CMS Posts Final Gapfill Codes for CY2019: Whole Genome Raised from $349 to $5031

On Friday evening, October 19, 2018, CMS published the final contractor gapfill pricing, which are effective 1/1/2019.  (Proposed prices had been released in early June with comments due in early August). 

The 18 codes were placed into the gapfill process last fall; some were codes with no pricing through PAMA and a few were new codes that couldn't be assigned a fall 2017 crosswalk.

• On the CMS CLFS webpage here, see the final "2018 Final Gapfill Determinations."

CMS provided summary rationales for each price.  MACs varied more from one another in the final price proposals than in the preliminary ones in June.  However, the final price is set by the median, which is controlled by MolDx-system MACs which essentially act as a voting bloc of 30 states.

Most of the codes being gapfilled were either "PLA" (new rapid) codes, ending in "U" such as 0001U, or administrative MAAA codes (ending in M, such as 0001M).  See table below.

Whole Genome Analysis

The biggest price change was for whole genome analysis (81425), sibling/family member analysis (81426), and reanalysis (81427).   These rose from a uniform first recommended price of $349 (?!) to $5031, $2709, and $2337, respectively.   (Over 20 comments letters were submitted to CMS, if I can summarize, generally portraying the $349 price as ridiculous.) 

The whole genome price of $5031 is a little higher than the whole exome price of $4780, as set by market rates under PAMA.  Use of these tests is likely to be rare in the Medicare population but a growing literature has documented the usefulness of whole genome in special cases including gravely ill newborns.

How the different MACs priced WGS-related codes is shown in the next table.   By my count, 32 MolDx-related CLFS zones proposed $5031 for 81425.  Novitas and FCSO had 14 zones, at $4780.   NGS MAC had 12 zones at $349.   See table:

click to enlarge

These are "final gapfill prices" but CMS is "accepting comments" until November 19 at  CLFS_Annual_Public_Meeting@cms.hhs.gov .  Elsewhere CMS refers to this as an (ill defined) chance to "appeal" the gapfill final amounts.  If CMS takes any action on such "appeals" there is not much outside evidence of it other than the final prices on the 2019 CLFS in November would be different than those shown here in the "final gapfill" values.  (And note that the November 19 deadline for comment means it is very close to the lockdown of 2019 fee schedules anyway).   This is in contrast to an appeal of a final crosswalk value, which kicks the whole code back into the next summer public meeting again.
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Disclosure:  I served as a consultant this summer to several entities working to raise the median price from the initial $349 to $5000 or better.

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See the original CMS spreadsheet at the link early in the blog.  I've put a slightly tricked-out Excel with highlighted tabs for short summary views and comments views in the cloud, here.
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MAC rationales for 81425, 81426 were stated to be:

Some contractors based initial recommendations on laboratories with similar test with charges of $349.00. Upon further review, however, several contractors revised their recommendations.  Some contractors looked to similar tests on the CLFS, specifically 81415, a Whole Exome Sequencing code, and adjusted the payment rate based on input from several laboratories.  Other contractors simply followed public recommendations to use CPT 81415 as a similar test on the CLFS to recommend a payment rate. 

MAC rationales for 81427 were stated to be:

Initially, several contractors felt this code represented interpretation only and thus averaged two comparable codes (G0452-26 and 88291).  Upon further review, some contractors followed public recommendations to use CPT 81417 as a similar test on the CLFS. Others did not recommend this similar payment rate and instead estimated a professional labor rates for the code. 

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The average price of clinical grade WGS was $5225, almost the CMS price for 81425, in a 2018 Harvard study (here).

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