Cystic Fibrosis Foundation Mutation Analysis Program

The Mutation Analysis Program (MAP), funded by the Cystic Fibrosis Foundation and administered by The Johns Hopkins Genomics DNA Diagnostic Laboratory (JHGDDL), is a free and confidential genetic testing program for people with a confirmed or strongly suspected diagnosis of cystic fibrosis. The program provides genetic testing to people who have not yet been tested to determine their CF variants, or who have been tested previously but still have one or more unknown CF-causing variants.

By knowing their CF-causing variants, your patients can make informed decisions with you—their health care provider—about the most appropriate treatment options for them.

Test Description

The MAP offers patients the most comprehensive clinical genetic test for CFTR that is currently available. The complete CFTR gene is sequenced (all exons and all introns along with 10 kb upstream and 5kb downstream of the gene) along with deletion/duplication analysis. Please be aware that ‘full gene’ or ‘whole gene sequencing’ of CFTR as described by other laboratories may not be equivalent to the testing provided by MAP (see below).


The JHGDDL is proud to provide patients with the advantages offered by the MAP:

  • Testing is fully funded by the Cystic Fibrosis Foundation. Enrolled patients receive whole CFTR gene sequencing at no cost, except for sample collection and shipping.
  • Complete analysis of the whole CFTR gene by an expert team with over 30 years’ experience interpreting variation in CFTR.
  • Increased sensitivity for individuals carrying unusual CF-causing variants such as gene rearrangements and intronic changes.
  • Previously enrolled patients with sweat chloride levels ≥40mM, clinical features of CF, and only one CF-causing variant are eligible for re-enrollment in the MAP (see re-enrollment eligibility). As our understanding of variant effect increases, re-analysis of sequence data may yield an answer.
  • Negative MAP testing provides compelling evidence that CFTR is not the cause of an individual’s elevated sweat chloride concentration and clinical features. Analysis of other genes known to cause elevated sweat chloride concentration (e.g. ENaC subunits and CA12) and clinical exome sequencing are also offered by the DNA Diagnostic Lab.
  • De-identified variant data collected by MAP may be used to understand CF pathophysiology. Rare variants of unknown effect can be evaluated by the CFTR2 project to ascertain effect on CFTR function and response to FDA-approved CFTR modulators.

Eligibility Guidelines

First-Time Enrollment

  1. Patients must be a resident of the US.
  2. Patients must be referred by a physician at an accredited CF Care Center. To find an accredited CF Care Center please refer to the Cystic Fibrosis Foundation’s directory.
  3. Patients must have not yet had genetic testing to determine their CF variants, or have been tested previously but still have one or more unknown variants. Patients must have a confirmed or strongly suspected diagnosis of CF.
  4. Lowest sweat chloride levels are required for enrollment consideration. If your patient is unable to have a sweat test, please contact the JHGDDL to provide additional clinical information supporting your patient’s diagnosis.

Qualified Re-Enrollment

Individuals previously enrolled in the program who meet both the following criteria will be allowed to re-enroll for whole gene sequencing:

  1. MAP testing identified a single CF-causing variant.
  2. Lowest sweat chloride concentration is greater than 40 mmol/L.

 Please note that individuals enrolled after February 15, 2021, who have already received whole gene sequencing are not eligible for re-enrollment.

Enrollment Process for Providers

  1. Provider submits a completed enrollment form

    Complete the enrollment form, also available on the Cystic Fibrosis Foundation patient portal. Completed forms should be faxed to the lab at 410-367-3266. Please note that incomplete or outdated forms will not be accepted for consideration.  
  2. JHGDDL reviews the enrollment and issues a decision

    This process may take up to 3 business days for first time enrollments, 2-3 weeks for re-enrollments. If your patient’s enrollment is denied the JHGDDL will issue a letter detailing the reasons for denial. If you would like to appeal a denial, please contact the JHGDDL to provide additional clinical information supporting your patient’s diagnosis. The JHGDDL will perform a secondary review of your patient’s credentials and issue a final enrollment decision.  
  3. Sample is collected from the approved individual and sent to the JHGDDL

    Once you receive an approval letter for your patient, a sample can be submitted for testing. For patients approved for re-enrollment, the JHGDDL will confirm whether there is sufficient DNA remaining from prior testing. If a new sample is required, this will be communicated in the re-enrollment approval letter. If you and your patient elected to submit a saliva sample, a collection kit will be shipped to the patient. If you choose to submit a blood sample, specimens may be shipped to:

    Johns Hopkins Genomics – DDL 
    1812 Ashland Ave. 
    Sample Intake; Room 245 
    Baltimore, MD 21205
  4. JHGDDL initiates testing and releases results within 90 days

    Once testing is complete, results will be faxed directly from the JHGDDL to the number provided on MAP enrollment form. Results may take up to 90 days to report.

Frequently Asked Questions

If you are unable to find the answer to your question, please contact the JHGDDL for assistance.