Description 
Cystic fibrosis (CF) is an autosomal recessive genetic disease in which dysfunctional epithelial chloride channels lead to excessively thick mucus affecting multiple organ systems. Common complications include mucous plugging of the airway, lung inflammation, chronic pulmonary infections, intestinal malabsorption, pancreatic insufficiency, and infertility.¹ 

When pursuing genetic testing for cystic fibrosis, genetic counseling is strongly recommended.  

For guidance on pre-implantation genetic testing, please see CAM 110-Pre-Implantation Genetic Testing. For guidance on prenatal screening and preconception screening for cystic fibrosis, please see CAM-358-Prenatal Screening (Genetic). 

Policy  
Application of coverage criteria is dependent upon an individual’s benefit coverage at the time of the request. 

1. Common variant testing (see Note 1) or comprehensive analysis of the CFTR gene (i.e., full gene sequencing, deletion/duplication analysis) is considered MEDICALLY NECESSARY in any of the following situations:
   1. In a newborn after an abnormal newborn screening result using immunoreactive trypsinogen.
   2. For infants with meconium ileus.
   3. For individuals with congenital absence of the vas deferens (CAVD).
   4. For individuals with idiopathic pancreatitis or bronchiectasis.
2. As an adjunct to sweat testing in an individual presenting with symptoms of cystic fibrosis, common variant testing (see Note 1) or comprehensive analysis of the CFTR gene (i.e., full gene sequencing, deletion/duplication analysis) is considered MEDICALLY NECESSARY in any of the following situations:
   1. When there are no known familial pathogenic or likely pathogenic (P/LP) variants.
   2. When one or more familial P/LP variants are known; testing must include the familial P/LP variants.
3. For individuals with congenital bilateral absence of the vas deferens (CBAVD), common variant testing (see Note 1) or comprehensive analysis of the CFTR gene (i.e., full gene sequencing, deletion/duplication analysis), including testing for the CFTR IVS8 5T/7T/9T variant, is considered MEDICALLY NECESSARY.
4. When the CFTR R117H variant is detected on carrier screening, reflex genetic testing for the CFTR IVS8 5T/7T/9T variant is considered MEDICALLY NECESSARY.
5. For individuals for whom common variant testing (see Note 1) identified no variants or only one variant, but for whom the clinical suspicion of cystic fibrosis still remains, comprehensive analysis of the CFTR gene (i.e., full gene sequencing, deletion/duplication analysis) is considered MEDICALLY NECESSARY in any of the following situations:
   1. For individuals that presented with symptoms of cystic fibrosis and who received panel testing as an adjunct to sweat testing.
   2. When a diagnosis of cystic fibrosis related CBAVD remains a consideration in individuals with CBAVD.
6. For the family members of individuals with CFTR-related metabolic disorder/cystic fibrosis screen positive, inconclusive diagnosis (CRMS/CFSPID), comprehensive analysis of the CFTR gene (i.e., full gene sequencing, deletion/duplication analysis) is considered MEDICALLY NECESSARY in any of the following situations:
   1. For parents of the individual: When phasing of the CFTR variants would inform the diagnostic status of the individuals by confirming the inheritance pattern.
   2. For siblings of the individual.
7. For all other situations not described above, genetic testing for variants in the CFTR gene is considered NOT MEDICALLY NECESSARY. 

NOTES:

Note 1: Common variant testing for CFTR mutations must include the American College of Medical Genetics’ (ACMG) CFTR carrier screening variant set (n = 100). Please see the “Guidelines and Recommendations” section of this policy for a table of ACMG’s CFTR minimum variant set.

Table of Terminology

Rationale
Cystic fibrosis (CF) is a common life-limiting autosomal recessive genetic disorder caused by the mutation of a gene that encodes an epithelial chloride-conducting transmembrane channel called the cystic fibrosis transmembrane conductance regulator (CFTR). This gene regulates anion (negatively charged ion) transport and mucociliary clearance. Mucociliary clearance is the process by which particles and gases dissolved in the mucus are moved unidirectionally from the respiratory tract. The CFTR protein was first identified as a chloride channel but has been shown to facilitate or regulate the transport of other ions, such as sodium, thiocyanate, bicarbonate, as well as water absorption and excretion.^2,3The CFTR protein is present in the epithelia of various tissues, including that of the lungs, sweat glands, gastrointestinal tract, and pancreas.⁴ CFTR dysfunction mainly affects epithelial cells; although, there is evidence of a role in immune cells.

Mutations in the CFTR gene which impede protein production, stability, or activity result in less available functional protein.³ Functional failure of CFTR results in defective mucociliary clearance, chronic infection, and abnormal inflammatory response leading to progressive, irreversible lung damage.² Other manifestations of dysfunctional CFTR include pancreatic insufficiency and meconium ileus.⁴The early identification and treatment of patients by multidisciplinary teams have resulted in improvements in both quality of life and clinical outcomes in patients with cystic fibrosis, with life expectancy reaching 50 or even 60 years.³

Most mutations of the CFTR gene are missense alterations, but other mutations, deletions and insertions have been described.⁵ Missense mutations occur when a single nucleotide is changed, resulting in a different amino acid which may affect the overall protein functionality. To date, over 2000 mutations have been identified in the CFTR gene.⁶CFTR mutations can be divided into six classes according to their effects on protein function as depicted in the figure below.⁵

Class I, II, and III mutations are associated with no residual CFTR function and patients with these mutations have a severe phenotype, whereas individuals with class IV, V, and VI mutations have some residual function of CFTR protein and have a mild lung phenotype and pancreatic sufficiency.^5,7

Due to the relatively high frequency in the U.S. population and studies demonstrating that early detection and care can improve outcomes, CF testing is included as part of the newborn screen in all states.⁸ Newborn screening (NBS) for CF can include testing for immunoreactive trypsinogen (IRT), which is a pancreatic enzyme found at elevated levels in the blood of some individuals with CF, genetic testing for common CF mutations, or a combination of IRT and genetic testing. Positive newborn screens are typically followed by genetic testing (if not already done), and a sweat test, which measures the chloride concentration in sweat. The sweat test historically has been considered the “gold standard” for CF diagnosis. The presence of two disease-causing mutations also may be considered diagnostic of the disease, even in the absence of classic symptoms or in the case of a negative or inconclusive sweat test.⁹

In addition to NBS, CF carrier screening (PCS) has become commonplace in the U.S., particularly among pregnant individuals and couples planning a pregnancy. PCS has been found to markedly reduce CF birth rates with a shift towards milder mutations, but it was often avoided for cultural reasons necessitating the use of complementary PCS and NBS.¹⁰

A subset of 23 mutations accounts for most cystic fibrosis cases in the U.S. and were accepted by most guidelines as the primary genes to be screened for diagnosis of CF and carrier status. The most common CF-causing mutation is F508del, which is present in over 70% of known CF cases. The Clinical and Functional Translation of CFTR (CFTR2) project continually evaluates genotype and phenotype correlations and has confirmed many additional mutations as being causative of CF.⁶ Information from over 88,000 patients with specific cystic fibrosis variants from the United States, Canada, and Europe was collected by the CFTR2 team from national CF Patient Registries and placed in the CFTR2 database and then compiled into the CFTR2 website that contains information about the 322 most common CFTR variants.⁶

Analysis of data from the CF Foundation Patient Registry found that patients of Hispanic, black, or Asian ancestry were less likely to have two identified CFTR variants and more likely to carry no mutations on the commonly used 23 mutation carrier screening panel.¹¹ Analysis of the Exome Aggregation Consortium dataset also found that none of the current genetic screening panels or existing CFTR mutation databases covered most deleterious variants in any geographical population outside of Europe. Both clinical annotation and mutation coverage by commercially available targeted screening panels for CF are strongly biased toward detection of reproductive risk in persons of European descent.¹² This research indicates the possible need for adjustment of this panel to facilitate equity in mutation detection between white and nonwhite or mixed-ethnicity CF patients, enabling an earlier diagnosis improving their quality of life.

Proprietary Testing
There are several traditional cystic fibrosis genotyping assays approved by the FDA. eSensor Cystic Fibrosis Carrier Detection System detects 24 CFTR variants,¹³ Tag-It™ Cystic Fibrosis Kit detects 39 variants,¹⁴ Cystic Fibrosis Genotyping Assay detects 30 variants,¹⁵ InPlex™ CF Molecular Test detects 32 variants,¹⁶ Verigene®CFTR and Verigene®CFTR PolyT Nucleic Acid Tests detect 26 variants,¹⁷ Diasorin xTAG® Cystic Fibrosis (CFTR) 39 kit v2 detects 39 variants and the Diasorin xTAG® Cystic Fibrosis (CFTR) 60 kit v2 detects an additional 21 variants,¹⁸  and Illumina MiSeqDx™ Cystic Fibrosis 139-Variant Assay detects 139 variants.¹⁹These panels target common mutations prevalent in certain populations, providing rapid and cost-effective results. However, they may miss rare or novel mutations not included in the panel, potentially leading to incomplete genetic assessments.

Next generation sequencing (NGS) offers a comprehensive analysis by sequencing the entire CFTR gene enabling the detection of both common and rare mutations, including novel variants that traditional panels might overlook.  FDA-approved platforms, such as the Illumina MiSeqDx Cystic Fibrosis Clinical Sequencing Assay, facilitate the detection of both common and rare CFTR mutations.²⁰ A study using NGS for NBS found that the NGS assay was 100% concordant with traditional methods. Retrospective analysis results indicate an IRT/NGS screening algorithm would enable high sensitivity, better specificity, and positive predictive value.²¹ Further studies have shown that implementing NGS has improved diagnostic accuracy and increased the positive predictive value in newborn screening.²² Additionally,  whole genome sequencing of the CFTR gene is also growing in popularity. This type of sequencing has revealed a high prevalence of the intronic variant c.3874-4522A>G in those affected by CF.²³

Cystic fibrosis transmembrane conductance regulator (CFTR) modulators are a new class of medications targeting the underlying defect in CF by improving production, intracellular processing, and/or function of the defective CFTR protein. Ivacaftor (IVA), which improves chloride channel function, IVA combined with lumacaftor (LUM), which partially corrects the CFTR misfolding, and IVA combined with tezacaftor, which improves the intracellular processing and trafficking of CFTR, have been approved by the U.S. Food and Drug Administration for use in patients with CF. Additional approval of Trikafta, a combination therapy of elexacaftor, tezacaftor, and ivacaftor, has expanded treatment options by demonstrating efficacy in patients with a broader spectrum of CFTR mutations.²⁴ The indications and efficacy of these drugs depend upon the CFTR mutation in the individual patient. For example, ivacaftor has been FDA-approved and Clinical Pharmacogenetics Implementation Consortium (CPIC)-recommended only for CF patients with the G551D mutation. It is not recommended for any other CF mutation.²⁵

Analytical Validity
Lyon, et al. (2014) assessed clinical laboratories’ proficiency at evaluating genetic alterations for CF. A total of 357 labs participated, performing approximately 120,000 tests monthly. Analytical sensitivity and specificity were 98.8% and 99.6%, respectively. Clinical interpretation matched intended response for zero, one, and two mutations. The authors concluded that laboratory testing for CF in the United States is of high quality.²⁶

Sugunaraj, et al. (2019) completed a cross-sectional study which included the analysis of CFTR variants in 50,778 exomes. Only 24 patients were identified to contain bi-allelic pathogenic CFTR variants; the authors identified 21 of these cases as true-positives and three as potential false positives. Therefore, “genomic screening exhibited a positive predictive value of 87.5%, negative predictive value of 99.9%, sensitivity of 95.5%, and a specificity of 99.9%.”²⁷ Overall, the presence and/or absence of CFTR variants was strongly related to a CF diagnosis.

Hendrix, et al. (2020) assessed the performance of dried blood spot DNA extraction methods in NGS for cystic fibrosis. A total of 20 DNA samples were used in this study and sequenced using Illumina's MiSeqDx™ Cystic Fibrosis 139-Variant Assay and Swift Biosciences’ Accel-Amplicon™ CFTR panel. The MiSeqDx CFTR Clinical Sequencing Assay identified 37 CF-causing variants in the 20 samples tested, for a total of 141 benign variants which were all confirmed with Sanger sequencing. The Swift Biosciences’ Accel-Amplicon™ CFTR panel identified 39 CF-causing variants for a total of 123 benign variants which were all confirmed with Sanger sequencing. Illumina's MiSeqDx performed well with a very high average coverage per method (>3000×) despite most DNA extraction methods being low-concentration and relatively crude. Because of the higher input of samples on a single flow cell, the average coverage per target was lower in the Accel-Amplicon™ CFTR panel in comparison to the clinical sequencing assay, but still often had >1000× coverage. The authors conclude that “both these tests are appropriate DNA extraction methods that can be used with dried blood spots that will result in consistent, high-quality sequencing results.”²⁸

Sicko, et al. (2021) validated the use of a custom NGS assay, Archer CF assay, for CF newborn screening. According to the New York State, CF NBS had high false positive rates. However, after the implementation of this three-tier IRT-DNA-SEQ approach using commercially available tests, the positive predictive value of CF NBS improved from 3.7% to 25.2%. The Archer CF assay involves full gene sequencing, analyzing a specific panel of 338 clinically relevant CFTR variants (second tier), followed by unblinding of all sequence variants and bioinformatic assessment of deletions/duplications (third tier). 227 infant samples were taken, and 190 of 227 carries one or more of the 338 panel variants. The second-tier panel variants were all called correctly, detecting 44 different variants with a 100% sensitivity and 100% specificity. All 227 samples also underwent third tier analysis which detected 62 additional unique SNV/indel variants.²²

Pedersen, et al. (2024) evaluated the 11-year performance of the cystic fibrosis newborn bloodspot screening (CF-NBS) and found strong sensitivity (96%) but moderate positive predictive value (PPV) (25%). The program uses an immunoreactive trypsinogen (IRT)-DNA algorithm with a second IRT (IRT-2) as a safety net. Optimal cut-offs for IRT-1 and IRT-2 were identified at 2.7 and 5.9 z-scores, respectively. Simulated algorithm modifications suggested that removing the safety net could increase PPV to 30%, reduce unnecessary second heel-prick tests, and maintain sensitivity at 95%. The findings highlight the potential for optimizing CF-NBS algorithms to improve PPV and reduce follow-up testing while maintaining high diagnostic sensitivity.²⁹

Clinical Utility and Validity 
Sosnay, et al. (2013) performed a comprehensive analysis of CF genotypes and phenotypes. The authors collected genotype and phenotype data from 39696 CF patients and found 159 variants with over 0.01% allele frequency, 127 of which met both the clinical and functional criteria for CF. The phenotypic criterion used to define the pathogenic threshold was sweat chloride conductance of 10%. These 127 pathogenic genetic variants were estimated to represent 95.4% of CF alleles, leaving only 0.21% of CF patients without an identified pathological CFTR variant. The phenotypes of these variants vary.³⁰

Wainwright, et al. (2015) evaluated the combination of IVA and LUM in CF patients homozygous for the F508D mutation (labeled Phe508del). A total of 1108 patients were examined. The mean baseline forced expiratory volume in one second “FEV1” was 61% of the predicted value. The absolute mean improvement in FEV1% was found to be 2.6-4%, which corresponded to a 4.3-6.7% relative treatment difference. The rate of pulmonary exacerbations was found to be 30-39% less in the treatment group compared to the placebo group. However, the rate of discontinuation due to an adverse event was 4.2% in the treatment group compared to the placebo group.³¹

Sharma, et al. (2018) performed a cost-effectiveness analysis of the FDA-approved IVA-LUM combination for the F508D mutation. The authors built a Markov-state model to assess the IVA-LUM for 12-year-old CF patients over several periods of time. “Markov states included mild CF (percentage of predicted forced expiratory volume in one second or FEV1 > 70%), moderate (FEV1 40–70%), severe (FEV1 < 40%) disease, post-transplant, and death. Pulmonary exacerbation and lung transplant were included as transition states.” The IVA-LUM combination resulted in higher quality adjusted life years (QALY, 7.29 vs 6.84 for usual care) but at a cost of $1,778,920.88 per QALY compared to $116,155.76 for usual care. Both monetary amounts were over a 10-year period. The IVA-LUM combination was cost-effective at a threshold of $150,000 / QALY, which was estimated to occur at an annual drug cost of $4153.³²