Cystic Fibrosis Pathogenic Variant Analysis
Polymerase Chain Reaction (PCR)
Single Nucleotide Extension (SNE)
Matrix-Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry
Lavender BD Hemogard™ K2EDTA Tubes
Ambient (within 48 hours)
7 days (stored at 2-8 °C)
Cystic fibrosis (CF) (OMIM#219700) is a multisystem genetic disease of sodium chloride transport that commonly involves the lungs, pancreas, intestines, liver, sweat glands, and male reproductive system. Respiratory failure is the leading cause of death among individuals with CF, with a median life expectancy of 41 years (CF Foundation).
CF is one of the most common inherited conditions among Caucasians and is diagnosed in approximately 1 in 3,000 individuals.[2-3] The condition is less common but does occur among all other racial groups. CF has an autosomal recessive inheritance pattern and heterozygous mutation carriers (1 in 25-30 Caucasians) are unaffected. If both partners in a couple are mutation carriers, there is a 25% chance for each child to have CF and a 50% chance for each child to be a carrier.
The cystic fibrosis transmembrane conductance regulator (CFTR) gene was isolated in 1989. The most common pathogenic variant, deltaF508, was identified in the same year and represents 70% of CF mutations among Caucasians. To date, more than 1,800 gene variants have been found, though most are quite rare. Mutations in CFTR have also been identified in individuals with atypical presentations, such as acute or chronic recurrent pancreatitis and isolated congenital absence of vas deferens (CAVD), as well as in individuals with late-onset or mild CF symptoms.
To identify couples at risk of having a child with CF, both the American College of Medical Genetics and Genomics and the American College of Obstetricians and Gynecologists recommend that CF carrier screening be offered routinely to women of reproductive age. Mutation screening should include the pan-ethnic panel of the 23 most common CTFR pathogenic variants.
In both pediatric and adult patients in whom CFTR-related disorders are suspected, genetic testing is routinely performed as an initial diagnostic test or as confirmation of clinical findings, or sweat chloride testing, which remains the standard diagnostic test.
Newborn screening (NBS) for cystic fibrosis is now offered universally in the United States through each state’s mandatory NBS program. Initial screening measures a digestive enzyme, immunoreactive trypsinogen (IRT). Because elevations in IRT may have other causes, a CFTR mutation analysis is often performed as a secondary screen, though this varies by state.
Since the advent of routine carrier screening and NBS, many individuals with CF are recognized at, or even before, birth.
DNA samples are amplified in a multiplex reaction for regions of interest in CFTR. Initial amplification is followed by single base extension (SBE) reactions to detect known CFTR variants. The extension products are analyzed using matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) mass spectrometry. Multiple variants may be detected because each CFTR variant assay contains a primer of unique length and mass, allowing specific genotypes to be assigned.
The variants included on the Cystic Fibrosis Pathogenic Variant Analysis assay represent clinically-validated variants classified as CF-causing in the CFTR2 database at Johns Hopkins University, a product of the Clinical and Functional Translation of CFTR (CFTR2) initiative. The assay tests for 140 CF-causing variants; one variant (F508C) associated with Congenital Absence of the Vas Deferens (CAVD); one ACMG-recommended panel variant (R117H) classified as a Mutation of Varying Clinical Consequence by CFTR2; one conditionally reported modifying variant (Poly T); and two conditionally-reported benign variants (I506V and I507V). This panel includes the 23 pathogenic variants recommended for universal carrier screening by the American College of Medical Genetics. The panel also encompasses all variants that are detected by the Ohio Newborn Screening Panel.
Results should be used and interpreted in the context of clinical evaluation. This test does not detect all variants in the CFTR gene and it is possible that this individual could have a CFTR variant not included in this test. Therefore, the failure to identify a variant does not guarantee that other CFTR variants are not present in the sample being analyzed.
Variants identified by this assay vary in frequency among different populations.[9, 11] Residual CF carrier risk following a negative Cystic Fibrosis Pathogenic Variant Analysis result is based on ethnicity and personal/family history.
Residual Cystic Fibrosis Carrier Risk after Negative Carrier Screen
Residual Carrier Risk
(with negative family history)
1 in 61
1 in 231
1 in 24
1 in 768
1 in 94
1 in 183
1 in 25
1 in 267
1 in 58
1 in 248
As with any hybridization-based assay, underlying gene variants in oligonucleotide-binding regions can affect the alleles being probed and, consequently, the calls made. The orientation of the Poly T variant, whether in cis/trans to the R117H variant, cannot be ascertained via this assay.
Due to the complex issues surrounding cystic fibrosis, informed consent and genetic counseling are recommended for all individuals undergoing testing.
Cystic Fibrosis (CFTR RefSeq# NM_000492.3)
Legacy names of 142 pathogenic variants with three *conditionally-reported variants are listed below:
1. Cystic Fibrosis Foundation Patient Registry: Annual Data Report 2017. Available at http://www.cff.org/
2. Comeau AM, Parad RB, Dorkin HL, Dovey M, Gerstle R, Haver K, Lapey A, O’Sullivan BP, Waltz DA, Zwerdling RG, Eaton RB. Population-based newborn screening for genetic disorders when multiple mutation DNA testing is incorporated: a cystic fibrosis newborn screening model demonstrating increased sensitivity but more carrier detections. Pediatr. 2004;113(6):1573-1581.
3. Sontag MK, Hammond KB, Zielenski J, Wagener JS, Accurso FJ. Two-tiered immunoreactive trypsinogen (IRT/IRT)-based newborn screening for cystic fibrosis in Colorado: screening efficacy and diagnostic outcomes. J Pediatr. 2005;147(Suppl):S83-8.
4. Rommens JM, Iannuzzi MC, Kerem BS, Drumm ML, Melmer G, Dean M, Rozmahel R, Cole JL, Kennedy D, Hidaka N, Zsiga M, Buchwald M, Riordan JR, Tsui LC, Collins FS. Identification of the cystic fibrosis gene: chromosome walking and jumping. Science. 1989;245:1059-1065.
5. Kerem BS, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, Charavarti A, Buchwald M, Tsui LC. Identification of the cystic fibrosis gene: genetic analysis. Science. 1989;245:1073-1080.
6. The Clinical and Functional Translation of CFTR (CFTR2). Available at http://www.cftr2.org/
7. Cutting GR. Cystic fibrosis genetics: from molecular understanding to clinical application. Nat Rev Genet. 2015;16(1):45-56.
8. Carrier screening for genetic conditions. Committee Opinion No. 691. American College of Obstetricians and Gynecologists. Obstet Gynecol. 2017;129:e41–55.
9. Farrell PM, Rosenstein BJ, White TB, Accurso FJ, Castellani C, Gutting GR, Burie PR, LeGrys VA, Massie J, Parad RB, Rock MJ, Campbell, III, PW. Guidelines for diagnosis of cystic fibrosis in newborns through older adults: Cystic Fibrosis Foundation consensus report. J Pediatr. 2008;153:S4-S14.
10. National Newborn Screening and Genetics Resource Center. National newborn screening status report. Austin (TX) Available at http://genes-r-us.uthscsa.edu/sites/genes-r-us/files/nbsdisorders.pdf Updated Nov 02, 2014.
11. Sugarman EA, Rohlfs EM, Silverman LM, Allitto BA. CFTR mutation distribution among U.S. Hispanic and African American individuals: Evaluation in cystic fibrosis patient and carrier screening populations. Genet Med. 2004;6(5):392-99.
Ong T, Marshall SG, Karczeski BA, Sternen DL, Cheng E, Cutting GR. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2018. Cystic Fibrosis and Congenital Absence of the Vas Deferens. 2001 Mar 26 [Updated 2017 Feb 2]. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1250/