Next Generation Sequencing Coding and Billing Guidelines (M00127, V3)
June 21, 2017
Next Generation Sequencing (NGS) NGS allows identification of somatic and/or germline alterations in multiple genes simultaneously. This guideline focuses on Targeted and Comprehensive Genomic Profile testing for somatic variant detection using tumor tissue only-based panels. Panels involving germline variants, matched tumor-normal, or “liquid biopsies” (including circulating tumor cells (CTCs) or DNA (ctDNA), or cell-free DNA (cfDNA)) will be addressed separately, but should be billed using CPT 81479.
Targeted (aka Hot Spot) Tumor Panels Targeted NGS panels identify somatic alterations known to occur in certain areas (i.e., 'hotspots') in specific genes of interest. Generally, these NGS panels can detect single nucleotide variants (SNVs or point mutations) and small (typically ≤40 bp) insertions or deletions (indels), but not copy number alterations (CNAs) or structural variants (SVs), such as gene rearrangements, fusions, or translocations. These alterations typically represent genomic targets with corresponding targeted cancer therapies. Identification of a somatic alteration guides use of the corresponding targeted therapy.
To bill for targeted NGS services for somatic variant detection, review CPT codes 81445, 81450 and 81455. Select the appropriate CPT code based on the number of genes in your laboratory’s NGS panel and the test indication for either solid organ or hematolymphoid neoplasms. The units of service (UOS) for an NGS panel is one (UOS=1).
Effective July 1, 2017, laboratories with 1 to 4 gene(s) on their targeted NGS panel should use CPT 81479 and one (1) UOS along with their test identifier (DEX Z-code) to represent this service on their claims. (Similarly, CPT 81479 should be used to bill for somatic variant detection performed by a targeted NGS panel on a “fluid” sample (e.g., KRAS in pancreatic cyst fluid). Reimbursement is based on the number of reported genes in these small NGS panels. Tier 1 and/or Tier 2 individual biomarker CPT codes should not be used for a single gene or any combination of genes when testing is performed as part of a NGS or other multiplexing technology panel.
Comprehensive Genomic Profile (CGP) TestingCGP refers to NGS-based testing that has been optimized to identify all types of molecular alterations (i.e., SNVs, small and large indels, CNAs, and SVs) in cancer-related genes in a single test using complex and often proprietary bioinformatics. CGP may also include testing for MSI (microsatellite instability) and TMB (tumor mutational burden).
Because CGP includes SNVs, small (≤40 bp) and large (> 40 bp) indels, CNAs, and SVs, CPT codes 81445, 81450, and 81455 do NOT describe a CGP service. Therefore, to report a CGP service, test providers should use CPT code 81479.