Cystic Fibrosis - CF

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

Indications for Testing

  • Individuals with one or more classic symptoms
    • If chronic recurrent infection, consider immunodeficiency evaluation in addition to CF testing (see Immunodeficiency Evaluation algorithms)
  • 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

  • Two elevated sweat chloride values (>60 mmol/L) by quantitative pilocarpine iontophoresis performed at an accredited CF care center or two known pathogenic CFTR mutations on opposite chromosomes
    • Nonclassic CF is caused by mild CFTR mutations; borderline or normal sweat chloride values are common
    • Sweat chloride testing often fails in infants >4.5 kg or 10 lbs

Laboratory Testing

  • Initial testing – panel of common CFTR gene mutations
  • May consider deletion/duplication testing for detection of rare mutations in atypical presentations

Differential Diagnosis

Immunodeficiency Evaluation for Chronic Infections in Adults and Older Children Testing Algorithm

Immunodeficiency Evaluation for Chronic Infections in Infants and Children Testing Algorithm

  • American College of Medical Genetics (ACMG, 2011) and American College of Obstetricians and Gynecologists (ACOG, 2011) recommend a 23-mutation panel for carrier screening; each mutation occurs with >1/1,000 frequency in 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 3-4 weeks later or perform CFTR mutation panel
      • If IRT is elevated on second specimen or ≥1 mutations are detected on the CF mutation panel, sweat testing  recommended for confirmation

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene; over 1,800 different CFTR mutations have been reported. CF is associated with recurrent pulmonary infections and pancreatic dysfunction.

Epidemiology

  • Incidence
    • Classic CF
      • 1/3,000 Caucasians or Ashkenazi Jews
      • 1/8,000 Hispanics
      • 1/15,000 African Americans
      • 1/32,000 Asians
    • Nonclassic CF – unknown
  • Age – classic disease usually diagnosed by newborn screening or in early childhood; nonclassic usually presents in adulthood
  • Ethnicity – >90% are Caucasian

Inheritance

  • Autosomal recessive
    • Classic CF – 2 severe pathogenic CFTR mutations on opposite chromosomes
    • Nonclassic CF – 1 severe and 1 mild/moderate on opposite chromosomes
    • Men with congenital bilateral absence of the vas deferens (CBAVD)
      • At least 1 CFTR mutation will be present in ~80%
      • 2 CFTR mutations − ~25%
      • 1 CFTR and 1 5T mutation − 25%
      • 1 CFTR mutation − 20%
      • 1 5T mutation − 10%
    • Individuals with idiopathic pancreatitis
      • Up to 40% are predicted to have at least 1 CFTR mutation
    • Purulent pansinusitis or nasal polyposis starting early in life or associated with chronic infection
      • 30% of adults have 1 CFTR mutation
      • 7% of adults have 2 CFTR mutations
  • Penetrance – high for severe mutations, variable for mild/moderate mutations
  • CFTR gene mutations
    • >1,800 mutations
    • Most are very rare and not well characterized
    • Most common in U.S. - F508del
  • Carrier frequency
    • 1/25 European Caucasians and Ashkenazi Jews
    • 1/46 Hispanics
    • 1/65 African Americans
    • 1/90 Asian Americans

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 eventual epithelial injury
  • Death typically occurs from obstructive airway disease at an average age of 38 years

Clinical Presentation

  • Classic CF – chronic sinopulmonary disease, gastrointestinal (GI) malabsorption, 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 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
  • Nonclassic CF – monosymptomatic disease such as idiopathic pancreatitis, CBAVD, nasal polyps, or bronchiectasis

Indications for Laboratory Testing

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) 32 Mutations 2001933
Method: Polymerase Chain Reaction/Oligonucleotide Ligation/Fragment Analysis

Limitations

Mutations other than the 32 tested will not be detected

Primer site mutations may affect this assay

Clinical sensitivity varies with ethnicity

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

Limitations

Rare diagnostic errors can occur due to primer site mutations

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

Cystic Fibrosis (CFTR) 32 Mutations with Reflex to Sequencing 2001968
Method: Polymerase Chain Reaction/Oligonucleotide Ligation/Fragment Analysis/Sequencing

Limitations

CFTR promoter mutations, deep intronic mutations and large gene deletions/duplications will not be detected

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

Limitations

Rare diagnostic errors can occur due to primer and probe site mutations

Breakpoints for large deletions/duplications will not be determined

Regulatory region and some deep intronic mutations will not be detected

Cystic Fibrosis (CFTR) 32 Mutations with Reflex to Sequencing and Reflex to Deletion/Duplication 2001967
Method: Polymerase Chain Reaction/Oligonucleotide Ligation/Fragment Analysis/Sequencing/Multiplex Ligation-dependent Probe Amplification

Limitations

CFTR promoter mutations and deep intronic mutations will not be detected

Cystic Fibrosis (CFTR) 3199del6 Mutation 0050098
Method: Polymerase Chain Reaction/Fluorescence Monitoring

Limitations

Other mutations in the CFTR gene will not be detected 

Cystic Fibrosis Cis-Trans (CFTR) R117H and 5T Mutations 0056006
Method: Polymerase Chain Reaction/Oligonucleotide Ligation

Cystic Fibrosis (CFTR) 32 Mutations, Fetal 2001970
Method: Polymerase Chain Reaction/Oligonucleotide Ligation/Fragment Analysis

Limitations

Only the 32 mutations tested will be detected; further mutations within the primer/probe regions could affect assay

Clinical sensitivity varies with ethnicity

Additional Tests Available

Pancreatic Elastase, Fecal 0080526
Method: Quantitative Enzyme-Linked Immunosorbent Assay

Comments

Screen for pancreatic insufficiency caused by CF

Cystic Fibrosis (CFTR) Deletion/Duplication 0051642
Method: Multiplex Ligation-dependent Probe Amplification

Comments

Tests for large deletions or duplications in CFTR gene accounting for 1-2% of mutations

Order for symptoms of classic or atypical CF without 2 identified mutations following CFTR sequencing

This is a second-tier test and requires permission from ARUP’s genetic counselor before ordering

Preferred test is CF sequencing with reflex to deletion/duplication

Cystic Fibrosis (CFTR) 32 Mutations, Atypical 2001969
Method: Polymerase Chain Reaction/Oligonucleotide Ligation/Fragment Analysis

Comments

Diagnostic testing for individuals with nonclassic CF presentation

Tests for 32 common CFTR gene mutations, including 5T

Mutations other than the 32 tested will not be detected

Primer site mutations may affect analytic sensitivity

Cystic Fibrosis (CFTR) 5T Mutation 0056003
Method: Polymerase Chain Reaction/Fragment Analysis

Comments

For patients with a previously identified R117H mutation or those with atypical CF symptoms who only have 1 mutation detected on the CF panel

Cystic Respiratory Culture 0060130
Method: Culture/Identification

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 J, Kerem E, Durie P, Tullis E, Assael B, Bombieri C, Brown A, Casals T, Claustres M, Cutting G, Dequeker E, Dodge J, Doull I, Farrell P, Ferec C, Girodon E, Johannesson M, Kerem B, Knowles M, Munck A, Pignatti P, Radojkovic D, Rizzotti P, Schwarz M, Stuhrmann M, Tzetis M, Zielenski J, Elborn J. 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 L, Barton D, Cutting G, Dallapiccola B, Dequeker E, Girodon E, Grody W, Highsmith E, Kääriäinen H, Kruip S, Morris M, Pignatti P, 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 P, Rosenstein B, White T, Accurso F, Castellani C, Cutting G, Durie P, Legrys V, Massie J, Parad R, Rock M, Campbell P, 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 M. Genetic screening and counseling. Curr Opin Obstet Gynecol. 2008; 20(2): 157-63. PubMed

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

Taylor C, Hardcastle J, Southern K. 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

Watson M, Cutting G, Desnick R, Driscoll D, Klinger K, Mennuti M, Palomaki G, Popovich B, Pratt V, Rohlfs E, Strom C, Richards S, Witt D, Grody W. Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel. Genet Med. 2004; 6(5): 387-91. PubMed

References from the ARUP Institute for Clinical and Experimental Pathology®

Bennett C, Campbell M, Cook C, Eyre D, Nay L, Nielsen D, Rasmussen R, Bernard P. 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 C. 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 T, Jama M, Ponek V, Lyon E, Wilson J, Hoffmann M, Bejjani B. 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 D, Flume P, Hamilton L, Lyon E, Wolff D. 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

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 C, Kent J, 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 P, Miller C, Bayrak-Toydemir P, Best H, Mao R, Swensen J, Lyon E, Voelkerding K. 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 S, Grosso L, Amos J, Schaefer F, Lyon E, Wolff D, Hajianpour A, Taylor A, Millson A, Stenzel T. 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

Wittwer C, Reed G, Gundry C, Vandersteen J, Pryor R. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem. 2003; 49(6 Pt 1): 853-60. PubMed

Zhou L, Palais R, Ye F, Chen J, Montgomery J, Wittwer C. 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: December 2015