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
  • 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

Screening

  • 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

Clinical Background

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

Screening for individuals with symptoms of CF

Carrier screening for

  • Expectant couples
  • Couples planning a pregnancy
  • Individuals with a positive family history of CF

Tests for 32 CFTR gene mutations (includes the 23 mutations recommended by ACOG and ACMG):

G85E (c.254G>A), R117H (c.350G>A), R334W (c.1000C>T), R347P (c.1040G>C), R347H (c.1040G>A), 394delTT (c.262_263delTT), A455E (c.1364C>A), I507del (c.1519_1521de;ATC), F508del (c.1521_1523de;CTT), V520F (c.1558G>T), G542X (c.1624G>T), S549N (c.1646G>A), S549R (c.1645A>C or c.1647T>G), G551D (c.1652G>A), R553X (c.1657C>T), R560T (c.1679G>C), 621+1G>T (c.489+1G>T), 711+1G>T (c.579+1G>T), 1078delT (c.948delT), R1162X (c.3484C>T), W1282X (c.3846G>A), N1303K (c.3909C>G), 1717-1G>A (c.1585-1G>A), 1898+1G>A (c.1766+1G>A), 2183AA>G (c.2051_2052delAAinsG), 2184delA (c.2052delA), 2789+5G>A (c.2657+5G>A), 3120+1G>A (c.2988+1G>A), 3659delC (c.3528delC), 3849+10kbC>T (c.3717+12191C>T), 3876delA (c.3744delA), 3905insT (c.3773_3774insT); for specimens positive for R117H, the IVS-8/poly T (c.1210-12T[5_9])

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

Order for patients with symptoms of classic or atypical CF but without 2 mutations identified by the CF mutation panel

Clinical sensitivity – 97%

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

Order for patients with

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

For individuals suspected to be affected with CF but without 2 mutations detected by CFTR 32 mutation panel

Detects CFTR sequence variations in exons and intron/exon borders

Large duplication/deletion analysis is performed if 2 pathogenic mutations are not detected by sequencing

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

Confirm suspected diagnosis of CF

Sequencing is performed if only 1 mutation is identified; deletion/duplication testing is performed if 2 CFTR mutations are not identified by sequencing

Clinical sensitivity – 99%

CFTR promoter mutations and deep intronic mutations will not be detected

 
Cystic Fibrosis (CFTR) 3199del6 Mutation 0050098
Method: Polymerase Chain Reaction/Fluorescence Monitoring
Order only for patients who have a previously identified I148T mutation to detect co-presence of I148T and 3199del6 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

Order only for patients who have a previously identified R117H mutation and 5T variant to determine if the 2 mutations are on the same chromosome

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

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

Order in fetal samples for the following indications

  • 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

 
Additional Tests Available
 
Click the plus sign to expand the table of additional tests.
Test Name and NumberComments
Pancreatic Elastase, Fecal 0080526
Method: Quantitative Enzyme-Linked Immunosorbent Assay

Screen for pancreatic insufficiency caused by CF

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

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

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

Order for patients with nonclassic presentation of CF

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

Approval by an ARUP genetic counselor required prior to ordering

Cystic Respiratory Culture 0060130
Method: Culture/Identification