Background:
Cystic Fibrosis (CF) is a rare multisystem disease affecting epithelia of the respiratory tract, exocrine pancreas, intestine, hepatobiliary system, and exocrine sweat glands (Savant et al. 2024). The Cystic Fibrosis Foundation reports approximately 40,000 children and adults are living with cystic fibrosis in the U.S., and an estimated 105,000 people have been diagnosed with CF across 94 countries. CF is inherited in an autosomal recessive manner meaning an affected individual has inherited two disease causing variants in the gene CFTR. In 2017, the American College of Obstetricians and Gynecologists’ Committee on Genetics recommended that CF carrier screening be offered to all women considering pregnancy or are currently pregnant regardless of race, ethnicity, and ancestry.
This carrier test is designed to detect >99% of disease-causing variants in CFTR, including the 100 CFTR variants recommended by the American College of Medical Genetics for Cystic Fibrosis for population screening (Deignan et al. 2023 Table 1). In accordance with these recommendations, only pathogenic and likely pathogenic variants will be reported. Reporting of a variant of uncertain significance (VUS) may occur if the individual’s reproductive partner is known to carry either a pathogenic or likely pathogenic variant, and is at the discretion of the laboratory director.
Please note that reporting of the poly-T tract will only occur when the R117H variant is detected and the poly-TG repeat will only be reported when the poly-5T allele is detected.
This test is a screen for CF and should not be used for individuals with phenotypic symptoms of CF or a CFTR related condition. Separate diagnostic testing is available if an individual is symptomatic of Cystic Fibrosis, a CFTR-related disorder, or has a Known Familial Variant in CFTR.
Reasons for Referral:
- Women considering pregnancy or are currently pregnant and have not previously had CF screening.
- Individuals whose reproductive partner has a clinical diagnosis of either CF or apparently isolated congenital bilateral absence of the vas deference (CBAVD).
- Carrier identification of unaffected persons with a positive family history of CF without known genetic variants.
- Sperm & egg donors without prior CF Screening.
- Parental screening if Echogenic bowel observed on fetal ultrasound.
Methodology:
Genomic DNA is analyzed using next-generation sequencing (NGS) on the Illumina NextSeq 2000 platform, with target enrichment performed using hybridization-based probes to capture exonic (coding) regions of the gene(s). Single nucleotide variants (SNVs) and small insertions or deletions (INDELs) are identified using the Illumina DRAGEN Enrichment Workflow, executed onboard the NextSeq2000. This pipeline combines software and hardware acceleration to generate high-confidence germline haplotype calls. Clinical and analytical validation of DRAGEN was performed in our laboratory. Based on validation study results, for SNVs, this assay achieves >96% analytical sensitivity and >99% positive predictive value (PPV). For INDELs <50 bp, the analytical sensitivity is >87% and the PPV is >97%. INDELs >50 bp may be detected but the sensitivity for these is reduced.
This test is not designed to detect polynucleotide repeats, low-level mosaicism, structural rearrangements, or balanced alterations (e.g. inversions, gene conversion events, translocations, etc.) or variants in difficult regions. Additionally, variants located in regions of insufficient coverage, including introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and of high GC content may not be detected. This test does not provide complete coverage of all exons and noncoding regions may have limited information and ability to interpret. Variants in introns that are greater than 10 bp from the intron-exon junction may be analyzed. Please contact the laboratory if interrogation of intronic sequence greater than 10 bp from the intron-exon boundary is desired.
Multiplex ligation-dependent probe amplification (MLPA) to detect large CFTR coding region deletions /duplications is performed. The frequency of large deletions in the CFTR gene is estimated to be 1-3% (Schneider M. et al).
Please note that this test is unable to determine phase of variants.
Specimen Requirements:
Blood: EDTA or ACD (Solution A or B):
- Adult: 6 mL
- Child: 6mL
- Infant: 2 mL
Saliva: 2 ORAgene™ Saliva Collection Kits (OGR-500) used according to manufacturer instructions. Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample.
Assisted Saliva: 4 ORAgene™ Assisted Saliva Collection Kits (OGR-575) used according to manufacturer instructions. Please contact KDL Client Services for an Assisted Saliva Collection Kit for patients that cannot provide a blood sample.
Skin Fibroblast: Punch Biopsy (Cell cultures will be prepared at KDL and used for testing), or 2 T-25 confluent flasks.
DNA: 1-2µg at a minimum of 100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS).
For routine testing of blood, saliva and buccal swabs, KDL does NOT accept samples from patients within two (2) weeks of a packed cell/platelet transfusion or within four (4) weeks of a whole blood transfusion. For extraordinary circumstances, where testing must be performed within the above windows, please contact our lab.
Test Performed (Days):
Weekly
Turn Around Time:
21 Days
Shipment Sensitivity Requirements:
- Keep specimen cold during transit, but do not ship on dry ice.
- Ship the specimen overnight express.
References:
- Savant A, Lyman B, Bojanowski C, et al. Cystic Fibrosis. 2001 Mar 26 [Updated 2024 Aug 8]. In: Adam MP, Feldman J, Mirzaa GM, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2025. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1250/
- https://www.cff.org/intro-cf/about-cystic-fibrosis
- Committee Opinion No. 691: Carrier Screening for Genetic Conditions. Obstet Gynecol. 2017 Mar;129(3):e41-e55.
- Deignan JL, Gregg AR, Grody WW, Guo MH, Kearney H, Monaghan KG, Raraigh KS, Taylor J, ZepedaMendoza CJ, Ziats C; ACMG Board of Directors. Electronic address: documents@acmg.net. Updated recommendations for CFTR carrier screening: A position statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2023 Aug;25(8):100867.
Additional Info:
Prior to any genetic testing we recommend genetic counseling. To receive forms and information about prenatal diagnostic testing, please contact Client Services at (855) 535-1522.