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Molecular diagnostics laboratory billing have become increasingly complex over time.  This trend continues with a whole series of additional codes and some revisions for 2015.  Molecular Pathology, MoPath, Molecular Diagnostics, MolDx are the names applied to a series of laboratory genomic / genetic tests.

For 2015 where there are 3 new Tier 1 codes, 6 new Tier 2 codes.  The AMA also added a new section for Genomic Sequencing Procedures (also known as Next Generation Sequencing or “NGS”) and Other Molecular Multianalyte Assays.  21 new CPT codes were added to the AMA list that are in this new section, which is most often called NGS lab billing.  There has also been the addition of one new multianalyte assay with algorithmic analyses (MAAAs) CPT 81490-81599.

Also, the AMA added one (1) new multianalyte assay with algorithmic analyses (MAAAs), which are procedures that utilize multiple results derived from assays of various types, including molecular pathology, FISH and non-nucleic acid based assays. In concert with the addition of this subsection, the CPT code set also contains an Administrative Code List (Appendix O of the code book). 

MOLECULAR PATHOLOGY TIER 1 MOLECULAR PATHOLOGY PROCEDURES

The following are the new codes for 2015 for gene-specific and genomic procedures.

Molecular pathology codes include all analytical services performed in the test. This includes cell lysis, nucleic acid stabilization, extraction, digestion, amplification, and detection. Any procedures required prior to cell lysis such as microdissection (CPTs 88380, 88381) are reported separately.

Medical coders should use CPTs 87149-87153, 87470-87801, and 87900-87904 for any molecular testing done for microbial identification, i.e. molecular testing for infectious agents, like HPV are NOT reported in the molecular pathology section of the code book. You should look to the Microbiology section for those codes.

For in situ hybridization, use the CPT code range 88271-88275 (when interpreted by scientist instead of pathologist) and 88365-88368 when interpreted by a pathologist. 

MOLECULAR PATHOLOGY TIER 1 MOLECULAR PATHOLOGY PROCEDURES

CPT 81246

FLT3 (fms-related tyrosine kinase 3) (eg, acute myeloid leukemia), gene analysis; tyrosine kinase domain (TKD) variants (eg, D835, I836) 

CPT 81288

MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; promoter methylation analysis 

CPT 81313

PCA3/KLK3 (prostate cancer antigen 3 [non-protein coding]/kallikrein-related peptidase 3 [prostate specific antigen]) ratio (eg, prostate cancer

TIER 2 MOLECULAR PATHOLOGY PROCEDURES

The following molecular pathology procedure (Tier 2) codes are used to report procedures not listed in the Tier 1 molecular pathology codes. 

They are arranged by level of technical resources and interpretive work by the physician or other qualified health care professional. The individual analyses listed under each code (i.e., level of procedure) utilize the definitions and coding principles as described in the introduction preceding the Tier 1 molecular pathology codes. The parenthetical examples of methodologies presented near the beginning of each code provide general guidelines used to group procedures for a given level and are not all-inclusive. 

Use the appropriate molecular pathology procedure level code that includes the specific analyte listed after the code descriptor. If the analyte tested is not listed under one of the Tier 2 codes or is not represented by a Tier 1 code, use the unlisted code 81479.

If the test is not listed in any of the Tier 2 codes, a coder cannot chose a CPT code because it is similar. The unlisted code 81479 should be selected. 

TIER 2 MOLECULAR PATHOLOGY PROCEDURES

CPT 81402

Molecular pathology procedure, Level 3 (eg, >10 SNPs, 2-10 methylated variants, or 2-10 somatic variants [typically using non-sequencing target variant analysis], immunoglobulin and T-cell receptor gene rearrangements, duplication/deletion variants of 1 exon, loss of heterozygosity [LOH], uniparental disomy [UPD])

Chromosome 1p-.19q- (eg, glial tumors), deletion analysis

CPT 81403

Molecular pathology procedure, Level 4 (eg, analysis of single exon by DNA sequence analysis, analysis of >10 amplicons using multiplex PCR in 2 or more independent reactions, mutation scanning or duplication/deletion variants of 2-5 exons)

Human erythrocyte antigen gene analyses (eg, SLC14A1 [Kidd blood group], BCAM [Lutheran blood group], ICAM4 [Landsteiner-wiener blood group], SLC4A1 [Diego blood group], AQP1 [Colton blood group], ERMAP [Scianna blood group], RHCE [Rh blood group, CcEe antigens], KEL [Kell blood group], DARCX [Duffy blood group], GYPA, GYPB, GYPE [MNS blood group], ART4 [Dombrock blood group]) (eg, sickle-cell disease, thalassemia, hemolytic transfusion reactions, hemolytic disease of the fetus or newborn), common variants RHD (Rh blood group, D antigen) (eg, hemolytic disease of the fetus and newborn, Rh maternalfetal compatibility), deletion analysis (eg, exons 4, 5, and 7, pseudogene) RHD (Rh blood group, D antigen) (eg, hemolytic disease of the fetus and newborn, Rh maternalfetal compatibility), deletion analysis (eg, exons 4, 5, and 7, pseudogene), performed on cell-free fetal DNA in maternal blood

(For human erythrocyte gene analysis of RHD, use a separate unit of 81403)

CPT 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)

MPV17 (MpV17 mitochondrial inner membrane protein) (eg, mitochondrial DNA depletion syndrome), duplication/deletion analysis

PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha) (eg, colorectal cancer), targeted sequence analysis (eg, exons 9 and 20)

Use 81426 in conjunction with 81425

GENOMIC SEQUENCING PROCEDURES AND OTHER MOLECULAR MULTIANALYTE ASSAYS

This new section Genomic sequencing procedures (GSPs) are DNA or RNA sequence analysis methods that simultaneously assay multiple genes or genetic regions relevant to a clinical situation. Most commonly referred to a “Next Gen Sequencing” (NGS) or “Massively Parallel Sequencing” (MPS) in the laboratory, the tests are intended to evaluate the genetic material in totality or near totality.

The codes in this section should be used when the components of the descriptor(s) are met regardless of the technique used, unless specifically noted in the code descriptor.

If all the components are NOT performed, then you must assign code(s) in the Tier 1 or Tier 2 section or if they aren’t listed in the Tier codes, use the unlisted code 81479. AMA provides two parenthetical statements after this introduction section 

  • For cytogenomic microarray analyses, see CPTs 81228, 81229, 81405, 81406.
  • For long QT syndrome gene analyses, see CPTs 81280, 81282 

GENOMIC SEQUENCING PROCEDURES AND OTHER MOLECULAR MULTIANALYTE ASSAYS

CPT 81410

Aortic dysfunction or dilation (eg, 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

CPT 81411

Aortic dysfunction or dilation (eg, Marfan syndrome, Loeys Dietz syndrome, Ehler Danlos syndrome type IV, arterial tortuosity syndrome); duplication/deletion analysis panel, must include analyses for TGFBR1, TGFBR2, MYH11, and COL3A1

CPT 81415

Exome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis

CPT +81416

Exome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis, each comparator exome (eg, parents, siblings) (List separately in addition to code for primary procedure)

Use 81416 in conjunction with 81415

CPT 81417

Exome (eg, unexplained constitutional or heritable disorder or syndrome); re-evaluation of previously obtained exome sequence (eg, updated knowledge or unrelated condition/syndrome)

Do not report 81417 for incidental findings

For exome-wide copy number assessment by microarray, see 81228, 81229

CPT 81420

Fetal chromosomal aneuploidy (eg, trisomy 21, monosomy X) genomic sequence analysis panel, circulating cell-free fetal DNA in maternal blood, must include analysis of chromosomes 13, 18, and 21

CPT 81425

Genome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis

CPT +81426

Genome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis, each comparator genome (eg, parents, siblings( (List separately in addition to code for primary procedure

CPT 81427

Genome (eg, unexplained constitutional or heritable disorder or syndrome); re-evaluation of previously obtained genome sequence (eg, updated knowledge or unrelated condition/syndrome)

Do not report 81427 for incidental findings

For genome-wide copy number assessment by microarray, see 81228, 81299

CPT 81430

Hearing loss (eg, nonsydromic hearing loss, Usher syndrome, Pendred syndrome); genomic sequence analysis panel, must include sequencing of at least 60 genes, including CDH23, CLRN1, GJB2, GPR98, MTRNR1, MYO7A, MYO15A, PCDH15, OTOF, SLC26A4, TMC1, TMPRSS3, USH1C, USH1G, USH2A, and WFS1

CPT 81431

Hearing loss (eg, nonsydromic hearing loss, Usher syndrome, Pendred syndrome); duplication/deletion analysis panel, must include copy number analyses for STRC and DFNB1 deletions in GJB2 and GJB6 genes 

CPT 81435

Hereditary colon cancer syndromes (eg, 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

CPT 81436

Hereditary colon cancer syndromes (eg, Lynch syndrome, familial adenomatosis polyposis); duplication/deletion gene analysis panel, must include analysis of at least 8 genes, including APC, MLH1, MSH2, MSH6, PMS2, EPCAM, CHEK2, and MUTYH 

CPT 81440

Nuclear encoded mitochondrial genes (eg, neurologic or myopathic phenotypes), genomic sequence panel, must include analysis of at least 100 genes, including BCS1L, C10orf2, COQ2, COX10, DGUOK, MPV17, OPA1, PDSS2, POLG, POLG2, RRM2B, SCO1, SCO2, SLC25A4, SUCLA2, SUCLG1, TAZ, TK2, and TYMP

CPT 81445

Targeted genomic sequence analysis panel, solid organ neoplasm, DNA analysis, 5-50 genes (eg, ALK, BRAF, CDKN2A, EGFR, ERBB2, KIT, KRAS, NRAS, MET, PDGFRA, PDGFRB, PGR, PIK3CA, PTEN, RET), interrogation for sequence variants and copy number variants or rearrangements, if performed

CPT 81450

Targeted genomic sequence analysis panel, hematolymphoid neoplasm or disorder, DNA and RNA analysis when performed, 5-50 genes (eg, BRAF, CEBPA, DNMT3A, EZH2, FLT3, IDH1, IDH2, JAK2, KRAS, KIT, MLL, NRAS, NPM1, NOTCH1), interrogation for sequence variants, and copy number variants or rearrangements, or isoform expression or mRNA expression levels, if performed.

CPT 81455

Targeted genomic sequence analysis panel, solid organ or hematolymphoid neoplasm, DNA and RNA analysis when performed, 51 or greater genes (eg, ALK, BRAF, CDKN2A, CEBPA, DNMT3A, EGFR, ERBB2, EZH2, RLT3, IDH1, IDH2, JAK2, KIT, KRAS, MLL, NPM1, NRAS, MET, NOTCH1, PDGRA, PDGFRB, PGR, PIK3CA, PTEN, RET), interrogation for sequence variants and copy number variants or rearrangements, if performed.

CPT 81460

Whole mitochondrial genome (eg, Leigh syndrome, mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes [MELAS], myoclonic epilepsy with ragged-red fibers [MERFF], neuropathy, ataxia, and retinitis pigmentosa [NARP], Leber hereditary optic neuropathy [LHON]), genomic sequence, must include sequence analysis of entire mitochrondrial genome with heteroplasmy detection.

CPT 81465

Whole mitochondrial genome large deletion analysis panel (eg, Kearns-Sayre syndrome, chronic progressive external ophthalmoplegia), including heteroplasmy detection, if performed.

CPT 81470

X-linked intellectual disability (XLID) (eg, syndromic and non-syndromic XLID); genomic sequence analysis panel, must include sequencing of at least 60 genes, including ARX, ATRX, CDKL5, FGD1, FMR1, HUWE1,IL1RAPL, KDM5C, L1CAM, MECP2, MED12, MID1, OCRL, RPS6KA3, and SLC16AZ.

CPT 81471

X-linked intellectual disability (XLID) (eg, syndromic and non-syndromic XLID); duplication;/deletion gene analysis, must include analysis of at least 60 genes, including ARX, ATRX, CDKL5, FGD1, FMR1, HUWE1,IL1RAPL, KDM5C, L1CAM, MECP2, MED12, MID1, OCRL, RPS6KA3, and SLC16AZ. 

MULTIANALYTE ASSAYS WITH ALGORITHMIC ANALYSES

Multianalyte Assays with Algorithmic Analyses (MAAAs) are procedures that utilize multiple results derived from assays of various types, including molecular pathology assays, fluorescent in situ hybridization assays and nonnucleic acid based assays (eg, proteins, polypeptides, lipids, carbohydrates). Algorithmic analysis using the results of these assays as well as other patient information, if used, is then performed and reported typically as a numeric score(s) or as a probability. MAAAs are typically unique to a single clinical laboratory or manufacturer. The results of individual component procedure(s) that are inputs to the MAAAs may be provided on the associated laboratory report; however, these assays are not reported separately using additional codes. For more information on these codes, please see Appendix O in your 2015 Code book.

MULTIANALYTE ASSAYS WITH MAAAs

12 Category I Codes for Multianalyte Assays with Algorithmic Analyses (MAAA) 

CPT 81519

Oncology (breast), mRNA, gene expression profiling by real-time RT-PCR of 21 genes, utilizing formalin-fixed paraffin embedded tissue, algorithm reported as recurrence score

REVISED CODES

The revised codes and parenthetical notes are indicated below. Items presented with “underlined” narratives represent the new/revised verbiage for 2015 while “strikethrough” verbiage was deleted from the narrative. When new or revised parenthetical statement(s) are shown, they will appear in green font.

There were numerous revisions throughout the pathology/laboratory section of the code book. Coders should pay very close attention to revised verbiage and parenthetical statements made (also pertains to deleted codes and those parenthetical statements). Many parenthetical statements were added for 2015 and appear in green font in the AMA 2015 Professional edition; close attention to those statements will determine the accurate code to use. 

CPT 81245

FLT3 (fms-related tyrosine kinase 3) (eg, acute myeloid leukemia), gene analysis, internal tandem duplication (ITD) variants (ie, exons 14, 15); internal tandem duplication (ITD) variants (ie, exons 14, 15) 

CPT 81405

Molecular pathology procedure, Level 6 (eg, analysis of 6-10 exons by DNA sequence analysis, mutation scanning or duplication/deletion variants of 11-25 exons, regionally targeted cytogenomic array analysis

SOURCE: AMA 

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