Top 20 genomic sequencing procedure codes

Advances in genomic sequencing have led to the development of over 30 Current Procedural Terminology (CPT) codes that are used to detect and diagnose genetic conditions.

How many genomic sequencing tests are done each year?

Reviewing data from the Definitive Healthcare ClaimsMx product, we analyzed the genomic sequencing and other molecular multianalyte assays medical procedure codes for the last two years. The total number of genomic sequencing claims decreased from about 65,000 in 2019 to 60,000 in 2020. Below are the top genomic sequencing procedure codes with the highest number of claims in 2020.

Genomic sequencing procedure codes with most claims in 2020

Rank CPT code CPT code description Total procedures 2020 Total procedures 2019
1 81479 Molecular pathology procedure without a specific code 23,090 28,965
2 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 17,431 13,572
3 81450 Targeted genomic sequence analysis panel, hematolymphoid neoplasm or disorder, DNA analysis, 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 4,872 5,623
4 81445 Targeted genomic sequence analysis panel, solid organ neoplasm, DNA analysis, and RNA analysis when performed, 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 4,605 5,842
5 81455 Targeted genomic sequence analysis panel, solid organ or hematolymphoid neoplasm, DNA analysis, and RNA analysis when performed, 51 or greater genes (eg, ALK, BRAF, CDKN2A, CEBPA, DNMT3A, EGFR, ERBB2, EZH2, FLT3, IDH1, IDH2, JAK2, KIT, KRAS, MLL, NPM1, NRAS, MET, NOTCH1, PDGFRA, PDGFRB, PGR, PIK3CA, PTEN, RET), interrogation for sequence variants and copy number variants or rearrangements, if performed 4,172 4,072
6 81443 Genetic testing for severe inherited conditions (eg, cystic fibrosis, Ashkenazi Jewish associated disorders, beta hemoglobinopathies, phenylketonuria, galactosemia), genomic sequence analysis panel, must include sequencing of at least 15 genes (eg, ACADM, ARSA, ASPA, ATP7B, BCKDHA, BCKDHB, BLM, CFTR, DHCR7, FANCC, G6PC, GAA, GALT, GBA, GBE1, HBB, HEXA, IKBKAP, MCOLN1, PAH) 2,125 1,550
7 81415 Exome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis 906 1,124
8 81416 Exome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis, each comparator exome (eg, parents, siblings) 754 840
9 81422 Fetal chromosomal microdeletion(s) genomic sequence analysis (eg, DiGeorge syndrome, Cri-du-chat syndrome), circulating cell-free fetal DNA in maternal blood 670 556
10 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 mitochondrial genome with heteroplasmy detection 314 413
11 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 SLC16A2 213 251
12 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 SLC16A2 201 248
13 81465 Whole mitochondrial genome large deletion analysis panel (eg, Kearns-Sayre syndrome, chronic progressive external ophthalmoplegia), including heteroplasmy detection, if performed 169 231
14 81430 Hearing loss (eg, nonsyndromic 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 112 203
15 81412 Ashkenazi Jewish associated disorders (eg, Bloom syndrome, Canavan disease, cystic fibrosis, familial dysautonomia, Fanconi anemia group C, Gaucher disease, Tay-Sachs disease), genomic sequence analysis panel, must include sequencing of at least 9 genes, including ASPA, BLM, CFTR, FANCC, GBA, HEXA, IKBKAP, MCOLN1, and SMPD1 89 123
16 81432 Hereditary breast cancer-related disorders (eg, hereditary breast cancer, hereditary ovarian cancer, hereditary endometrial cancer); genomic sequence analysis panel, must include sequencing of at least 10 genes, always including BRCA1, BRCA2, CDH1, MLH1, MSH2, MSH6, PALB2, PTEN, STK11, and TP53 89 106
17 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 82 119
18 81425 Genome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis 82 88
19 81433 Hereditary breast cancer-related disorders (eg, hereditary breast cancer, hereditary ovarian cancer, hereditary endometrial cancer); duplication/deletion analysis panel, must include analyses for BRCA1, BRCA2, MLH1, MSH2, and STK11 66 58
20 81431 Hearing loss (eg, nonsyndromic 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 60 94

Fig. 1 Data from the Definitive Healthcare ClaimsMx product for calendar year 2019 and 2020. Commercial claims data is sourced from multiple medical claims clearinghouses in the United States and updated monthly. Data accurate as of October 2021.

Which genomic sequencing test has the highest number of claims?

The decrease in the overall number of genomic sequencing claims between 2019 and 2020 is largely seen in about 5,000 less claims for molecular pathology procedures without a specific code (81479). This generic category may be better represented with more specific codes or may also reflect sample retests. Representing precision medicine in maternal fetal care, tests for fetal chromosomal aneuploidy (81420) increased by nearly 4,000 procedures year-over-year, potentially reflecting the rising age in patients giving birth and the higher risk of associated chromosomal disorders.

The same codes for sequencing genomic DNA appear in the top ten by number of claims for both 2019 and 2020. Targeted genomic sequence analysis panel, hematolymphoid neoplasm or disorder (81450) and targeted genomic sequence analysis panel, solid organ neoplasm (81445) switched 3rd and 4th place between 2019 and 2020. These types of somatic testing of tumors are helping to shape a personalized approach to cancer care. The total number of these two procedures decreased by about 2,000 claims in that timeframe – potentially due to delays of care during the COVID-19 pandemic. Tests for hereditary colon cancer disorders including analysis of at least 5 genes (81436) was ranked 11th in 2019 but 28th in 2020.

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