Wednesday, November 21, 2018






original blog follows (October 2018)

Original Title from 2018:
CMS Posts CY2019 New Molecular Coding Rules!  Envisions More, Not Less, Use of 81479

Every November CMS updates a national coding rulebook called "National Correct Coding Initiative Edits."   This include massive excel spreadsheets, but also a zip file of PDF coding instructions.

The new files for CY2019 are now posted here and have some big changes for genetic coding.   NCCI edits and rules may be used by private payers as well.


At the CMS website here, click on the download for "NCCI Policy Manual...January 1, 2019...Zip".

Inside that Zip, the file for laboratory (codes 80000-89999) is Chapter X (10).  Inside that, Section F is Molecular Pathology (p9 ff).  I've also put up a cloud copy of Chapter X here, as it was on November 21.

Revisions in Chapter X, Labs, Section F, Paragraphs 7, 8, 9

The three revisions are new section 7, section 8, section 9. 

Section 7 states that individual Tier 1 or Tier 2 CPT codes (e.g. "EGFR") shall not be reported with a genomic sequencing procedure, when the CPT descriptor for GSP procedure includes a descriptor for the Tier 1, Tier 2 analyte.   E.g. don't report BRCA testing (81162) along with a Hereditary Breast Cancer gene panel (81432).   Don't report individual Lynch genes along with a Lynch panel (81435).

Section 8 states that if a lab analyzes multiple genes by "a next generation sequencing procedure," report only one unit of service of GSP, MAA, or PLA code.  "If no CPT code accurately describes the procedure performed, report CPT 81479 x 1."   And:  "The laboratory shall not report multiple CPT codes describing the component results."   

  • My joint reading of the two rules above, if you bill the 10 or more genes for an AMA CPT breast cancer or colon cancer panel, bill the panel codes (81432 or 81435) not individual CPT codes.   If you bill some subset, like 8 of the 10 breast panel codes, do not code stack them, but bill 81479.  Presumably, a MAC would not pay more for the subset panel as 81479 than it would pay for the whole panel (81432).  This fits recent Congressional instructions for CMS to handle panel unbundling (here).

Section 9 states that the NCCI Excel tables, or procedure-to-procedure edits, describes CPT codes that "should not be routinely reported together."   They give the example of 91292 MLH1 gene and 81292 MLH1 dup/del analysis, adding, "it may be appropriate to perform dup/del testing if the disease variant is not identified by full gene sequencing."

These are summaries and for this article I'll ignore some probably very esoteric or obscure or likely unintentional readings of the text.   Readers should refer to the full CMS text.

Molecular section F, new points 7,8,9.

They also include a similar paragraph, not in the molecular section, but in the introductory section "A" on page 4:


Section 7:  Don't report CPT codes that are found inside GSP (gene panel) codes  This seems like commonsensical coding advice.   I've been puzzled in the past by CMS data that MAC payments didn't seem to follow this rule.   There is a general principle to use the best-fit CPT code rather than components that add up to the same CPT code.    However, particularly MolDx may have given lab-specific instructions in the past in unpredictable combinations. 

Section 8:  Use of 81479 rather than code stacking Here, I think the key sentence is: "The laboratory shall not report multiple individual CPT codes describing the component-test results."   The most obvious fact here is that CMS seems to be nationalizing a MolDx rule called "Genetic Test Panel Alert" that multiple CPT codes (e.g. EGFR gene + KRAS gene + BRAF gene) should not be added up one by one, but coded as 81479 (unlisted procedure, unpriced procedure).   The MolDx rule is here (and cloud archive 11/21/18, here.)

  • Nationalizing a Quirky MolDx Coding Rule.  In the past, I felt the MolDx rule (that flipped every group of several genes into 81479 coding) violated the normal national correct coding rules and concepts, but now, the NCCI CMS manual appears to be updated to more or less match the MolDx multi-gene rule.
  • Labs May Complain There Isn't Time to Do This.   Labs may complain that this rule comes out near December 1, for implementation January 1, and there isn't enough time to recode LIS and billing systems to conform.  
  • I Predict Payment Chaos Without Further Instructions.  Without a payment rule, this creates huge opportunities for unfairness.  
    • What if one lab bills EGFR+KRAS+BRAF, let's pretend they historically add up to $200+$200+$200 =$600, and gets paid $100 for this use of 81479 and the lab across the street under the same MAC gets paid $500 for the same use of 81479?  
    • Remember that 81479 is unpriced and there is no pricing rule for it.  
    • Or different MACs across state lines might bundle and reprice genes under 81479 in very different ways.  This is inconsistent with the new nationwide fee schedules, which were deliberately meant to reduce state-to-state variation in lab test pricing.
    • Plus, there is a huge manual activity burden when 81479 is used, a burden on the MACs that process the claim.
    • Plus, if all payers follow this rule, PAMA genetic pricing surveys(which is based on individual genes for lab tests and ignores 81479) go haywire.
    • Auditors can't audit.  Let's say an OIG auditor finds a lab was billing for and getting paid for three CPT gene codes in 2019, and this instruction says to use 81479.  What overpayment would OIG assign?  It's undefined.  Would they just guess?  Spin a wheel?
    • In October 2017, CMS issued an instructions to MACs to "report to CMS" those labs that were using 81479.  Here.  At the time, my best guess is that CMS wanted to centrally track those labs doing a lot of 81479 billing, perhaps to encourage them to use specific codes or get a PLA code.   (Of course, CMS could always track labs billing 81479 anyway, since CMS has access to its own claims data.)  This November 2018 instruction would boost, not reduce, claims with 81479.   
    • Data dive:  CMS CY2016 data for 81479 billing by lab can be obtained here.   Total 81479 Part B payments were about $108M.  All but about 7% went through MolDx states.  The largest 81479 biller in CY2016 was (Assurex + Myriad) at $39M (36%; Myriad acquired Assurex in mid-year CY2016).  See screenshot of the top 18 81479 billers in CY2016, here.  8 labs provided 90% of 81479 billing.  Excel in cloud here.
    • Claims for some CPT codes that might have autopaid without further editing might be slowed down (requests for records, orders, physician notes) through the 81479 process.
  • Perverse Incentive to Tilt Away from NGS Sequencing.  These rules could be an incentive to do Sanger or PCR hotspot testing, as the bundling and down-payment applies only if an NGS method is used.  
    • The same incentive to Sanger or PCR  methods  is found in the CMS national NCD for NGS testing in cancer, which makes some types of genetic testing literally unpayable unless if performed by methods other than NGS, since the NCD applies only to NGS.
Section 9:  Dup Del analysis can be a reflex test, but don't report routinely with sequencing.  This is the only new rule that doesn't cite NGS as a method.   This is actually an improvement in some ways, because until recently MolDx had a published rule against paying for dup del testing such as 81433 (breast cancer panel dup del) at all; it was on a list of MolDx unpayable codes.   Here, NCCN says that Dup Del should be a reflex test, however, in most cases -- such as BRCA syndrome testing or Lynch/Colon syndrome testing -- the sequencing code will be negative >95% of the time so you will indeed reach the Dup Del code almost all the time. 

What I'm saying is that a new rule paying Dup Del 95% of the time on reflex is better than an old rule paying it never.   I've been told that some private payers paid Dup Del coding irregularly, but this confirms a payable role for Dup Del code use and payment. 

Since the sequencing code is typically negative 95% of the time, there will be a lot of endorsed use of modifiers to pay the second code, the dup del code, in those 95% of instances, at least when no other rule like use of a comprehensive code (e.g. 81162 or 81455) is available.

While Dup Del is sometimes reflected by a separate code (whether a separate single gene Dup Del code like 81294 or a separate gene panel Dup Del code like 81436) there are other times when Dup Del is already part of the CPT code (e.g. Dup Del is already inside the sequencing codes 81162 or 81455).