Mutation Analysis Program

The Mutation Analysis Program provides free genetic testing to people with cystic fibrosis to help identify their CF gene variants.

7 min read

The Mutation Analysis Program (MAP), funded by the Cystic Fibrosis Foundation and administered by The John Hopkins DNA Diagnostic Laboratory (JHGDDL), is a free and confidential genetic testing program for people with a strongly suspected or confirmed 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 variants, your patients can make informed decisions with you, their health care provider, about the most appropriate treatment options for them.

Frequently Asked Questions

What are the eligibility requirements for participating in the MAP?

Patients must be referred by a physician at an accredited CF care center. 

Patients must have a confirmed or strongly suspected CF diagnosis. 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.

Lowest sweat chloride levels are required for enrollment consideration. If your patient is unable to have a sweat test and you strongly suspect a CF diagnosis, please contact JHGDDL to provide additional clinical information supporting your patient’s diagnosis.

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

  • MAP testing identified a single CF-causing variant. Patients enrolled after February 15, 2021 who have already received full gene sequencing are not eligible.

•    Lowest sweat chloride concentration is greater than 60 mmol/L.

What types of genetic testing are performed?

MAP offers patients the most comprehensive clinical genetic test for CFTR 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 is not as extensive as provided by MAP, as shown in this table.

How do I enroll my patient in MAP?

Complete the enrollment form, also available on the Cystic Fibrosis Foundation patient portal. Fax completed forms to JHGDDL at 410-367-3266. Please note that incomplete or outdated forms will not be accepted.

JHGDDL will review the enrollment and issue 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, JHGDDL will issue a letter detailing the reasons for denial. If you would like to appeal a denial, please contact JHGDDL to provide additional clinical information supporting your patient’s diagnosis. JHGDDL will perform a secondary review of your patient’s credentials and issue a final enrollment decision.

When you receive an approval letter for your patient, a sample can be submitted for testing. 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, ship specimens to:

Johns Hopkins Genomics – DDL
1812 Ashland Ave.
Sample Intake Room 245
Baltimore, MD 21205

For patients approved for re-enrollment, JHGDDL will confirm whether there is sufficient DNA remaining from prior testing. We will inform you if we requires a new sample in the re-enrollment approval letter.

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

What kind of sample is acceptable for testing?

JHGDDL accepts blood or saliva from individuals older than 5 years for testing. Saliva samples must be submitted in a CFFMAP-provided collection kit.

Where can my CF patient get a blood sample taken?

Patients can get their blood drawn at their care center lab, if available. Otherwise, it is at the provider's and patient's discretion to use a lab that is most convenient and affordable.

Who covers the cost of the genetic testing?

The cost of the genetic testing is covered under a grant provided by the CF Foundation. However, the patient or CF care center is responsible for the cost of the blood sample and for shipping and postage for mailing the sample to the lab.

Is testing offered by the MAP New York State approved?

No. If the patient is from the state of New York, the ordering provider is required to complete and submit the New York State Non-Permitted Laboratory Test Request Approval Form. This approval must be completed and sent to JHGDDL before testing can begin. 

Will the patient's name and test results be released to the public?

No, patients' names and corresponding test results will not be released to the public. Test results will be released only to the referring doctor or CF care center.

When can providers expect test results?

For efficiency, testing occurs in batches. It can take up to 90 days to receive results.

Can a person participate in this program more than once?

Generally, individuals may participate only once. Individuals previously enrolled in the program who meet the following criteria may re-enroll for full gene sequencing:

  • MAP testing identified a single CF-causing variant for patients enrolled prior to February 15, 2021
  • Lowest sweat chloride concentration is greater than 60 mmol/L

To re-enroll your patient please complete the enrollment form and fax it to the lab at 410-367-3266.

How is MAP different than other testing options?

MAP offers the following advantages over other testing options:

  • Testing is fully funded by the Cystic Fibrosis Foundation. Enrolled patients receive full CFTR gene sequencing at no cost, except for sample collection and shipping.
  • Complete analysis of the CFTR gene by an expert team with more than 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 60mM or greater, clinical features of CF, and only one CF-causing variant are eligible for re-enrollment in 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 whole 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.
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