Cystic Fibrosis - CF

  • Diagnosis
  • Algorithms
  • Screening
  • Background
  • Lab Tests
  • References
  • Related Topics

Indications for Testing

  • Individuals with one or more classic symptoms of cystic fibrosis (CF)
  • Individuals with a CFTR gene-related disorder, such as congenital bilateral absence of the vas deferens (CBAVD), pancreatitis, or recurrent bronchiectasis
  • Children with an affected sibling
  • Infants with a positive newborn screen
  • Carrier screening
    • Expectant couples
    • Couples planning a pregnancy
    • Individuals with positive family history of CF

Criteria for Diagnosis

  • Classic CF
    • Two elevated sweat chloride values (>60 mmol/L) on two separate days by quantitative pilocarpine iontophoresis performed at an accredited CF care center or two known severe (or one moderate and one severe) pathogenic CFTR gene variants on opposite chromosomes
    • Sweat chloride testing often fails for infants <4.5 kg or 10 lbs
  • Other CFTR-related disorders
    • One mild and one pathogenic CFTR variant of any severity on opposite chromosomes
    • Borderline or normal sweat chloride values are common

Laboratory Testing

  • Initial testing – panel of at least the 23 common pathogenic CFTR gene variants recommended for carrier screening or diagnostic testing by the American College of Medical Genetics (ACMG, 2011)
  • If two panel variants are not identified for individuals with symptoms of CF or another CFTR-related disorder, reflex testing to CFTR gene sequencing and deletion/duplication testing is recommended

Differential Diagnosis

  • American College of Medical Genetics (ACMG, 2011) and American College of Obstetricians and Gynecologists (ACOG, 2011) recommend a 23-variants panel for carrier screening; each variant occurs with >1/1,000 frequency in cystic fibrosis (CF) patients in a pan-ethnic U.S. population
    • Offer screening to the following
      • All expectant couples or those planning a pregnancy
      • Men with congenital bilateral absence of the vas deferens (CBAVD) and their reproductive partners
      • Individuals with a positive family history
  • CF newborn screening – supported by U.S. Centers for Disease Control and Prevention and currently practiced in all 50 states
    • Measurement of immunoreactive trypsinogen (IRT) in blood spots
      • If IRT is elevated, repeat testing 2 weeks later or perform a CFTR variants panel test  
      • If IRT is elevated on second specimen or ≥1 variant is detected by the CFTR variants panel, sweat chloride testing is recommended for confirmation

Cystic fibrosis (CF) is caused by the presence of two severe pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene on opposite chromosomes; over 2,000 different CFTR variants have been reported, but most are very rare and of unknown significance. CF is typically associated with recurrent pulmonary infections and exocrine pancreatic insufficiency

Epidemiology

  • Incidence
    • Classic CF
      • Ashkenazi Jews – 1/2,300
      • Caucasians – 1/2,500
      • Hispanics – 1/13,500
      • African Americans – 1/15,100
      • Asians – 1/35,100
    • Other CFTR-related disorders – unknown
  • Age – classic CF is usually diagnosed by newborn screening or in early childhood; other CFTR-related disorders usually present in adulthood
  • Ethnicity – >90% are Caucasian

Inheritance

  • Autosomal recessive
    • Classic CF – two severe, or one severe and one moderate, pathogenic CFTR variants on opposite chromosomes
    • Other CFTR-related disorders – one severe and one mild pathogenic variant on opposite chromosomes
    • Men with congenital bilateral absence of the vas deferens (CBAVD)
      • At least one pathogenic CFTR variant will be present in ~75%
      • Two pathogenic CFTR variants − ~20%
      • One pathogenic CFTR and one mild 5T variant − 25%
      • One pathogenic CFTR variant − 20%
      • One mild 5T variant − 10%
    • Individuals with idiopathic pancreatitis
      • Up to 40% are predicted to have at least one pathogenic CFTR variant
    • Purulent pansinusitis or nasal polyposis starting early in life or associated with chronic infection
      • 30% of adults have one pathogenic CFTR variant
      • 7% of adults have two pathogenic CFTR variants
  • Penetrance – high for severe pathogenic variants, variable for mild/moderate variants
  • CFTR gene
    • >2,000 variants
    • Most are very rare and not well characterized
    • Most common - F508del
  • Carrier frequency
    • Ashkenazi Jews – 1/24
    • European Caucasians – 1/25
    • Hispanic Americans – 1/58
    • African Americans – 1/61
    • Asian Americans – 1/94

Pathophysiology

  • CFTR codes for a cAMP-regulated chloride channel in the apical membrane of epithelial cells
    • Without enough functional CFTR protein, the salt concentration in sweat is elevated, and the viscosity of the mucous in the lungs and pancreas is increased, leading to obstruction
    • Obstruction sets the stage for chronic infection, inflammation, and epithelial injury
  • Death typically occurs from obstructive airway disease at an average age of 38 years

Clinical Presentation

  • Classic CF – chronic sinopulmonary disease, exocrine pancreatic insufficiency, and obstructive azoospermia
    • Sinopulmonary disease
      • Chronic lung infections – bronchiectasis, dyspnea, wheezing, nasal polyps, clubbing of fingers
      • Infectious organisms typically involved
      • Eventual pulmonary complications may include massive hemoptysis, pneumothorax, and respiratory failure
    • Pancreas/liver/gallbladder/GI disease
      • Pancreas
        • ≥85% have exocrine pancreatic insufficiency
        • Reduced absorption of lipids and fat-soluble vitamins
        • Steatorrhea and malabsorption result in malnutrition
        • If pancreatic sufficiency, chronic/recurrent bouts of pancreatitis
        • 25% of adults develop diabetes
      • Liver
        • Clogging of biliary ducts leads to liver and biliary cirrhosis
        • Liver congestion secondary to hypoxia-induced cor pulmonale
      • Gallbladder disease
        • Fecal loss of bile acids leads to reduction in bile-salt pool with increased incidence of gallstones
      • GI
        • Distal intestinal obstruction
        • Constipation, intussusception, colonic strictures, hypotonic colon
        • Meconium ileus in 15% of infants
    • Endocrine system dysfunction
      • Male – azoospermia due to CBAVD in >95%
      • Female – modest reduction in fertility
  • Other CFTR-related disorders  – monosymptomatic disease such as idiopathic pancreatitis, CBAVD, nasal polyps, or bronchiectasis
Tests generally appear in the order most useful for common clinical situations. Click on number for test-specific information in the ARUP Laboratory Test Directory.

Cystic Fibrosis (CFTR) 165 Pathogenic Variants 2013661
Method: Polymerase Chain Reaction/Fluorescence Monitoring

Limitations 

Diagnostic errors can occur due to rare sequence variations

Only the 165 pathogenic CFTR variants (see Additional Technical Information) will be interrogated

Cystic Fibrosis (CFTR) 165 Pathogenic Variants with Reflex to Sequencing and Reflex to Deletion/Duplication 2013664
Method: Polymerase Chain Reaction/Fluorescence Monitoring/Sequencing/Multiplex Ligation-dependent Probe Amplification

Limitations 

Diagnostic errors can occur due to rare sequence variations

Breakpoints of large deletions/duplications and regulatory region and deep intronic variants are not detected

Variants of unknown clinical significance may be detected

Cystic Fibrosis (CFTR) Sequencing 0051110
Method: Polymerase Chain Reaction/Sequencing

Limitations 

Diagnostic errors can occur due to rare sequence variations

Variants of unknown clinical significance may be detected

Regulatory region variants, large deletions/duplications, and some deep intronic variants will not be detected

Cystic Fibrosis (CFTR) 165 Pathogenic Variants with Reflex to Sequencing 2013663
Method: Polymerase Chain Reaction/Fluorescence Monitoring/Sequencing

Limitations 

Diagnostic errors can occur due to rare sequence variations

Pathogenic (CTFR) promoter variants and large deletions/duplications will not be detected

Variants of unknown clinical significance may be identified 

Cystic Fibrosis (CFTR) Sequencing with Reflex to Deletion/Duplication 0051640
Method: Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification

Limitations 

Diagnostic errors can occur due to rare sequence variations

Breakpoints for large deletions/duplications will not be determined

Regulatory region and some deep intronic variants will not be detected

Cystic Fibrosis (CFTR) 165 Pathogenic Variants, Fetal 2013662
Method: Polymerase Chain Reaction/Fluorescence Monitoring

Limitations 

Diagnostic errors can occur due to rare sequence variations

Only the 165 pathogenic CFTR variants (see Additional Technical Information) will be interrogated

Guidelines

American College of Obstetricians and Gynecologists Committee on Genetics. ACOG Committee Opinion No. 486: Update on carrier screening for cystic fibrosis. Obstet Gynecol. 2011; 117(4): 1028-31. PubMed

Castellani C, Cuppens H, Macek M, Cassiman JJ, Kerem E, Durie P, Tullis E, Assael BM, Bombieri C, Brown A, Casals T, Claustres M, Cutting GR, Dequeker E, Dodge J, Doull I, Farrell P, Ferec C, Girodon E, Johannesson M, Kerem B, Knowles M, Munck A, Pignatti PF, Radojkovic D, Rizzotti P, Schwarz M, Stuhrmann M, Tzetis M, Zielenski J, Elborn JS. Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. J Cyst Fibros. 2008; 7(3): 179-96. PubMed

Castellani C, Macek M, Cassiman J, Duff A, Massie J, Kate LP, Barton D, Cutting G, Dallapiccola B, Dequeker E, Girodon E, Grody W, Highsmith EW, Kääriäinen H, Kruip S, Morris M, Pignatti PF, Pypops U, Schwarz M, Soller M, Stuhrman M, Cuppens H. Benchmarks for cystic fibrosis carrier screening: a European consensus document. J Cyst Fibros. 2010; 9(3): 165-78. PubMed

Farrell PM, Rosenstein BJ, White TB, Accurso FJ, Castellani C, Cutting GR, Durie PR, Legrys VA, Massie J, Parad RB, Rock MJ, Campbell PW, Cystic Fibrosis Foundation. Guidelines for diagnosis of cystic fibrosis in newborns through older adults: Cystic Fibrosis Foundation consensus report. J Pediatr. 2008; 153(2): S4-S14. PubMed

Green A, Kirk J, Guidelines Development Group. Guidelines for the performance of the sweat test for the diagnosis of cystic fibrosis. Ann Clin Biochem. 2007; 44(Pt 1): 25-34. PubMed

Standards and Guidelines for Clinical Genetics Laboratories . American College of Medical Genetics. [Revised Mar 2011; Accessed: Nov 2015]

General References

Culling B, Ogle R. Genetic counselling issues in cystic fibrosis. Paediatr Respir Rev. 2010; 11(2): 75-9. PubMed

Kerem E. Atypical CF and CF related diseases. Paediatr Respir Rev. 2006; 7 Suppl 1: S144-6. PubMed

Norton ME. Genetic screening and counseling. Curr Opin Obstet Gynecol. 2008; 20(2): 157-63. PubMed

O'Sullivan BP, Freedman SD. Cystic fibrosis. Lancet. 2009; 373(9678): 1891-904. PubMed

Taylor CJ, Hardcastle J, Southern KW. Physiological measurements confirming the diagnosis of cystic fibrosis: the sweat test and measurements of transepithelial potential difference. Paediatr Respir Rev. 2009; 10(4): 220-6. PubMed

References from the ARUP Institute for Clinical and Experimental Pathology®

Bennett CD, Campbell MN, Cook CJ, Eyre DJ, Nay LM, Nielsen DR, Rasmussen RP, Bernard PS. The LightTyper: high-throughput genotyping using fluorescent melting curve analysis. Biotechniques. 2003; 34(6): 1288-92, 1294-5. PubMed

Chou L, Gedge F, Lyon E. Complete gene scanning by temperature gradient capillary electrophoresis using the cystic fibrosis transmembrane conductance regulator gene as a model. J Mol Diagn. 2005; 7(1): 111-20. PubMed

Chou L, Lyon E, Wittwer CT. A comparison of high-resolution melting analysis with denaturing high-performance liquid chromatography for mutation scanning: cystic fibrosis transmembrane conductance regulator gene as a model. Am J Clin Pathol. 2005; 124(3): 330-8. PubMed

Christensen TM, Jama M, Ponek V, Lyon E, Wilson JA, Hoffmann ML, Bejjani BA. Design, development, validation, and use of synthetic nucleic acid controls for diagnostic purposes and application to cystic fibrosis testing. J Mol Diagn. 2007; 9(3): 315-9. PubMed

Heaney DL, Flume P, Hamilton L, Lyon E, Wolff DJ. Detection of an apparent homozygous 3120G>A cystic fibrosis mutation on a routine carrier screen. J Mol Diagn. 2006; 8(1): 137-40. PubMed

Lyon E, Miller C. Current challenges in cystic fibrosis screening. Arch Pathol Lab Med. 2003; 127(9): 1133-9. PubMed

Lyon E, Schrijver I, Weck KE, Ferreira-Gonzalez A, Richards S, Palomaki GE, CAP/ACMG Biochemical and Molecular Genetics Committee. Molecular genetic testing for cystic fibrosis: laboratory performance on the College of American Pathologists external proficiency surveys Genet Med. 2015; 17(3): 219-25. PubMed

Millson A, Pont-Kingdon G, Page S, Lyon E. Direct molecular haplotyping of the IVS-8 poly(TG) and polyT repeat tracts in the cystic fibrosis gene by melting curve analysis of hybridization probes. Clin Chem. 2005; 51(9): 1619-23. PubMed

Montgomery J, Wittwer CT, Kent JO, Zhou L. Scanning the cystic fibrosis transmembrane conductance regulator gene using high-resolution DNA melting analysis. Clin Chem. 2007; 53(11): 1891-8. PubMed

Pont-Kingdon G, Jama M, Miller C, Millson A, Lyon E. Long-range (17.7 kb) allele-specific polymerase chain reaction method for direct haplotyping of R117H and IVS-8 mutations of the cystic fibrosis transmembrane regulator gene. J Mol Diagn. 2004; 6(3): 264-70. PubMed

Ridge PG, Miller C, Bayrak-Toydemir P, Best H, Mao R, Swensen JJ, Lyon E, Voelkerding KV. Cystic fibrosis testing in a referral laboratory: results and lessons from a six-year period. J Clin Bioinforma. 2013; 3(1): 3. PubMed

Sebastian S, Spitzer SG, Grosso LE, Amos J, Schaefer FV, Lyon E, Wolff DJ, Hajianpour A, Taylor AK, Millson A, Stenzel TT. Multicenter characterization and validation of the intron-8 poly(T) tract (IVS8-T) status in 25 Coriell cell repository cystic fibrosis reference cell lines for cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation assays. Clin Chem. 2004; 50(1): 251-4. PubMed

Siryani I, Jama M, Rumman N, Marzouqa H, Kannan M, Lyon E, Hindiyeh M. Distribution of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mutations in a Cohort of Patients Residing in Palestine PLoS One. 2015; 10(7): e0133890. PubMed

Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem. 2003; 49(6 Pt 1): 853-60. PubMed

Zhou L, Palais RA, Ye F, Chen J, Montgomery JL, Wittwer CT. Symmetric snapback primers for scanning and genotyping of the cystic fibrosis transmembrane conductance regulator gene. Clin Chem. 2013; 59(7): 1052-61. PubMed

Medical Reviewers

Last Update: August 2016