Pathology/Lab Coding Alert

Don’t miss Tier 2 to Tier 1 conversions.

If your lab performs gene analyses, you need to upgrade your coding toolkit for 2020. As of Jan. 1, you have four new and four revised molecular pathology CPT^® codes you need to know if you don’t want to miss out on pay you deserve. 

Discover the Codes

The four new molecular pathology codes are all found in the Tier 1 subsection, which designate gene-specific or genomic procedures.

Some of these new codes represent a procedure that was formerly described by a Tier 2 molecular pathology code, but now warrants a specific Tier 1 code because it has become more commonly used, according to Lee Hilborne, MD, MPH, professor of pathology and laboratory medicine, UCLA school of medicine in his CPT^® and RBRVS 2020 Annual Symposium presentation. You’ll read about the revised Tier 2 codes in the next section.

Here are the new Tier 1 codes:

• 81277 (Cytogenomic neoplasia (genome-wide) microarray analysis, interrogation of genomic regions for copy number and loss-of-heterozygosity variants for chromosomal abnormalities)
• 81307 (PALB2 (partner and localizer of BRCA2) (eg, breast and pancreatic cancer) gene analysis; full gene sequence)
• 81308 (… known familial variant)
• 81309 (PIK3CA (phosphatidylinositol-4, 5-biphosphate 3-kinase, catalytic subunit alpha) (eg, colorectal and breast cancer) gene analysis, targeted sequence analysis (eg, exons 7, 9, 20))

Purpose: Your lab might perform one of these tests for various clinical applications related to somatic or germline mutations, using methods such as amplification by polymerase chain reaction (PCR) and gene mapping by Sanger sequencing.

For instance: Codes 81307 and 81308 describe interrogation of the PALB2 gene, which clinicians may order to evaluate for autosomal-dominant forms of breast or pancreatic cancer, especially in patients with a strong family history of these conditions. The ordering physician may be looking for a mutation known to occur in a family member, therefore requesting an 81308 test. Or the clinician may order 81307 to cast a wider net, evaluating the full PALB2 gene sequence for other possible mutations that may impact specific cancers or other conditions such as Fanconi anemia.

Caution: If the lab performs a gene panel test that includes PALB2, such as the hereditary breast cancer-related disorders panel 81432, the PALB2 test is included and you should not additionally report 81307.

PIK3CA: CPT^® 2020 introduces 81309 to describe an analysis of specific sequences in the PIK3CA gene. Clinicians may order the test to analyze tumor tissue from breast or colorectal cancer patients for mutations that may impact treatment recommendations and prognosis.

Although the code lists exons 7, 9, and 20 as examples of gene sequences that the targeted test may evaluate, you should use 81309 even if the specific analysis interrogates additional sequences, fewer sequences, or different sequences of the PIK3CA gene. The code definition specifies only that you perform a targeted analysis (not full gene sequence), but doesn’t specify required targets.

81277: The final new CPT^® 2020 molecular pathology code describes a cytogenomic microarray analysis (CMA) rather than interrogation of a specific gene. Clinicians may order this test using blood or tissue specimens from a cancer patient to help identify chromosomal abnormalities. The test evaluates the entire genome for variations in the number of copies of a gene sequence (called copy number variants, or CNV) or other chromosomal abnormalities, such as long sequences of homozygous DNA (called loss of heterozygosity, or LOH). The test may identify clinically significant CNV or LOH that may impact prognosis or treatment options.

CPT^® 2020 instruction reminds you that the test is comprehensive, and you should not additionally report gene-specific codes for genetic regions included in the test. Nor should you additionally report molecular cytogenetics code 88271 (Molecular cytogenetics; DNA probe, each (eg, FISH)) with 81277.

Grasp Code Revisions

You’ll find four revised molecular pathology codes that you need to know for 2020.

“Coders must understand the importance of reviewing the revised CPT^® codes the AMA publishes each year — since the result of using a code description that has been revised could be that the claim does not get paid,” says Ronda Tews, CPC, CHC, CCS-P, AAPC Fellow, director of billing and coding compliance at Modernizing Medicine in Boca Raton, Florida.

Update Tier 2: Molecular pathology procedures assigned to Tier 2 represent less-common tests than those assigned a unique Tier 1 code. CPT^® assigns the tests to different levels (codes 81400-81408 for levels 1 through 9) based on technical and interpretive resources required. However, you can report one of the codes only for a specific test listed under the code, not for just any test that requires the described level of resources.

That’s why it’s particularly important to look at Tier 2 changes every year. Your lab may be performing a test that has been “promoted” to a Tier 1 code, or has been added or deleted to the list under a particular Tier 2 code.

In fact: The four new Tier 1 codes discussed earlier in this article involve Tier 2 revisions as follows (emphasis added):

81404 (Molecular pathology procedure, Level 5 (eg, analysis of 2-5 exons by DNA sequence analysis, mutation scanning or duplication/deletion variants of 6-10 exons, or characterization of a dynamic mutation disorder/triplet repeat by Southern blot analysis) PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha) (eg, colorectal cancer), targeted sequence analysis (eg, exons 9 and 20) UGT1A1 (UDP glucuronosyltransferase 1 family, polypeptide A1) (eg, hereditary unconjugated hyperbilirubinemia [Crigler-Najjar syndrome]) full gene sequence)

• The deleted PIK3CA test becomes code 81309, with the minor addition of exon 7 to the parenthetic example of targeted regions.
• The newly listed test for UGT1A1 full sequence analysis complements revisions to 81350 for UGT1A1 common variant analysis.

81406 (Molecular pathology procedure, Level 7 (eg, analysis of 11-25 exons by DNA sequence analysis, mutation scanning or duplication/deletion variants of 26-50 exons, cytogenomic array analysis for neoplasia) Cytogenomic microarray analysis, neoplasia (eg, interrogation of copy number, and loss-of-heterozygosity via single nucleotide polymorphism [SNP]-based comparative genomic hybridization [CGH] microarray analysis) PALB2 (partner and localizer of BRCA2) (eg, breast and pancreatic cancer), full gene sequence)

• The deleted test for cytogenomic microarray, neoplasia becomes code 81277 with changes to the descriptor. Notice that CPT^® also removes “cytogenomic array analysis for neoplasia” from the description of the type of procedures included in the code.
• The deleted PALB2 full gene sequence test becomes code 81307.

81407 (Molecular pathology procedure, Level 8 (eg, analysis of 26-50 exons by DNA sequence analysis, mutation scanning or duplication/deletion variants of >50 exons, sequence analysis of multiple genes on one platform) APOB (apolipoprotein B) (eg, familial hypercholesterolemia type B) full gene sequence)

• CPT^® adds the test for APOB full gene sequence analysis, which you would have previously reported as 81479 (Unlisted molecular pathology procedure). Identifying mutations in this gene can aid in diagnosis of familial hypercholesterolemia, according to Hilborne in his CPT^® and RBRVS 2020 Annual Symposium presentation.

Minor change: CPT^® 2020 makes the following revisions to 81350: UGT1A1 (UDP glucuronosyltransferase 1 family, polypeptide A1) (eg, irinotecan drug metabolism, hereditary unconjugated hyperbilirubinemia [Gilbert syndrome]), gene analysis, common variants (eg, *28, *36, *37). The changes broaden the example of conditions for which clinicians might order this test to include Gilbert syndrome and broader drug metabolism issues, and should not change the way you use the code. The test interrogates some of the most common changes in the gene, such as *28, *36, and *37, but may include other, non-listed variants. The mutations may reduce function of an enzyme that metabolizes bilirubin and certain drugs, allowing metabolites to accumulate to toxic levels.