[Medicare Administrative Contractor (MAC) Name]


[City, State, Zipcode]

RE:Accurate Gapfillingfor Cystic Fibrosis Genetic Testing under the 2013 Clinical Laboratory Fee Schedule (CLFS)

Dear Sir/Madam,

On November 6, 2012, the Centers for Medicare and Medicaid Services (CMS) announced that the Tier 1 and Tier 2 molecular pathology (MoPath) CPT®[1] codes (81201-81408) will be gapfilled for Medicare reimbursement under the Clinical Laboratory Fee Schedule (CLFS) in 2013. This includes the following Tier 1 codes for cystic fibrosis genetic testing:

81220CFTR (cystic fibrosis transmembrane conductance regulator) (e.g., cystic fibrosis) gene analysis; common variants (e.g., ACMG/ACOG guidelines)

81221CFTRknown familial variants

81222CFTRduplication/deletion variants

81223CFTRfull gene sequence

81224CFTRintron 8 poly-T analysis (eg, male infertility)

The following clinical vignettes issued by the American Medical Association (AMA) provide examples of common patient scenarios in which each type of test/code may be performed/billed[2]:

CPT / Clinical Vignette
81220 / A 26-year–old Caucasian female, approximately eight weeks pregnant and other wise in good health, visits her obstetrician for a first prenatal visit. After discussing advantages and limitations of prenatal cystic fibrosis carrier screening with her obstetrician, an anticoagulated peripheral blood sample is sent to the laboratory to be tested for common mutations and variants associated with cystic fibrosis.
81221 / A 1-year–old Caucasian male, whose 6-year–old brother was previously diagnosed with cystic fibrosis is brought by his mother to the pediatrician for genetic testing. The brother was previously demonstrated to be a compound heterozygote carrying one copy each of the common CFTR DeltaF508 mutation as well as a rare variant not included in assays which test for common variants of CFTR but known to cause cystic fibrosis. An anticoagulated peripheral blood sample is sent to the laboratory for testing of these known mutations.
81222 / A 17-year–old Caucasian female, previously diagnosed with cystic fibrosis based on convincing clinical criteria and two elevated sweat chloride results, visits her pediatrician with her father to discuss potential additional genetic testing. Previous tests with a screening assay for common mutations and variants followed by CFTR full gene sequence analysis revealed only heterozygosity for the DeltaF508 mutation. An anticoagulated peripheral blood sample is forwarded to a reference laboratory for deletion/duplication analysis for an uncommon CFTR mutation.
81223 / A 17-year–old Caucasian female with chronic rhino-sinusitis, idiopathic bronchiectasis, and two sweat chloride measurements in the intermediate range (40-60meq/L) is suspected by her pediatrician of having an atypical form of cystic fibrosis. A tube of anticoagulated peripheral blood is submitted to the laboratory for full CFTR gene sequence analysis.
81224 / Following recent consultation with his family physician regarding his wife’s difficulty in conceiving a child, a 34-year–old Caucasian male is referred to a urologist for infertility workup. Physical further examination and testing reveals bilateral absence of the vas deferens. The urologist recommends genetic analysis of the CFTR gene to look for common CFTR mutations and assess the intron 8 poly-T region frequently associated with male infertility. An anticoagulated peripheral blood sample is forwarded to the laboratory for testing.

While genetic testing for cystic fibrosis is not a high-volume test withinthe Medicare patient population, Medicare payment determinations are influential and often used as a benchmark by other payers in establishing rates for new CPT codes. Therefore, it is critical that [MAC Name] utilizes the appropriate information and inputs in the gapfilling process in order to derive accurate payment rates for these codes.

Background on CFTR Gene Analysis

Cystic fibrosis (CF) is a multisystem disease affecting the pulmonary and digestive systems, sweat glands, and, in males, the reproductive tract. It is the most common monogenic disorder in Caucasians of Northern European heritage, with a prevalence of 1 in 2,500 to 3,300 live births. CF is caused by mutations in a single large gene on chromosome 7 that encodes the cystic fibrosis transmembrane conductance regulator (CFTR) protein[3]. Genetic testing for mutations in the CFTR gene may beordered for carrier screening, newborn screening, or confirmatory diagnostic testing in individuals with suspected CF.

Supporting the Gapfilling Process for CFTR Gene Analysis

To ensure that [MAC Name] has the necessary information to make accurate payment determinations for the CFTR gene analysis codes, [Lab Name] is providing the following materials that reflect our own experience in providing these tests (please see enclosed):

[Select the materials that will be provided to the MAC]

  • Submitted charges and routine discounts to charges
  • Analysis of the costs of resources required to perform the test
  • Payment rates provided by other payers [specify which payers]
  • Previously billed CPT code stacks

Although we are glad to share this information with [MAC Name] to support the gapfilling process, we request that it be kept strictly confidential at this time.

[Lab Name] believes that inaccurate rate-setting for the CFTR gene analysiscodes under the Medicare gap-filling process could lead to similarly inaccuraterates being set by Medicaid and other payers, which would ultimately impede patient access to this medically necessary service. Therefore, we ask that [MAC Name] consider the information provided here, and adopt an appropriate methodology that will ensure accurate payment rates for these codes.

In summary:

  • Although CFTR gene analysis is not ordered in high volumesforMedicare patients, the outcome of Medicare gap-filling for the relevant CPT codes is likely to influence Medicaid and private payer rate-setting as well.
  • Therefore, accurate Medicare rate-setting for CPT 81220-81224 will be critical to ensuring sustainable reimbursement by other payers,and therefore continued patient access to CFTR gene analysis when medically necessary.

[Lab Name] appreciates the opportunity to submit this information to [MAC Name] to support the gap-filling process for CPT codes 81220-81224, and would be glad to assist if any questions arise.

Yours sincerely,



[Phone Number]

[Email Address]

[1]CPT is a registered trademark of the American Medical Association. ©2012 American Medical Association. All rights reserved.

[2]© American Medical Association 2011. All rights reserved.

[3]Wenstrom, KD. Cystic fibrosis: prenatal genetic testing. UpToDate. Last updated July 9, 2012.