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Healthcare Insights

Top genomic sequencing procedure codes

Medical advancements in genomic sequencing have led to the development of more than 40 Current Procedural Terminology (CPT) codes that are used to detect and diagnose genetic conditions.

What is genomic sequencing?

Genomic sequencing is a method of determining the genetic makeup of an organism or cell type. Using genomic sequencing to identify changes in areas of genomes can help scientists understand how diseases form and help to develop methods of diagnosing and treating them.

Using the Atlas All-Payor Claims dataset, we ranked the top 20 most common genomic sequencing CPT codes by percentage of total genomic sequencing procedures. The chart below represents claims filed in 2023 through October.

Top 20 genomic sequencing procedure codes in 2023

Rank CPT code CPT code description Percent of procedures Explore dataset
81479 Unlisted molecular pathology procedure 37.9% Explore
81420 Fetal chromosomal aneuploidy genomic sequence analysis 33.3% Explore
81455 Genomic sequence analysis of solid organ or hematolymphoid neoplasm or disorder   7.7% Explore
81443 Genetic testing for severe inherited conditions  5.5% Explore
81450 Genomic sequence analysis of hematolymphoid neoplasm or disorder 3.4% Explore
81422 Fetal chromosomal microdeletion(S) genomic sequence analysis  1.8% Explore
81445 Solid Organ Neoplasm, genomic sequence analysis panel 1.7% Explore
81456 Genomic sequence analysis panel of solid organ or hematolymphoid neoplasm or disorder, 51 or greater genes 1.5% Explore
81432 Genomic sequence analysis panel for hereditary breast cancer-related disorders of at least 10 genes 1.2% Explore
10 81418 Genomic sequence analysis plan for drug metabolism of a least 6 genes 1.2% Explore
11 81433 Duplication/deletion analysis panel for hereditary breast cancer-related disorders 1.0% Explore
12 81415 Exome (Eg., unexplained constitutional or heritable disorder or syndrome); Sequence analysis 0.7% Explore
13 81416 Exome (Eg., unexplained constitutional or heritable disorder or syndrome); Sequence analysis, each comparator exome (Eg., parents, siblings) 0.6% Explore
14 81460 Whole mitochondrial genome; Sequence analysis of entire mitochondrial genome with heteroplasmy detection   0.3% Explore
15 81465 Whole mitochondrial genome large deletion analysis panel  0.3% Explore
16 81412 Genomic sequence analysis panel for Ashkenazi Jewish associated disorders of at least 9 genes 0.2% Explore
17 81449 Genomic sequence analysis panel of solid organ neoplasm 0.2% Explore
18 81435 Genomic sequence panel for hereditary colon cancer disorders of at least 10 genes 0.2% Explore
19 81419 Genomic sequence analysis panel for epilepsy  0.2% Explore
20 81425 Genome; Sequence analysis 0.1% Explore

Fig. 1 Data is from the Atlas All-Payor Claims dataset and represents claims filed in 2023 through October. Data accessed December 2023.

What are the top CPT codes for genomic sequencing in 2023?

The most common genomic sequencing CPT code was unlisted molecular pathology procedures, accounting for 37.9% of all procedures billed in 2023 through October. This CPT code is used for molecular pathology procedures that do not have a designated code. Given the rapid growth of the number of molecular tests, insurers struggle to keep up with innovation in the field, leading some tests to not yet have their own billing codes. This top code on our list likely ranks so high because it encompasses this large array of procedures that do not yet have unique assigned CPT codes.

The second most common genetic sequencing procedure is fetal chromosomal aneuploidy genomic sequence analysis panel, accounting for 33.3% of all genomic sequencing CPT codes billed this year. This genetic testing procedure involves performing an analysis panel to evaluate fetal DNA in maternal blood, specifically looking at chromosomes 13, 18, and 21. These three chromosomes are commonly examined in noninvasive prenatal testing (NIPT) for trisomy, which is the presence of three chromosomes and may help identify potential fetal conditions such as Patau Syndrome, Edward Syndrome, and Down Syndrome.

Solid organ or hematolymphoid or disorder genomic sequence analysis panel was the third top genomic CPT code, accounting for 7.7% of all billed procedures. This procedure involves evaluating a patient specimen, like a tumor or bone marrow, for any DNA or RNA alterations in genes linked to organ, blood, and lymph cancers and disorders.

How does genome sequencing work?

In addition to aiding in the diagnosis and treatment of conditions and diseases, genome sequencing can be critical in identifying disease outbreaks. Scientists conduct genome sequencing tests in laboratories and follow four main steps:

  • DNA shearing: Scientists cut the DNA into small pieces using molecular scissors. DNA pieces must be small enough for the machine to read.
  • DNA barcoding: Scientists tag DNA pieces with identification to match sheared DNA to its respective bacteria.
  • DNA sequencing: Multiple barcoded DNA are combined in a DNA sequencer which identifies the bases that make up each sequence. The sequencer uses the barcode to track which base belongs to which bacteria.
  • Data analysis: Scientists compare sequences between bacteria to identify any differences.

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