians is not necessarily a physician service. Its costs—software development, proprietary algorithms, maintenance, and updating—do not correspond to the physician work and practice-expense inputs used to construct PFS RVUs.
Moving SaMS to the PFS would also make these products compete with physician services under budget neutrality. Thus, payments to software companies could effectively reduce payments to physicians. Contractor pricing rather than RVU valuation, as CMS proposes, only underscores how awkwardly SaMS fits into the PFS.
CAP therefore recommends:
Leave the affected services on the CLFS for now.
Do not treat either the CLFS or PFS as the permanent solution.
Develop a separate SaMS payment framework, budgetarily isolated from the PFS.
Create a clinically informed expert process for determining whether individual codes really qualify as stand-alone SaMS.
CAP points to 81416 as a cautionary example: its descriptor includes both next-generation sequencing of a patient specimen and subsequent analysis. Calling the entire service stand-alone software based on a superficial reading of the descriptor could misclassify substantial laboratory work.
This may be CAP’s most forward-looking position: SaMS is neither conventional laboratory testing nor physician work and ultimately may require a third Medicare payment architecture.
3. CAP Defends AMA CPT Against the CMS RFI
CMS asked whether CPT should continue as the national coding standard for physician and other professional services—an RFI that implicitly raises questions about AMA ownership and monopoly power.
CAP offers an emphatic defense. It rejects the “monopoly” framing and characterizes CPT instead as a uniform, clinically grounded, continuously maintained national standard. One vocabulary allows Medicare and other payers to process, audit, and compare claims consistently across specialties and settings.
CAP uses MolDx DEX Z-codes as a real-world warning about competing coding systems. Requiring both CPT codes and separate Z-code registration has been disruptive, administratively burdensome, and expensive for laboratories; multiplying such systems nationally could increase billing uncertainty and delay access to testing.
CAP also emphasizes distinctions that are frequently blurred:
CPT describes services.
The RUC recommends relative resource values.
CMS controls Medicare coverage and payment.
Nor does CAP see ICD-10-PCS as a plausible substitute: it was designed for inpatient hospital procedures and cannot describe the full range of professional services.
CAP therefore supports retaining CPT while encouraging CMS, AMA, and the medical specialty societies to identify improvements within the existing framework.
The Short Version
Across all three subjects, CAP defends established systems against changes based on incomplete analytic or conceptual foundations. Don’t cut 88305 from anomalous claims data. Don’t force software into the PFS simply because it no longer looks like a traditional laboratory test. And don’t discard CPT without an alternative capable of serving as a genuinely national clinical vocabulary.
Source: CAP comments on CMS-1848-P, September 14, 2026, especially pp. 2–10.
