Cystic Fibrosis

Algorithm(s)

PDF algorithm(s) available at www.arupconsult.com.

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 1500 different CFTR mutations have been reported.

Epidemiology

Classic CF affects 1:3000 Caucasians and Ashkenazi Jews, 1:8000 Hispanics, 1:15,000 African Americans, 1:32,000 Asians
4% of Caucasians are carriers

Inheritance

Autosomal recessive
- 2 deleterious CFTR mutations on different chromosomes
  - Classical symptoms of cystic fibrosis - 2 severe mutations
  - Atypical symptoms - 1 severe and 1 mild mutation, 2 mild mutations, or 1 mutation and 1 5T variant
- Penetrance - high for severe mutations, variable for mild mutations

Pathophysiology

CFTR codes for a cAMP-regulated chloride channel in the apical membrane of epithelial cells
Without enough functional CFTR, 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 results from obstructive airway disease in the fourth decade of life

Clinical Presentation

Classic - chronic sinopulmonary disease, gastrointestinal malabsorption, pancreatic insufficiency and obstructive azoospermia
Atypical - monosymptomatic disease such as chronic pancreatitis, bilateral absence of the vas deferens, nasal polyps or bronchiectasis
Sinopulmonary disease
- Chronic lung infections - bronchiectasis, dyspnea, wheezing, chest pain, nasal polyps, clubbing
- Infectious organisms
  - Pseudomonas aeruginosa
  - Staphylococcus aureus
  - Burkholderia cepacia
Pancreas/liver/gallbladder/gastrointestinal (GI) disease
- Pancreas
  - 85% or more have pancreatic insufficiency
  - Absorption of lipids and fat soluble vitamins is reduced
Chronic or recurrent abdominal pain from pancreatitis
Steatorrhea and malnutrition result
Meconium ileus in 15% of infants
25% of adults develop diabetes
- Liver
  - Clogging of biliary ducts leads to liver and biliary cirrhosis
  - Congestion of liver secondary to hypoxia-induced cor pulmonale
- Gallbladder
  - 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
Endocrine systems dysfunctions
- Male - azoospermia due to congenital bilateral absence of vas deferens (CBAVD) in >95%
- Female - modest reduction in fertility

Screening

American College of Medical Genetics (ACMG) recommends a 23 mutation panel for carrier screening; each mutation occurs with greater than 1 in 1000 frequency in panethnic US population
- Offer screening for the following indications:
  - 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

Treatment

Respiratory therapy - chest physiotherapy
Antibiotic treatment of infections
Inhalant treatment - Dornase alfa
Nutritional supplementation when necessary
Lung transplantation
- Improves quality of life, but not survival

See Also

Malabsorption

Pancreatitis, Acute

Algorithm(s)

PDF algorithm(s) available at www.arupconsult.com.

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

Immunodeficiency Evaluation for Chronic Infections in Infants and Children Testing Algorithm

Tests

Tests generally appear in the order most useful for common clinical situations

Test name: Cystic Fibrosis (CFTR) 32 Mutations

ARUP #: 0056040

Methodology: Polymerase Chain Reaction/Oligonucleotide Ligation

Use:

Tests for 32 of the most common CF gene mutations

Order for any of the following indications:

Carrier testing in an expectant couple or those planning a pregnancy
Patient with symptoms of CF
Patient with family history of CF

Limitations:

Mutations other than the 32 tested will not be detected

Primer site mutations may affect this assay

Follow-up:

Test name: Cystic Fibrosis (CFTR) 32 Mutations with Reflex to Sequencing

ARUP #: 0051150

Methodology: Polymerase Chain Reaction/Oligonucleotide Ligation/Scanning/Sequencing

Use:

Tests for 32 of the most common CF gene mutations; full gene sequencing is performed if two CF mutations are not identified on the panel

Order for patients with either of the following indications who have not been previously tested:

Patients with symptoms of classic CF
Patients with a positive sweat chloride

Clinical sensitivity: 97%

Limitations:

CFTR promoter mutations and larger gene deletions/duplications will not be detected

Follow-up:

Test name: Cystic Fibrosis (CFTR) 32 Mutations with Reflex to Sequencing and Reflex to Deletion/Duplication

ARUP #: 0051732

Methodology: Polymerase Chain Reaction/Fragment Analysis/Sequencing/Multiplex Ligation-dependent Probe Amplification

Use:

Tests for 32 of the most common CF gene mutations; full gene sequencing is performed if two CF panel mutations are not identified; deletion/duplication testing is performed if two mutations have not be identified by sequencing

Order for patients with either of the following indications who have not been previously tested:

Patients with symptoms of classic CF
Patients with a positive sweat chloride

Clinical sensitivity: 99%

Test name: Cystic Fibrosis, Mutation Panel, Fetal

ARUP #: 0050393

Methodology: Polymerase Chain Reaction/Oligonucleotide Ligation

Use:

Test amniocytes for 32 of the most common CF gene mutations

Order in fetal samples for the following indications:

Both parents have known CF panel mutations
One parent has a known CF panel mutation and the other parent is unavailable
Echogenic or cystic dilatation of the fetal bowel on ultrasound

Limitations:

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

Follow-up:

Test name: Cystic Fibrosis (CFTR) Deletion/Duplication

ARUP #: 0051642

Methodology: Multiplex Ligation Probe Amplification

Use:

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

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

Approximately 1-2% of CFTR mutations are large deletions or duplications

Limitations:

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

Test name: Cystic Fibrosis (CFTR) Sequencing

ARUP #: 0051110

Methodology: Polymerase Chain Reaction/Scanning/Sequencing

Use:

Detects point mutations and small insertions/deletions within the coding region intron/exon boundaries

Order for patients with positive sweat chloride or CF symptoms without two detectable mutations on the CF mutation panel

Clinical sensitivity: 97%

Limitations:

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

Test name: Cystic Fibrosis (CFTR) Sequencing with Reflex to Deletion/Duplication

ARUP #: 0051640

Methodology: Polymerase Chain Reaction/Sequencing/Multiplex Ligation Probe Amplification

Use:

Detects mutations in CFTR exons and intron/exon borders

Order for patients with positive sweat chloride or CF symptoms without two detectable mutations on the CF mutation panel

Clinical sensitivity: 99%

Limitations:

CFTR promoter mutations and rare intronic mutations will not be detected

Test name: Cystic Fibrosis Cis-Trans

ARUP #: 0056006

Methodology: Polymerase Chain Reaction/Oligonucleotide Ligation

Use:

Tests whether 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

Limitations:

Follow-up:

Test name: Cystic Fibrosis Mutation Panel, Atypical

ARUP #: 0050756

Methodology: Polymerase Chain Reaction/Oligonucleotide Ligation

Use:

Tests for 32 of the most common CF gene mutations and the 5T variant

Order in patients with one or more of the following symptoms:

Recurrent pancreatitis
Bilateral absence of the vas deferens
Nasal polyps
Bronchiectasis

Limitations:

Mutations other than the 32 CFTR panel mutations and the 5T variant will not be detected

Primer site mutations may affect the analytic sensitivity of this assay

Follow-up:

Test name: Cystic Fibrosis 3199del6 Only (ARUP Medical Director or Genetic Counselor approval required prior to testing)

ARUP #: 0050098

Methodology: Polymerase Chain Reaction/Fluorescence Monitoring

Use:

Tests for 3199del6 mutation only
Order only for patients who have a previously identified I148T mutation

Limitations:

Follow-up:

Test name: Trypsin, Fecal

ARUP #: 0020383

Methodology: Film Digestion

Use:

Screen for pancreatic insufficiency caused by cystic fibrosis

Limitations:

Follow-up:

Test name: Pancreatic Elastase, Fecal

ARUP #: 0080526

Methodology: Enzyme-Linked Immunosorbent Assay

Use:

Screen for pancreatic insufficiency caused by cystic fibrosis

Limitations:

Watery stool samples may produce falsely decreased results due to a dilution effect

Additional Tests Available

Test name: Cystic Fibrosis (CFTR) 5T Mutation

ARUP #: 0056003

Methodology: Polymerase Chain Reaction/Fragment Analysis

Comments: Do not order without ARUP's genetic counselor approval

Test name: Cystic Respiratory Culture

ARUP #: 0060130

Methodology: Standard reference procedure for aerobic bacterial culture and identification

Comments:

References

Guidelines

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

Watson MS, Cutting GR, Desnick RJ, Driscoll DA, Klinger K, Mennuti M, Palomaki GE, Popovich BW, Pratt VM, Rohlfs EM, Strom CM, Richards CS, Witt DR, Grody WW. Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel. Genet Med. 2004;6(5):387-391.

General References

Accurso FJ. Update in cystic fibrosis 2005. Am J Respir Crit Care Med. 2006;173(9):944-947.

Biagioli FE, DeVoe JE, Hamilton A, WinklerPrins V. Clinical inquiries. What are appropriate screening tests for infants and children?. J Fam Pract. 2006;55(9):803-808.

Davies JC. New tests for cystic fibrosis. Paediatr Respir Rev. 2006;7 Suppl 1:S141-S143.

Kerem E. Atypical CF and CF related diseases. Paediatr Respir Rev. 2006;7 Suppl 1:S144-S146.

Lyon E, Miller C. Current challenges in cystic fibrosis screening. Arch Pathol Lab Med. 2003;127(9):1133-1139.

Quinton HB, O'Connor GT. Current issues in quality improvement in cystic fibrosis. Clin Chest Med. 2007;28(2):459-472.

Rowe SM, Clancy JP. Advances in cystic fibrosis therapies. Curr Opin Pediatr. 2006;18(6):604-613.

Smyth R, Jahnke N. Cochrane systematic reviews in cystic fibrosis. J R Soc Med. 2006;99 Suppl 46:6-12.

Southern KW, Peckham D. Establishing a diagnosis of cystic fibrosis. Chron Respir Dis. 2004;1(4):205-210.

Strausbaugh SD, Davis PB. Cystic fibrosis: a review of epidemiology and pathobiology. Clin Chest Med. 2007;28(2):279-288.

References from the ARUP Institute for Clinical and Experimental Pathology Research®

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):1288-5.

Chou LS, 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):111-120.

Chou LS, 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):330-338.

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):315-319.

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):137-140.

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):1619-1623.

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):1891-1898.

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):264-270.

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):251-254.

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):853-860.

Medical Reviewers

Grenache, David G., Ph.D. Medical Director, Special Chemistry at ARUP Laboratories; Assistant Professor, Clinical Pathology, University of Utah

Lyon, Elaine, Ph.D. Medical Director, Molecular Genetics at ARUP Laboratories; Associate Professor, Pathology, University of Utah

Mao, Rong , M.D. Co-Medical Director, Molecular Genetics at ARUP Laboratories; Assistant Professor, Pathology, University of Utah

Roberts, William L. , M.D., Ph.D. Medical Director, Automated Core Laboratory at ARUP Laboratories; Professor, Pathology, University of Utah

Comprehensive Review: May 2008
Last Update: July 2008