Pathology/Lab Coding Alert

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If your molecular lab performs genetic sequencing procedures (GSP), you have 21 new codes to choose from this year — 81410-81471 — but do you know how to use them? 

Problem: The codes may seem straightforward, but knowing the gene name or even knowing whether the lab uses next generation sequencing isn’t enough to ensure that you choose the correct code. 

Solution: We have the tips you need to make sure you select the proper code, and understand the payment pitfalls that could impact your lab. 

Tip 1: Distinguish Next Generation

The introduction to the new CPT® section “Genomic Sequencing Procedures and Other Molecular Multianalyte Assays” names a lab process you need to understand: “next-generation sequencing.” NGS is a newer technology that provides a method to read many DNA or RNA sequences simultaneously. Also called massive parallel sequencing, the procedure allows the lab analyst to interrogate, or assay, multiple genes or regions of interest within the genome at the same time. This process potentially allows greater ability to identify variant changes that may be relevant to the patient’s clinical situation. 

Compare: Prior to the advent of NGS, labs relied on polymerase chain reaction (PCR) to make multiple accurate copies of the DNA or RNA, and Sanger sequencing methods to identify the nucleotide sequence.

Potential: The NGS method allows whole exome sequencing and multi-gene panels that involve evaluating much more of the patient’s genome than was feasible using older methods. The 21 new CPT® 2015 codes represent a group of these newer tests that have clinical significance in treating somatic or germ-line conditions, such as neoplasm or heritable disorders. Table 1 summarizes the tests described by the new codes (see table on page 35).

Results stand alone: Although the tests in the new section represent molecular tests that analyze multiple analytes, these panels differ from tests in the CPT® section, “Multianalyte Assays with Algorithmic Analyses,” (MAAAs). Each panel test in the range 81410-81471 involves individual genetic analyses that potentially have medical significance apart from the other tests in the panel. That’s different from MAAAs, which rely on an algorithm to generate a prognostic “score” from the individual test results. 

Tip 2: Code for Genes Interrogated

Although the new section emphasizes NGS technology, you might use one of the codes even if your lab doesn’t perform the test using next generation. 

Example: The lab analyzes a colon cancer specimen for seven genes, APC, CHEK2, MLH1, MSH2, MSH6, MUTYH, and PMS2 using PCR methods. 

Question: New code 81435 (Hereditary colon cancer syndromes (e.g., Lynch syndrome, familial adenomatosis polyposis); genomic sequence analysis panel, must include analysis of at least 7 genes, including APC, CHEK2, MLH1, MSH2, MSH6, MUTYH, and PMS2) describes this gene panel. But several Tier 1 and Tier 2 codes also describe tests for these specific genes (MLH1, 81292-81294; MSH2, 81295-81297; MSH6, 81298-81300; PMS2, 81317-81319; MUTYH, 81401 and 81406). How should you code the panel?

Answer: Even if the lab uses PCR instead of next generation to interrogate these seven genes, you should report 81435, according to Diana Voorhees, MA, CLS, MT(ASCP), SH, CLCP, principal at DV & Associates Inc., in Salt Lake City during her presentation at the Coding Institute’s CodingCon 2014.

That’s because the new CPT® 2015 instructions for the GSP section states that “the analyses may also be performed by other molecular techniques (PCR methods and microarrays).” The instructions go on to state that you should use one of the new codes when the lab analyzes all the components of the test, “regardless of technique.” 

Tip 3: Code Describes Minimum

You’ll notice that the descriptor for many of the new codes in the range 81410-81471 state, “must include … analysis of at least [x number of] genes, including …” In other words, you should use these codes when the lab performs all of the listed genes, and at least the number of genes specified — or more. Don’t charge an additional code for additional genes in the panel.

For instance: If the physician orders a full genomic sequence analysis panel for aortic dysfunction or dilation, such as Marfan syndrome, the test must include at least the nine genes listed in the code (81410, Aortic dysfunction or dilation [e.g., Marfan syndrome, Loeys Dietz syndrome, Ehler Danlos syndrome type IV, arterial tortuosity syndrome); genomic sequence analysis panel, must include sequencing of at least 9 genes, including FBN1, TGFBR1, TGFBR2, COL3A1, MYH11, ACTA2, SLC2A10, SMAD3, and MYLK]). But if the lab performs an aortic dysfunction or dilation panel analyzing 20 genes, including the nine listed, you should still report 81410.

Tip 4: Look for Tier 1 or 2 Alternative

You need to know what to do if your lab performs a panel that analyzes most — but not all — of the genes described by a new code

For example: If your lab performs a hereditary colon cancer panel that includes full sequence analysis of MLH1, MSH2, MSH6, MUTYH, how should you report the service?

Restriction: Don’t code 81435, because the panel doesn’t include the other listed genes APC, CHEK2, and PMS2. “When all components of the descriptor are not fulfilled, use: Tier 1 code(s), Tier 2 code(s), and/or unlisted molecular pathology procedure code (81479, Unlisted molecular pathology procedure),” stated Roger D. Klein, MD, JD, FCAP, AMA CPT® Molecular Pathology Advisory Committee Member (MPAG) at the American Medical Association’s (AMA) annual CPT® and RBRVS Symposium.  

Solution: Instead of 81435, you should report the following codes for the listed panel:

• 81292 — MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2) (e.g., hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; full sequence analysis
  
• 81295 — MSH2 (mutS homolog 2, colon cancer, nonpolyposis type 1) (e.g., hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; full sequence analysis
  
• 81298 — MSH6 (mutS homolog 6 [E. coli]) (e.g., hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; full sequence analysis
  
• 81406 — Molecular pathology procedure, Level 7 (e.g., analysis of 11-25 exons by DNA sequence analysis, mutation scanning or duplication/deletion variants of 26-50 exons, cytogenomic array analysis for neoplasia),… MUTYH (mutY homolog [E. coli]) (e.g., MYH-associated polyposis), full gene sequence…