Cystic Fibrosis - CF

Diagnosis

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

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

  • Begin with panel of common CFTR mutations and reflex to sequencing and duplication/deletion testing for detection of rare mutations

Differential Diagnosis

Screening

  • American College of Medical Genetics (ACMG) and American College of Obstetricians and Gynecologists (ACOG) 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 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

Clinical Background

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene; over 1,600 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
  • Ethnicity – >90% are Caucasian

Inheritance

  • Autosomal recessive
    • 2 pathogenic CFTR mutations on opposite chromosomes
      • Classic CF – 2 severe mutations
      • Nonclassic CF – 1 severe and 1 mild/moderate or 2 mild/moderate mutations
    • Penetrance – high for severe mutations, variable for mild/moderate mutations
    • Most common mutation in U.S. is F508del
      • >1,600 mutations have been identified
  • 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 sufficient, 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 systems dysfunction
      • Male – azoospermia due to congenital bilateral absence of vas deferens (CBAVD) in >95%
      • Female – modest reduction in fertility
  • Nonclassic CF – monosymptomatic disease such as chronic pancreatitis, bilateral absence of the vas deferens, nasal polyps, or bronchiectasis

Treatment

  • Respiratory therapy – chest physiotherapy
  • Antibiotic treatment of infections
  • Inhalant treatment – Dornase alfa
  • Pancreatic enzymes taken with meals to increase nutrient absorption
  • Lung transplant
    • Improves quality of life but not survival

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
Test Name and Number Recommended Use Limitations Follow Up
Cystic Fibrosis (CFTR) 32 Mutations 2001933
Method: Polymerase Chain Reaction/Oligonucleotide Ligation/Fragment Analysis

Tests for 32 common CFTR gene mutations

Order for any of the following indications

  • Carrier testing in a healthy patient
  • Patient with symptoms of CF
  • Patient with family history of CF

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

Tests for 32 common CFTR gene mutations

Sequencing detects 97% of the described CF mutations (currently >1,600)

Order for patients with either of the following indications (if not previously tested using the CF mutation panel)

  • Symptoms of classic CF
  • Positive sweat chloride test

If only one pathogenic mutation is identified, CFTR gene sequencing will be added

Clinical sensitivity: 97% in all ethnicities

CFTR promoter mutations, deep intronic mutations and large gene deletions/duplications 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

Tests for 32 common CFTR gene mutations

Sequencing is performed if only 1 mutation is identified; deletion/duplication testing is performed if two CFTR mutations are not identified by sequencing

Clinical sensitivity is 99%

Cost-effective method for determining causative mutations in patients with a clinical diagnosis of CF

CFTR promoter mutations and deep intronic mutations will not be detected

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

Test amniocyte for 32 common CF gene mutations

Order in fetal samples for the following indications

  • One or both parents have CFTR mutations included on the panel
  • Echogenic or cystic dilatation of the fetal bowel on ultrasound

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

Clinical sensitivity varies with ethnicity

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

Detects large CFTR duplications and deletions within the exons and intron/exon borders

Order for patients who have a positive sweat chloride test or atypical CF symptoms but have only one or no detectable mutations on CFTR sequencing

Deletion/duplication breakpoints will not be determined

CFTR single-base pair substitutions, small deletions/duplications, and deep intronic and promoter mutations will not be detected

Mutations within the primer/probe regions could affect this assay

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

Detects 97% of described CFTR gene mutations (currently >1,600)

Order for patients with symptoms of classic or atypical CF but without two mutations identified by the CF mutation panel

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

Tests for nearly all described CFTR gene mutations (currently >1,600)

If sequencing identifies fewer than 2 pathogenic mutations, CFTR deletion/duplication will be added

Order for patients with symptoms of classic or atypical CF but without two mutations identified using the CF mutation panel

Clinical sensitivity: 99%

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

Determines if the R117H mutation and 5T variant are on the same chromosome

Order only for patients who have a previously identified R117H mutation and 5T variant

Analytic sensitivity and specificity for detection of these mutations are 99%

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

Tests for 3199del6 mutation only

Order only for patients who have a previously identified I148T mutation

 Other mutations in the CFTR gene will not be detected  
Pancreatic Elastase, Fecal 0080526
Method: Quantitative Enzyme-Linked Immunosorbent Assay

Screen for pancreatic insufficiency caused by CF

 Watery stool samples may produce falsely decreased results due to a dilution effect   
Additional Tests Available
 
 
Click the plus sign to expand the table of additional tests.
Test Name and NumberComments
Cystic Fibrosis (CFTR) 32 Mutations, Atypical 2001969
Method: Polymerase Chain Reaction/Oligonucleotide Ligation/Fragment Analysis

Tests for 32 common CFTR gene mutations, including 5T

Order for patients with one or more of the following symptoms

  • Bilateral absence of the vas deferens
  • Nasal polyps
  • Bronchiectasis

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

Approval by an ARUP genetic counselor required prior to ordering
Cystic Respiratory Culture 0060130
Method: Culture/Identification