Cystic Fibrosis (CF) Mutation Panel - Clinical Genetic Test - GTR

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Cystic Fibrosis (CF) Mutation Panel

Clinical Genetic Test

offered by

Mayo Clinic Laboratories

View lab's test page

GTR Test Accession: GTR000607860.2

CAP

INHERITED DISEASERESPIRATORY DISEASE

Last updated in GTR: 2024-04-09

Last annual review date for the lab: 2024-05-28

At a Glance

Test purpose:

Diagnosis; Screening; Therapeutic management

Conditions (1):

Cystic fibrosis

Genes (1):

CFTR (7q31.2)

Methods (1):

Molecular Genetics - Targeted variant analysis: PCR with allele specific hybridization

Target population:

Confirmation of a clinical diagnosis of cystic fibrosis. Reproductive risk …

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

Mayo Clinic Laboratories
View lab's website
View lab's test page

Test short name:

CFMP

Specimen Source:

Peripheral (whole) blood
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Dentist
Licensed Physician
Nurse Practitioner
Physician Assistant
Public Health Mandate
Registered Nurse

Test Order Code:

CFMP
View other test codes

LOINC codes:

**LOINC codes notice

CPT codes:

**AMA CPT codes notice

Lab contact:

Huong Cabral, MS, Certified Genetic counselor, CGC, Genetic Counselor
GCMolgen@mayo.edu
1-800-533-1710

Contact Policy:

Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.

How to Order:

https://www.mayocliniclabs.com/test-catalog/Overview/605197#Specimen
Order URL

Test development:

Test developed by laboratory (no manufacturer test name)

Informed consent required:

Based on applicable state law

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Recommended fields not provided:

Test strategy

Conditions

Total conditions: 1

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 1

Gene	Associated Condition	Germline or Somatic	Allele (Lab-provided)	Variant in NCBI

Methodology

Total methods: 1

Method Category

Test method

Instrument

Targeted variant analysis

PCR with allele specific hybridization

ThermoFisher GeneTitan platform

Clinical Information

Test purpose:

Diagnosis; Screening; Therapeutic management

Target population:

Confirmation of a clinical diagnosis of cystic fibrosis. Reproductive risk refinement via carrier screening for individuals in the general population. Reproductive risk refinement via carrier screening for individuals with a family history when familial variants are not available. Identification of patients who may respond to cystic fibrosis transmembrane conductance regulator … View more

View citations (8)

Improved detection of cystic fibrosis mutations in the heterogeneous U.S. population using an expanded, pan-ethnic mutation panel. Heim RA, et al. Genet Med. 2001;3(3):168-76. doi:10.1097/00125817-200105000-00004. PMID: 11388756.
Cystic fibrosis: a worldwide analysis of CFTR mutations--correlation with incidence data and application to screening. Bobadilla JL, et al. Hum Mutat. 2002;19(6):575-606. doi:10.1002/humu.10041. PMID: 12007216.
Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel. Watson MS, et al. Genet Med. 2004;6(5):387-91. doi:10.1097/01.gim.0000139506.11694.7c. PMID: 15371902.
CFTR mutation distribution among U.S. Hispanic and African American individuals: evaluation in cystic fibrosis patient and carrier screening populations. Sugarman EA, et al. Genet Med. 2004;6(5):392-9. doi:10.1097/01.gim.0000139503.22088.66. PMID: 15371903.
Mutation spectrum in Jewish cystic fibrosis patients in Israel: implication to carrier screening. Quint A, et al. Am J Med Genet A. 2005;136(3):246-8. doi:10.1002/ajmg.a.30823. PMID: 15948195.
De Boeck K, Munck A, Walker S, Faro A, Hiatt P, Gilmartin G, Higgins M. Efficacy and safety of ivacaftor in patients with cystic fibrosis and a non-G551D gating mutation. J Cyst Fibros. 2014;13(6):674-80. doi:10.1016/j.jcf.2014.09.005. Epub 2014 Sep 26. PMID: 25266159.
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, . Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-24. doi:10.1038/gim.2015.30. Epub 2015 Mar 05. PMID: 25741868.
Carrier Testing for Cystic Fibrosis. Cystic Fibrosis Foundation; Accessed May 24, 2021. Available at www.cff.org/What-is-CF/Testing/Carrier-Testing-for-Cystic-Fibrosis/

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Are family members with defined clinical status recruited to assess significance of VUS without charge?
No.

Will the lab re-contact the ordering physician if variant interpretation changes?
No. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.

Research:

Is research allowed on the sample after clinical testing is complete?
Research testing is only performed under IRB approved protocol with an opt-out policy in place.

Recommended fields not provided:

Clinical validity, Clinical utility, Sample negative report, Sample positive report

Technical Information

Test Procedure:

The targeted genotyping assay utilizing the ThermoFisher GeneTitan platform is used to detect 500 plus genetic targets, including the 23 disease-causing variants specified in the American College of Medical Genetics standards for population-based carrier screening.

Test Confirmation:

Multiplex ligation-dependent probe amplification, polymerase chain reaction (PCR), relative quantitative PCR, and Sanger sequencing are used to confirm alterations detected by array when appropriate.

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

Analytical sensitivity, specificity, and accuracy are ≥ 99%.

Assay limitations:

This assay will not detect all known disease-associated variants that cause cystic fibrosis or CFTR-related disorders. Therefore, the absence of a detectable variant does not rule out the possibility that an individual is a carrier of or affected with this disease. A negative result does not eliminate the risk of … This assay will not detect all known disease-associated variants that cause cystic fibrosis or CFTR-related disorders. Therefore, the absence of a detectable variant does not rule out the possibility that an individual is a carrier of or affected with this disease. A negative result does not eliminate the risk of carrier status for any of the included conditions, due to the possibility that the patient carries a variant that is not interrogated with this assay or the rare chance of a false-negative result for a tested variant. For tested variants, the negative predictive value of this screen is greater than 98%. The patient's residual risk to be a carrier after a negative screen is dependent on ethnic background and family history. A positive control was not available for all variants targeted on this panel. For more information regarding availability of a positive control for each variant see Targeted Variants Interrogated by Cystic Fibrosis Variant Panel. The negative predictive value of these targets is unknown. Rare variants (ie, polymorphisms) exist that could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, additional testing should be considered. All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(1) This assay was designed to specifically target known disease-causing or likely disease-causing variants. In rare cases, DNA variants of undetermined significance may be identified. The laboratory encourages healthcare providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time. Multiple in-silico evaluation tools may have been used to assist in the interpretation of these results. Of note, the sensitivity and specificity of these tools for the determination of pathogenicity is currently unvalidated. Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete. Bone Marrow transplants from allogenic donors will interfere with testing. Call Mayo Clinic Laboratories for instructions for testing patients who have received a bone marrow transplant. An online research opportunity called GenomeConnect (genomeconnect.org), a project of ClinGen, is available for the recipient of this genetic test. This patient registry collects deidentified genetic and health information to advance the knowledge of genetic variants. Mayo Clinic is a collaborator of ClinGen. This may not be applicable for all tests. View more

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Formal PT program

PT Provider:
American College of Medical Genetics / College of American Pathologists, ACMG/CAP

VUS:

Software used to interpret novel variations
Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, gene-specific online databases, ISCA, UCSC Genome Browser

Laboratory's policy on reporting novel variations
All novel alterations and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.

Recommended fields not provided:

Citations to support assay limitations, Description of internal test validation method, Citations for Analytical validity, Description of PT method, Major CAP category, CAP category, CAP test list

Regulatory Approval

FDA Review:

Category: FDA exercises enforcement discretion

Additional Information

Reviews:

Genereviews

PubMed Clinical Queries

Reviews in PubMed