Gene test interpretation: CFTR

INTRODUCTION — This monograph discusses the interpretation of genetic testing for the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene and possible actions based on results. It does not discuss the indications for testing and is not intended to replace clinical judgment in the decision to test or in the clinical care of the individual who was tested. These subjects are discussed separately in UpToDate [1]. (See 'UpToDate topics' below.)

HOW TO READ THE REPORT

General principles

●Assess report for accuracy and interpretation (table 1).

●If the report is from direct-to-consumer testing or a research study and the results would impact clinical care, the patient should be retested using a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory with established procedures assuring proper specimen collection and labeling.

Though >2100 DNA sequence variants have been identified in the CFTR gene, certainty regarding the potential to cause disease exists for only a subset. When genetic testing consists of genotyping a specific panel of CFTR variants known to cause CF, the report typically describes positive results as either mutations or pathogenic variants (table 2). When CFTR gene sequencing is performed, the report may call all identified changes variants. The testing laboratory classifies each variant as pathogenic, likely pathogenic, benign, or likely benign based on accumulated data (table 3) [2]. Variants that cannot be characterized this way are called variants of uncertain significance (VUS) and are likely to be reclassified as more data emerge. (See "Secondary findings from genetic testing", section on 'Definitions and classification of variants'.)

CF-specific caveats

●Negative results – The clinical implication of a negative test depends on the method used:

•Genotyping – A negative CF genotyping panel only means that the individual does not carry any of the CFTR mutations tested. Panels test 23 to >100 of the more commonly observed pathogenic variants (table 4). Though uncommon, patients can have one or more rare variants that are not represented on such panels, and thus a negative result does not eliminate the possibility of being a CF carrier or, in the case of fetal testing, of having an affected child. The uncertainty is greatest in individuals of non-European ancestry, for whom extensive sequence data are lacking. (See 'Negative screen' below.)

•Sequencing – A negative sequencing test means that no variants were identified in the parts of the gene that were adequately sequenced or that the only identified variants are ones known to be benign (ie, ones that do not cause disease). False negative results can arise if a pathogenic variant is missed in a gene region poorly covered by the sequencing assay. If a diagnosis of CF is suspected clinically, practitioners should verify the adequacy of sequence coverage (comments are often included in the report) and consult with a specialist if suspicions remain.

Regardless of assay type, if the patient has a family history of CF or of family members who are CFTR-variant carriers, the patient should be tested explicitly for the variants known to exist in the family. If such information is not available, sequencing is recommended over genotyping.

●False positives – Additional testing may be necessary to exclude false positives. As an example, variants I506V, I507V, and F508C may lead to false positive reports of F508del or F507del. The laboratory usually performs this testing automatically (ie, reflex testing).

●5T/7T/9T testing – Additional testing, usually performed automatically (ie, reflex testing), helps predict the phenotype for certain variants. For example, when R117H is identified, testing for 5T/7T/9T variants helps predict the likelihood of congenital bilateral absence of the vas deferens.

●Compound heterozygotes – If genetic testing reveals two or more pathogenic variants at different positions within the gene, further evaluation is needed to evaluate whether the variants reside on the same chromosome (ie, they are in "cis," both inherited from one parent) or if each are on separate chromosomes (ie, in "trans," inherited from each parent separately) (figure 1). Because CF is autosomal recessive, only variants in trans cause disease.

SPECTRUM OF DISEASE — CF is a life-limiting, systemic disease with an autosomal recessive transmission pattern. Features of classic CF include bronchiectasis, sinusitis, pancreatitis, pancreatic exocrine insufficiency, malabsorption, CF-related diabetes mellitus, hepatobiliary disease with cirrhosis and/or portal hypertension, and absence of the vas deferens in males. Disease severity varies widely and is impacted by both the inherited variants and environmental factors. (See "Cystic fibrosis: Clinical manifestations and diagnosis".)

Disease-modifying therapies have dramatically improved the prognosis for CF. Shared decision-making must acknowledge uncertainties regarding our ability to predict the future of patients born with CF today.

The most common pathogenic CFTR variants (mutations), F508del and W1282X, are highly penetrant and result in a consistent phenotype; all patients with F508del or W1282X who have another pathogenic variant will develop classic CF. In contrast, it is difficult to predict the phenotype if there is one pathogenic variant and one variant of uncertain significance (VUS). This may result in classic CF, clinical disease limited to one organ system (a CFTR-related disorder), or a carrier state. VUS may be reclassified at any time as pathogenic or benign, so clinicians must seek an updated interpretation before providing counseling.

For the purpose of prenatal screening and fetal diagnosis, predicting the potential fetal phenotype can be difficult. If the fetus shares at least one CFTR variant with an affected family member, the phenotype may be similar to that of the affected relative. However, there can be significant interindividual phenotype variation among family members with the same genotype, and the phenotype may be modified by the variant inherited from the other parent and other factors. These uncertainties must be shared with the patient. (See "Cystic fibrosis: Carrier screening", section on 'Prediction of phenotype'.)

Information on predicted phenotype is presented in separate searchable databases. (See 'Genetics resources' below.)

ASYMPTOMATIC ADULTS

Carrier screening — Carrier screening is routinely offered to all women planning pregnancy or in early pregnancy. At a minimum, screening examines a panel of the 23 most common mutations (pathogenic variants) in the United States (table 4). (See "Cystic fibrosis: Carrier screening".)

The clinical implication of mutations identified depends on the specific mutations and background risk (eg, family history, ethnicity). Partner testing informs the risk of having a child affected with CF with each pregnancy. Patient values and preferences will impact decisions about pregnancy. Some pregnant women will use the screening results to avoid the birth of an affected child, while others will use it to plan for the birth of an affected child. Couples at risk who are not pregnant may elect to conceive using noncarrier donor gametes or in vitro fertilization with preimplantation genetic testing and selection of unaffected embryos. (See "Preimplantation genetic testing".)

Positive screen — Individuals with a positive screening test should receive genetic counseling, and testing of the partner is indicated (algorithm 1).

If the father is unavailable for testing, the risk of an affected child is calculated based on the mother's test results and the background carrier rate for her partner's ethnicity (table 5).

If both partners carry a known mutation (pathogenic variant), there is a one in four chance that their child will be affected. Affected offspring can be identified prenatally using chorionic villus sampling or amniocentesis. Because obstetric and neonatal management is not changed by the prenatal diagnosis of CF, couples who would not terminate an affected pregnancy may elect to delay testing until after birth to avoid the small risk of miscarriage from invasive diagnostic procedures. (See 'Newborn screening' below.)

Negative screen — A negative screening test only means that the individual does not carry any of the CF mutations included in the screening panel; a negative result does not eliminate the possibility of being a CF carrier. The degree to which the risk of being a carrier is reduced after a negative test is determined by the number of mutations screened and the patient's ethnicity. There is considerable variability across ethnicity and race with regard to the most common CF-causing mutations (table 5).

If there is a family history of CF, carrier screening should include the mutations present in the affected family member in addition to those in the standard panel. If the affected family member had no or incomplete CF testing and is not available for testing, and standard screening of the member of the couple who is related is negative, CFTR sequencing should be offered.

When a CF carrier's partner has a negative screen, further testing of the screen negative partner may be indicated. A genetic counselor can help determine the next step (eg, CFTR sequencing versus expanded screening panels followed by CFTR sequencing, if negative), taking into account background risk and insurance coverage.

Incidental finding — An individual may unexpectedly discover that he or she carries a pathogenic or likely pathogenic CFTR variant through testing done for research purposes, exome or genome testing performed for other clinical indications, or direct-to-consumer testing. If confirmed by repeat testing, genetic counseling is indicated (algorithm 1). Those with two copies of a pathogenic or likely pathogenic variant should be evaluated at a certified CF center.

NEWBORN SCREENING — Newborn screening typically measures blood levels of immunoreactive trypsinogen (IRT), with or without concurrent CFTR gene testing. If IRT is abnormal, genetic testing is indicated. (See "Cystic fibrosis: Clinical manifestations and diagnosis", section on 'Diagnosis'.)

Infants with one or more pathogenic CFTR variants are referred for sweat chloride testing, which distinguishes affected children from carriers in most cases. Infants with indeterminate results may be given a provisional diagnosis of CFTR-related metabolic syndrome (CRMS), also referred to as CF screen positive, inconclusive diagnosis (CFSPID).

Some cases of CF will be missed by newborn screening. CF should be suspected in individuals with suggestive symptoms, even when results of the newborn screen are negative or equivocal. CFTR gene sequencing may identify pathogenic variants in this setting.

SYMPTOMATIC INDIVIDUALS — CFTR gene testing may be performed in individuals with a chronic condition that can be associated with CF such as pulmonary disease, recurrent pancreatitis, nasal polyps, chronic sinusitis, or male infertility due to absence of the vas deferens.

Such testing is usually conducted by a subspecialist. Genetic testing and counseling of such patients is complicated and often benefits from CF center expertise.

Since the universal adoption of newborn screening for CF in the United States, it is much less common for adults to have undiagnosed CF. However, individuals with milder CF or only a single feature of CF are more likely to present later in childhood or adulthood, and to have uncommon CFTR variants not included in the standard screening panels. (See "Cystic fibrosis: Clinical manifestations and diagnosis", section on 'Regional variation in screening'.)

Results of CFTR gene testing helps guide treatment of CF as mutation class impacts treatment options (table 6). (See "Cystic fibrosis: Genetics and pathogenesis" and "Cystic fibrosis: Treatment with CFTR modulators".)

CONSIDERATIONS FOR THE FAMILY — CF is an autosomal recessive disorder. Relatives of individuals with pathogenic CFTR variants are at increased risk of being carriers and should be offered genetic counseling.

●Parents of patients with CF – Unaffected parents of individuals with CF are usually obligate carriers.

●Siblings of patients with CF – Each full sibling of an individual with CF has a 25 percent chance of being affected, a 50 percent chance of being an asymptomatic carrier, and a 25 percent chance of being a noncarrier. This means unaffected siblings of a child with classic CF have a two in three chance (66 percent) of being a carrier.

●Offspring of patients with CF – An affected individual will transmit one pathogenic variant to offspring; therefore, offspring will either be asymptomatic carriers or will have CF depending on the genotype of the other parent.

●Siblings of a CFTR carrier – Each full sibling of a known carrier has a 50 percent chance of being a carrier.

RESOURCES

UpToDate topics

●(See "Cystic fibrosis: Carrier screening".)

●(See "Cystic fibrosis: Genetics and pathogenesis".)

●(See "Cystic fibrosis: Clinical manifestations and diagnosis".)

Genetics resources

Resources for locating a genetic counselor or specialized CF center:

●National Society of Genetic Counselors (NSGC)

●Cystic Fibrosis Foundation (www.cff.org)

Resources for determining pathogenicity of variants:

●Clinical and functional translation of CFTR international consortium (cftr2.org)

●CF mutation database (www.genet.sickkids.on.ca/cftr/)