Cystic Fibrosis - CF

Background
Dx
Screen
Lab Tests
Algorithm

Diagnostic Algorithm

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

Immunodeficiency Evaluation for Chronic Infections in Infants and Children Testing Algorithm

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
- Incidence of nonclassic CF is unknown
Age – 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
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
    - Pseudomonas aeruginosa
    - Staphylococcus aureus
    - Burkholderia cepacia
  - 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
    - Reduction may lead to gallstones
  - GI
    - Distal intestinal obstruction (meconium ileus equivalent)
    - Constipation, intussusception, colonic strictures, hypotonic colon
    - Meconium ileus in 15% of infants
- Endocrine systems dysfunctions
  - 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

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

Infectious GI disease
- Diarrhea – viral, bacterial, parasitic
Immunodeficiency syndromes
AAT deficiency
Mucopolysaccharidosis
Malnutrition
Glycogen storage diseases
Celiac disease

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 one or more mutations are detected on the CF mutation panel, sweat testing recommended for confirmation

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
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 Clinical sensitivity varies with ethnicity	Mutations other than the 32 tested will not be detected Primer site mutations may affect this assay
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; if two CFTR mutations are not identified sequencing is performed 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 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 two CFTR mutations are not 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 amniocytes 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 Clinical sensitivity varies with ethnicity	Only the 32 mutations tested will be detected; further mutations within the primer/probe regions could affect this assay
Cystic Fibrosis (CFTR) Deletion/Duplication 0051642 Method: Multiplex Ligation 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 ~1-2% of CFTR mutations are large deletions or duplications	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/Scanning/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 Probe Amplification	Tests for nearly all described CFTR gene mutations (currently >1,600) If two CFTR mutations are not identified by sequencing, deletion/duplication testing is performed 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 & 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
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) 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: 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 Number	Comments
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: Standard reference procedure for aerobic bacterial culture and identification