PAMA 2027: Genome Prices Fall Below Exome—and Rapid Genome Codes Have Missing Data
CMS’s preliminary PAMA results point toward a notable reversal in genomic testing reimbursement: standard genome sequencing has a lower private-payor median than exome sequencing.
The broader genome assay currently receives higher Medicare payment. Under the new medians, genome sequencing would ultimately receive substantially less. However, Medicare’s annual reduction limit delays the payment crossover: genome remains more expensive in 2027, with the genome-exome price reversal projected to begin in 2028.
Rapid and ultra-rapid genome sequencing present a different situation. Several established proprietary codes have current Medicare prices, but no private-payor medians in the preliminary workbook. A newly announced rapid genome code, effective January 2027, adds another pricing question. (It will enter pricing meetings in June 2027).
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Standard exome and genome: different reductions, reversed targets
The central comparison involves 81415, exome sequence analysis, and 81425, genome sequence analysis.
| Code | Service | 2026 Medicare rate | Preliminary private-payor median | Median versus 2026 | Preliminary 2027 payment considering cap |
|---|---|---|---|---|---|
| 81415 | Exome sequencing | $4,780.00 | $3,680.60 | −23% | $4,063.00 |
| 81425 | Genome sequencing | $5,031.20 | $3,018.72 | −40% | $4,276.52 |
These figures appear in CMS’s preliminary weighted-median and payment-calculation workbook, released September 21, 2026.
In 2026, genome sequencing receives $251.20 more than exome sequencing. The new medians reverse that relationship: genome’s median will reach $3018, is $661.88 lower, approximately 18% below exome’s median.
That is a pricing inversion worth distinguishing from the cuts themselves.
Why genome still pays more - just in 2027
The private-payor median is the pricing target, but Medicare does not necessarily move to that target immediately.
Current law limits annual payment reductions to 15% for 2027 through 2029. Both codes qualify for the full 15% reduction in 2027. Because both start above their medians, their first-year payments retain the existing relationship: $4,276.52 for genome versus $4,063.00 for exome.
Applying the reduction limit to subsequent years illustrates when the inversion would reach actual payment.
| Year or pricing target | Exome, 81415 | Genome, 81425 | Genome minus exome |
|---|---|---|---|
| 2026 current rate | $4,780.00 | $5,031.20 | +$251.20 |
| 2027 preliminary capped payment | $4,063.00 | $4,276.52 | +$213.52 |
| 2028 projected payment | $3,680.60 | $3,635.04 | −$45.56 |
| 2029 projected payment | $3,680.60 | $3,089.78 | −$590.82 |
| Current preliminary median target | $3,680.60 | $3,018.72 | −$661.88 |
The 2028–2029 figures are calculations assuming the preliminary medians and current reduction limits remain unchanged. They are not separately announced CMS rates.
Exome reaches its median in 2028, while genome continues declining. Consequently, genome becomes slightly less expensive in 2028 and markedly less expensive in 2029.
The important distinction is therefore between an inversion already visible in the medians and an inversion delayed in Medicare payment by the phase-in rules.
Different reporting populations—and no QC change
The two medians also arise from different reporting populations. Before additional quality-control exclusions, CMS reports:
| Reported private-payor data | Exome, 81415 | Genome, 81425 |
|---|---|---|
| Reporting entities, measured by TIN | 30 | 12 |
| Reporting laboratory NPIs | 30 | 13 |
| Reported test volume | 14,666 | 2,164 |
These are private-payor volumes submitted for PAMA pricing, not Medicare utilization or spending.
The populations may differ in laboratories, contracts, payer mix, and payment distributions. The summary data do not identify which factors explain genome’s lower median.
Additional QC changes neither median. These are minor CMS adjustments for duplicate reporting. Exome remains $3,680.60, and genome remains $3,018.72. The price reversal survives the additional data cleaning.
Rapid genome codes: current prices, missing medians
The rapid-sequencing codes should be distinguished carefully. 0094U describes rapid genome analysis; 0425U describes each rapid comparator genome, such as a parent’s or sibling’s; 0426U describes ultra-rapid genome analysis. Newly announced 0699U describes another proprietary rapid genome service.
| Code | Service, abbreviated | Code effective date | 2026 Medicare rate | Preliminary PAMA median |
|---|---|---|---|---|
| 0094U | Rapid genome analysis [Rady] | July 1, 2019 | $7,582.20 | No data obtained |
| 0425U | Rapid analysis, each comparator genome | January 1, 2024 | $4,094.39 | No data obtained |
| 0426U | Ultra-rapid genome analysis | January 1, 2024 | $7,582.20 | No data obtained |
| 0699U | Phoenix Children’s rapid genome analysis | January 1, 2027 | Not effective in 2026 | Not in the workbook |
The effective dates are documented in CMS code-update materials and AMA’s October 2026 PLA release.
0094U "Rapid" currently receives $2,551 more than standard genome sequencing—approximately a 51% premium. MolDx set this by the Gapfill method several years ago. Ultra-rapid code 0426U has the same current rate as 0094U. The $4,094.39 rate for 0425U applies to each comparator genome, rather than representing an alternative price for the patient’s primary genome analysis.
The established codes are associated with Rady Children’s Institute for Genomic Medicine’s services. They should not all be labeled “ultra-rapid”: that designation specifically belongs to 0426U.
A blank median does not establish the 2027 payment
For 0094U, 0425U, and 0426U, CMS’s workbook explicitly indicates that it obtained no private-payor data. The median cells and corresponding 2027 payment calculations are blank.
Those blanks establish a limitation of this dataset. They do not establish a zero payment, a permanent exemption from PAMA, or automatic continuation of the current price.
CMS has prevented any codes with blank PAMA data from being used as crosswalk codes.
CMS states that existing tests without applicable information are considered through crosswalking or gapfilling. Crosswalking uses comparable existing tests to establish payment; gapfilling develops prices through Medicare contractors. The no-data codes therefore require attention to CMS’s separate payment determinations, rather than an assumption drawn from empty spreadsheet cells.
Genome codes 0658U, 0659U
Both of these new codes are in the summer crosswalk/gapfill new code process (not PAMA), both have CMS re commendations for gapfill in 2027. As noted, 0699U comes even later, for initial price discussion June 2027.
A new rapid genome code enters in January
AMA’s October 2026 release introduces 0699U for Phoenix Children’s Clinical Genomics Laboratory, effective January 1, 2027. AMA identifies its clinical descriptor as identical to that of 0094U and adds reciprocal cross-references between the codes.
The separate code reflects the proprietary service and laboratory identification. An identical clinical descriptor does not itself establish an identical Medicare price. Because 0699U becomes effective in 2027, it has no 2026 rate in the workbook and no code-specific median in this PAMA dataset.
CMS expects to publish final 2027 rates in November. Standard exome and genome already have a clear preliminary trajectory: both decline, and genome’s lower median ultimately reverses their payment relationship. For the rapid and ultra-rapid proprietary services, current prices are known, but the missing medians leave their next payment determination as a separate issue to follow.
Source workbook for the numerical comparisons:
