Pathology/Lab Coding Alert

Learn ‘algorithm’ distinction from MAAA codes.

Although CPT^® 2021 introduces just one new Category 1 code in the Genomic Sequencing Procedures [GSPs] and Other Molecular Multianalyte Assays section, there’s more you need to know about these services.

You’ll also find GSPs in CPT^® Appendix O and in the Proprietary Laboratory Analyses (PLA) section where they mingle with Multianalyte Assays with Algorithmic Analyses (MAAA) codes and other proprietary lab tests.

Let our experts help you sort out the new GSP codes, what makes the procedures unique, and how to use the codes relative to other molecular pathology procedures that may involve the same genes.

Look for New GSP Codes

CPT^® 2021 adds 81419 (Epilepsy genomic sequence analysis panel, must include analyses for ALDH7A1, CACNA1A, CDKL5, CHD2, GABRG2, GRIN2A, KCNQ2, MECP2, PCDH19, POLG, PRRT2, SCN1A, SCN1B, SCN2A, SCN8A, SLC2A1, SLC9A6, STXBP1, SYNGAP1, TCF4, TPP1, TSC1, TSC2, and ZEB2) to the GSPs section. The code involves a panel of genes associated with epilepsy and includes some genes that have gene-specific treatments, according to M. Laura Cremona, PhD, FACMG, representing American College of Medical Genetics and Genomics at the Clinical Laboratory Fee Schedule Annual Laboratory Meeting last year.

You’ll also find multiple new GSPs in the CPT^® 2021 Proprietary Laboratory Analyses (PLA) section. Several new proprietary codes come from Variantyx, Inc., for the following Genomic Unity^® tests:

• For constitutional/heritable disorders, codes 0212U and 0213U describe whole genome analysis for the patient (proband) and a relative (comparator), respectively; codes 0214U and 0215U describe whole exome analysis for proband and comparator, respectively.
• For heritable neurological conditions, codes 0216U and 0217U describe genomic DNA sequence analysis of 12 or 51 relevant genes, respectively; code 0218U describes sequence analysis of the DMD gene associated with muscular dystrophy.

The Genomic Unity^® tests use polymerase-chain-reaction-(PCR)-free whole genome sequencing (WGS) to detect a range of genetic mutations such as base sequence changes, large deletions and expansions, duplications, and chromosomal abnormalities, according to Daryl Spinner PhD, and Christine Stanley PhD FACMG, representing Variantyx, Inc., at the Clinical Laboratory Fee Schedule Annual Laboratory Meeting last year. The testing also includes computer data analysis and interpretation by clinical and molecular geneticists.

Update: The AMA released additional Genomic Unity^® PLA codes effective Jan. 1, 2021 that are in the CPT^® 2021 code book. The nine new codes are in the range 0230U-0238U and include tests for genes associated with cardiac ion channelopathies (0237U) and Lynch syndrome (0238U), which is a heritable condition that increases the likelihood of a patient developing certain cancers, particularly colorectal cancer.

Distinguish GSPs from MAAAs and More

GSPs evaluate the genetic “umbrella” for a specific clinical condition, so many of the codes start with descriptors for the condition, such as cardiac ion channelopathies, hearing loss, hereditary colon cancer, and Noonan spectrum disorders, to name a few.

Specifically: GSPs analyze DNA or RNA sequences but are distinct from other molecular pathology tests including MAAAs and Tier 1 and Tier 2 codes in the following ways:

• The tests analyze multiple genes or genetic regions simultaneously, up to and including whole exome or genome analyses.
• The genes evaluated relate to a specific condition or clinical scenario.
• The analysis may go beyond gene sequencing to include copy number variations, structural changes, and chromosomal differences.
• If desired, the method allows clinicians to “re-query” the data generated from the initial lab test, such as when clinical understanding of relevant mutations has changed.
• Each finding from the test can stand alone as independently significant for a clinical situation. This characteristic is unlike MAAA tests that algorithmically combine results for a separate, distinct value such as a risk score.
• The tests commonly use advanced methods such as next generation sequencing (NGS), but the method does not limit the code.

Notice repeat genes: When billing a molecular test, just knowing the gene(s) evaluated might not get you to the correct code. For instance, the following codes all list genes KCNH2 and KCNQ1: 81413, 81414 and 0237U (Cardiac ion channelopathies …) and 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) …).

Do this: Choose the code that most specifically describes the entire procedure. That means if you have a duplication/deletion gene analysis panel for KCNH2 and KCNQ1 to evaluate cardiac ion channelopathies, you should report 81414 (… duplication/ deletion gene analysis panel, must include analysis of at least 2 genes, including KCNH2 and KCNQ1) instead of 81406 (… KCNH2, full gene sequence … KCNQ1, full gene sequence …) for each of the genes. Inversely, if a GSP code lists specific genes and your lab evaluates some — but not all — of those genes, you should bill the appropriate Tier 1 or Tier 2 molecular pathology code(s) instead of the GSP code.

Beware single outcome: If a gene analysis test results in a single finding reported as some kind of risk score based on the test results and an algorithmic analysis, you should code a MAAA test rather than a GSP test, even if a GSP code lists the same genes. If there’s no specific code for the MAAA test, you should use the unlisted code (81599, Unlisted multianalyte assay with algorithmic analysis).

Know Where to Find GSPs

Don’t get confused by the various categories for GSPs, because you need to know where to find the code numbers, definitions, and proprietary lab names within the CPT^® code book.

Contents: You’ll find GSPs in three places within CPT^®:

• First, look in the GSPs and Other Molecular Multianalyte Assays section of Category I codes numbered 81410-81471.
• Some, but not all, PLA codes describe GSP tests. You’ll find the PLA codes in the final section of the Pathology and Laboratory chapter in the CPT^® code book, numbered 0001U-0222U.
• Appendix O now also includes a complete listing of PLA codes, whether or not the analysis is a GSP procedure.

Proprietary name: Appendix O lists the proprietary name for each PLA procedure. If the GSP test is proprietary, you must use the associated administrative or PLA code shown in Appendix O, which takes priority over any Category I code. Conversely, you should not use a proprietary code for any procedure other than the specified test.

For instance: For the specific whole genome sequence analysis for constitutional/heritable disorders by Variantyx, Inc., you should report 0212U (Rare diseases (constitutional/ heritable disorders), whole genome and mitochondrial DNA sequence analysis, including small sequence changes, deletions, duplications, short tandem repeat gene expansions, and variants in non-uniquely mappable regions, blood or saliva, identification and categorization of genetic variants, proband) for testing the patient and 0213U (… each comparator genome (eg, parent, sibling)) for testing a relative. You should not report 81425 (Genome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis) and +81426 (… sequence analysis, each comparator genome (eg, parents, siblings) (List separately in addition to code for primary procedure) instead of or in addition to the specific PLA codes.