CPT Codes for Genomic Sequencing Procedures

The following CPT codes are for GENOMIC SEQUENCING PROCEDURES AND OTHER MOLECULAR MULTIANALYTE ASSAYS

The 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 ofthe 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:

1.For cytogenomic microarray analyses, see CPT 81228, CPT 81229, CPT 81405, CPT 81406.
2.For long QT syndrome gene analyses, see CPT 81280, CPT 81282

GENOMIC SEQUENCING PROCEDURES AND OTHER MOLECULAR MULTIANALYTE ASSAYS

CPT Code: 81410 
Code Description:           

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 Code: 81411 

Code Description:  
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 Code: 81415

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

CPT Code: 81416
Code Description:  
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 CPT 81416 in conjunction with CPT 81415

CPT Code: 81417

Code Description: 
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 CPT 81417 for incidental findings
For exome-wide copy number assessment by microarray, see CPT 81228, CPT 81229

CPT Code: 81420

Code Description: 
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 Code: 81425

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

CPT Code: 81426

Code Description: 
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
Use CPT 81426 in conjunction with CPT 81425

CPT Code: 81427

Code Description:
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 CPT 81427 for incidental findingsGenome (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 CPT 81427 for incidental findings For genome-wide copy number assessment by microarray, see CPT 81228, CPT 81299

CPT Code: 81430

Code Description:
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 Code: 81431

Code Description:
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 Code: 81435

Code Description:
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 Code: 81436

Code Description: 
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 Code: 81440

Code Description:
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 Code: 81445

Code Description:
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 Code: 81460

Code Description:
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 Code: 81465

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

CPT Code: 81470

Code Description:
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 Code: 81471

Code Description:
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.

Reference: www.ama-assn.org