Cystic Fibrosis and CF-Related Disorders via the CFTR Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 3035 | CFTR | 81223 | 81223,81222 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
Turnaround Time
3 weeks on average for standard orders or 2 weeks on average for STAT orders.
Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.
Targeted Testing
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
Clinical Features and Genetics
Clinical Features
Cystic Fibrosis (CF) is a severe disorder with typical onset in infancy. Main features include chronic, debilitating lung infections, pancreatic insufficiency connected to dietary malabsorption; excess Cl- in sweat, and absence of the vas deferens. Severity varies widely; genetic and non-genetic modifying factors exist. Average survival in patients is currently ~37 years. Today, many U.S. CF cases are detected through routine neonatal screening (http://genes-r-us.uthscsa.edu/). CF is one of the most common “single gene” disorders with carrier frequencies up to 1/25 in individuals with Northern European ancestry.
CF-Related disorders include chronic pancreatitis due to pancreatic insufficiency and congenital bilateral absence of the vas deferens (CBAVD) in the absence of other CF features (Lebo and Grody, 2007). In the case of CBAVD, nearly all male patients are infertile.
Genetics
Cystic Fibrosis is caused by mutations in the cystic fibrosis conductance regulator (CFTR) gene. Inheritance is autosomal recessive. Over 1300 causative CFTR mutations have been reported; most are very rare (http://genes-r-us.uthscsa.edu/). Missense mutations predominate, but there are also substantial numbers of nonsense, frameshift, and splicing mutations. A relatively small number of larger deletions and other major gene rearrangements have been reported. One major mutation, ΔF508, comprises about 70% of all mutant alleles in Northern Europeans. Correlations between genotyping and phenotype are beginning to be made (Moskowitz et al. 2005; McKone et al. 2006).
The CFTR gene encodes a membrane channel protein which transports chloride ions across cells that produce mucus, saliva, sweat, tears and digestive enzymes (Kreda, S. et al., 2012). CFTR also regulates the function of sodium ion channels, which is necessary for the function of the lungs and pancreas. Though CFTR mutations are typically associated with cystic fibrosis, and CBAVD, recent literature has demonstrated the presence of CFTR variants in individuals with chronic pancreatitis (Masson, E. et al., 2013).
Clinical Sensitivity - Sequencing with CNV PG-Select
Our full gene sequencing test is expected to detect >98% of CFTR causative mutations involved in Cystic Fibrosis or CF-related disorders like CBAVD and pancreatitis.
To date, no gross duplications or deletions have been reported for CFTR-associated pancreatitis and a relatively small number of large deletions and other major gene rearrangements have been reported to cause cystic fibrosis and CBAVD (Human Gene Mutation Database).
Testing Strategy
This test provides full coverage of all coding exons of the CFTR gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
This test also includes sequencing of regions within intron 11 and intron 21, along with a complete analysis of the compound (TG)n(T)n sequence (5T/TG tract) in intron 8. Variations in the 5T/TG tract have been reported to cause CBAVD (Chillon et al. 1995). Our 5T/TG tract analysis involves bidirectional sequencing along with allele length measurement.
Indications for Test
Most CF patients and many potential CFTR mutation carriers will first receive testing for a collection of ≥23 specific, well characterized mutations (Amos et al., 2011). PreventionGenetics does not offer such a panel at this time. Patients, who carry no more than one of the mutations within the panel, are candidates for our full gene sequencing test. CF patients with Native American, African or Asian ancestry may also be candidates for the full sequencing test, as the standard panel of mutations was designed for White patients. CBAVD patients are also good candidates for our full sequencing test, especially since the 5T/TG tract has a particularly strong effect on this phenotype. The 5T/TG tract analysis may be ordered alone. To rule out CF related pancreatitis, individuals with the following criteria should consider testing for mutations in CFTR (Ellis et al., 2001):
Recurrent unexplained attacks of acute pancreatitis and a positive family history Unexplained chronic pancreatitis and a positive family history Unexplained chronic pancreatitis without a positive family history after exclusion of other causes such as hyperlipidaemia type I, familiar hypercalciuric hypercalcemia (FBH), hereditary hyperthyroidism and autoimmune pancreatitis. Unexplained pancreatitis episodes in children Individuals who test negative for mutations in the PRSS1 gene or have a single, heterozygous mutation in either SPINK1 or CTRC. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CFTR.
Most CF patients and many potential CFTR mutation carriers will first receive testing for a collection of ≥23 specific, well characterized mutations (Amos et al., 2011). PreventionGenetics does not offer such a panel at this time. Patients, who carry no more than one of the mutations within the panel, are candidates for our full gene sequencing test. CF patients with Native American, African or Asian ancestry may also be candidates for the full sequencing test, as the standard panel of mutations was designed for White patients. CBAVD patients are also good candidates for our full sequencing test, especially since the 5T/TG tract has a particularly strong effect on this phenotype. The 5T/TG tract analysis may be ordered alone. To rule out CF related pancreatitis, individuals with the following criteria should consider testing for mutations in CFTR (Ellis et al., 2001):
Recurrent unexplained attacks of acute pancreatitis and a positive family history Unexplained chronic pancreatitis and a positive family history Unexplained chronic pancreatitis without a positive family history after exclusion of other causes such as hyperlipidaemia type I, familiar hypercalciuric hypercalcemia (FBH), hereditary hyperthyroidism and autoimmune pancreatitis. Unexplained pancreatitis episodes in children Individuals who test negative for mutations in the PRSS1 gene or have a single, heterozygous mutation in either SPINK1 or CTRC. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CFTR.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| CFTR | 602421 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Diseases
| Name | Inheritance | OMIM ID |
|---|---|---|
| Congenital Bilateral Absence Of The Vas Deferens | AR | 277180 |
| Cystic Fibrosis | AR | 219700 |
| Pancreatitis, Chronic | AD | 167800 |
Related Tests
| Name |
|---|
| Chronic Granulomatous Disease via the CYBA Gene |
| Chronic Granulomatous Disease via the NCF2 Gene |
| Chronic Pancreatitis Panel |
| Interstitial Lung Disease Panel |
Citations
- Amos, J, Feldman, GL, Grody, WW, Monaghan, K, Palomaki, GE, Prior, TW, Richards, CS, Watson, MS. 20011. Technical Standards and Guidelines for CFTR Mutation Testing.
- Chillon, M, Casals, T, Mercier, B, Bassas, L, Lissens, W, Silber, S, Romey, MC, Ruiz-Romero, J, Verlingue, C, Claustres, M, et al. 1995. Mutations in the cystic fibrosis gene in patients with congenital absence of the vas deferens. N. Engl. J. Med. 332: 1475-1480. PubMed ID: 7739684
- Ellis, I, Lerch, MM, Whitcomb, DC. 2001. Genetic testing for hereditary pancreatitis: guidelines for indications, counselling, consent and privacy issues. Pancreatology 1:405-415. PubMed ID: 12120217
- Human Gene Mutation Database (Bio-base).
- Joergensen, MT, Brusgaard, K, Crüger, DG, Gerdes, AM, Schaffalitzky de Muckadell, OB. 2010. Genetic, epidemiological, and clinical aspects of hereditary pancreatitis: a population-based cohort study in Denmark. Am. J. Gastroenterol. 105:1876-1883. PubMed ID: 20502448
- Kreda, SM, Davis, CW, Rose, MC. 2012. CFTR, mucins, and mucus obstruction in cystic fibrosis. Cold Spring Harb. Perspect. Med. 2:a009589. PubMed ID: 22951447
- Lebo, RV, Grody, WW. 2007. Variable penetrance and expressivity of the splice altering 5T sequence in the cystic fibrosis gene. Genet. Test 11: 32-44. PubMed ID: 17394391
- Masson, E, Chen, JM, Audrézet, MP, Cooper, DN, Férec, C. 2013. A Conservative Assessment of the Major Genetic Causes of Idiopathic Chronic Pancreatitis: Data from a Comprehensive Analysis of PRSS1, SPINK1, CTRC and CFTR Genes in 253 Young French Patients. PLoS One 8:e73522. PubMed ID: 23951356
- McKone, EF, Goss, CH, Aitken, ML. 2006. CFTR genotype as a predictor of prognosis in cystic fibrosis. Chest 130: 1441-1447. PubMed ID: 17099022
- Moskowitz, SM, Chmiel, JF, Sternen, DL, Cheng, E, Cutting, GR. 2008. CFTR-Related Disorders. GeneReviews. PubMed ID: 20301428
Ordering/Specimens
Ordering Options
We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
- PGnome sequencing panels can be ordered via the myPrevent portal only at this time.
Requisition Form
- A completed requisition form must accompany all specimens.
- Billing information along with specimen and shipping instructions are within the requisition form.
- All testing must be ordered by a qualified healthcare provider.
For Requisition Forms, visit our Forms page
If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.
Specimen Types
Specimen Requirements and Shipping Details
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