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Pathologist Group Asks Medicare to Reconsider Payment for BRCA Genetic Testing CPT Codes

NEW YORK (GenomeWeb) – The Association for Molecular Pathology has asked Medicare to increase the payment amounts for two CPT codes attached to testing procedures for BRCA1 and BRCA2 genes by considering the work and resources that labs invest in analyzing these large and variable genes. 

The Centers for Medicare & Medicaid Services in December 2018 released the clinical lab fee schedule final payment amounts to take effect Jan.1, 2019. Among the priced CPT codes, CMS said Medicare would pay $468 for CPT code 81163 describing full sequencing of BRCA1/2 and $283 for CPT code 81165 describing sequencing of just BRCA1.

"Following careful review of the final determinations, AMP requests reconsideration of new CPT codes 81163 and 81165 on the basis of final payment amount," the organization said in a letter to CMS.

CMS arrived at the payment amount for CPT code 81163 by crosswalking to codes 81406 and 81216, to account for sequencing BRCA1 and BRCA2, respectively. However, AMP said in its letter that crosswalking to these codes fails to account for the work and costs labs incur by performing full sequencing of these two genes. As such, the pathologists' organization asked CMS to reconsider crosswalking this code to CPT code 81408 describing sequencing of similarly large genes, such as the dystrophin (DMD) gene. In the 2019 clinical lab fee schedule, this code is priced at $2,000.

"Code 81163 is a single procedure done by bi-directional sequencing of coding regions, as well as exon-intron junctions by Sanger or next generation sequencing. Laboratories analyzing for sequence variations in the BRCA1 and BRCA2 genes do so at the same time rather than in separate single gene analyses," AMP told CMS in its letter. "Thus, the most direct crosswalk is code 81408, which assesses 50 or more exons as the methodology and the amount of DNA sequencing of the large genes, such as DMD, is most similar to new code, 81163."

For CPT code 81165 describing full sequencing of BRCA1, CMS decided to crosswalk to code 81406, which describes sequencing analysis of 11 to 25 exons for genes such as RAF1 and ACADVL. AMP told CMS that 81406 describes some but not all the work required to fully sequence BRCA1, which is a large and variable gene with 24 exons and more than 7,000 base pairs. In comparison, RAF1 and ACADVL contain around 3,300 base pairs and 2,200 base pairs, respectively.

"BRCA analysis is particularly notorious for the diversity of abnormalities that occur, including frequent novel changes requiring substantial resources both to confirm the sequence variation and give an interpretation of its clinical significance," AMP said, estimating that the work and resources required to sequence this gene is two to three times greater than other genes currently billed under CPT code 81406.

"We do not feel this is a reasonable crosswalk," AMP wrote and suggested CMS crosswalk to CPT code 81408, and price it 50 percent less at $1,000 to more accurately reflect the resources required.  

For reference, when a patient receives full sequencing of BRCA1/2 with deletion and duplication analysis, CMS has instructed labs to bill CPT code 81162 priced at $2,028. When only BRCA1 and BRCA2 are sequenced, CPT code 81163 is used, priced at $468, and when only deletion and duplication analysis is done of the two genes, CPT code 81164 is used at $584. In addition to pricing full sequencing of BRCA1 at $283 via CPT code 81165, just deletion and duplication analysis of this gene using CPT code 81166 is $301. Meanwhile, full sequencing of BRCA2 using CPT code 81216 is reimbursed at $185 and deletion/duplication analysis of this gene using CPT code 81167 is reimbursed at $283.

If CMS agrees to increase the value of CPT code 81163 to $2,000, then billing separately for BRCA1/2 full sequencing and del/dup analysis will be more profitable for labs than billing only CPT code 81162 that accounts for both types of analysis together ($2,584 versus $2,028). As reimbursement experts have pointed out in comments to CMS, this type of pricing could incentivize labs to stack codes, a practice CMS has been trying to rein in.

AMP said that at the upcoming 2019 clinical lab fee schedule meeting, stakeholders intend to provide additional input on CPT codes 81163 and 81165 and discuss the payment amounts that appropriately reflect the work needed to analyse these genes.