Genetic Testing For Cystic Fibrosis Research Articles

Hereditary lung diseases and modern possibilities of genetic testing

The European Respiratory Society website gives the following criterion for the disease to be classified as rare (orphan) - the disease occurs in 1 person per 2 000. One of the well-studied rare lung diseases is cystic fibrosis (CF), which is often considered a medical care model for patients with other orphan diseases. However, effective diagnostics and therapies have not yet been developed for many other rare diseases. Moreover, their true prevalence remains unknown because these diseases often go undiagnosed. One of the problems in diagnosing rare diseases is the lack of knowledge among physicians.The aim of this review is to provide a brief clinical and genetic description of rare hereditary lung diseases and to show modern genetic diagnostics to raise awareness among physicians. Data from 95 articles on hereditary lung diseases were used.Results. The results of the analysis of lung diseases associated with bronchiectasis, fibrosis, pneumothorax, and hereditary storage diseases are presented. Genetics and diagnostics, including the three-step molecular genetic testing for cystic fibrosis, are considered in detail. The diagnosis has been developed for both neonatal screening and clinical manifestations. The emergence of targeted therapy based on genetic diagnosis makes neonatal screening even more relevant and leads to an increase in life expectancy. A patient registry was established within 10 years. A detailed analysis of the diagnosis of primary ciliary dyskinesia (PCD) is given, taking into account the absence of a single “golden” standard for the diagnosis of PCD. The genetic basis of the most common hereditary diseases and modern possibilities of their diagnosis are discussed, including sequencing of genes responsible for the development of orphan diseases using standard Sanger sequencing methods and next-generation sequencing, and creating multigene panels.Conclusion. New molecular diagnostic methods will help to understand the nature of orphan lung diseases, study their epidemiology, and develop new diagnostic algorithms. The study of the genetic causes of rare diseases may serve as a basis for the development of targeted therapy.

Efficacia dello screening preconcezionale del portatore di fibrosi cistica: revisione sistematica.

genetic testing for cystic fibrosis (CF) has been offered to people with higher risk of being carrier. to assess the effectiveness of population-based CF carrier screening for adults of reproductive age and its optimal organizational features. systematic review. MedLine, Embase, Cochrane Library, CINAHL and LILACS (1990-2022) were searched to retrieve primary and secondary studies on adults (16 years and older), with no clinical indication or genetic risk, eligible for genetic testing for CF carrier status. attitude to screening, uptake of screening offered, informed reproductive choices. a total of 3,326 records were screened and 292 potentially eligible full-text publications assessed. The review included 71 publications, corresponding to 3 reviews, 40 cohort studies (11 comparative, 29 single-arm), and 6 model studies, published between 1992 and 2021 (median 1998). Only one study compared screening or no screening. This study suggested an association between carrier screening and a lower incidence of CF. Comparative studies examined different approaches for invitation and testing, i.e., settings, target population (individuals/couples, prenatal/preconceptional), how invitations are organized (primary care/maternal hospitals), and format and content of the pre-test information. However, no firm conclusions can be drawn on the impact of these features on informed reproductive choices, uptake, and attitude, because of the limitations of the evidence collected. the broad heterogeneity of the studies, methodological weaknesses, and the limited transferability of the results mean there is still uncertainty about the effectiveness of preconceptional and prenatal CF carrier screening in the general population.

Een zeldzame oorzaak van meconium ileus

A rare cause of meconium ileus A newborn was admitted to the neonatal intensive care unit due to a gastrointestinal obstruction and respiratory failure. Based on a diagnostic laparoscopy, the diagnosis of meconium ileus was made and 2 ileostomies were created. Genetic testing for cystic fibrosis was performed. Postoperatively, respiratory failure persisted with extubation failure on day 5. A few days later, a new attempt was successful. Because of repeated apnea and severe hypoventilation, BiPAP (bilevel positive airway pressure) was necessary. Genetic testing for cystic fibrosis turned out to be negative on day 13. The hypoventilation, the negative genetics for cystic fibrosis and a new gastrointestinal obstruction led to an alternative and more rare diagnosis: Haddad syndrome. This condition was first described by G. Haddad as the combination of congenital central hypoventilation syndrome (CCHS) and Hirschsprung’s disease. Both are the result of autonomic dysfunction and are due to a mutation in the PHOX2B gene, which plays a role in the embryological development of the autonomic nervous system from the neural crest. Different types of mutations have been described with implications for the clinic, comorbidities and prognosis.

Prenatal genetic testing for cystic fibrosis: a systematic review of clinical effectiveness and an ethics review

PurposeWe aimed to assess the clinical value of prenatal testing for cystic fibrosis (CF) and whether ethical considerations would affect endpoint selection. MethodsTo determine effectiveness, we conducted a systematic literature review whose protocol outlined search strategies across eight databases, study inclusion criteria, and prespecified literature screening, data extraction, and synthesis processes. We conducted a scoping search on ethical considerations. ResultsThe genetic test showed good diagnostic performance. A change in clinical management was observed: termination of pregnancy (TOP) occurred in most cases where two pathogenic variants were identified in a fetus of carrier parents (158/167; 94.6%). The TOP rate was lower in pregnancies where CF was diagnosed after fetal echogenic bowel detection (~65%). TOP and caring for a child with CF were both associated with poor short-term parental psychological outcomes. Ethical analyses indicated that informed decisions should have been the main endpoint, rather than CF-affected births prevented. ConclusionCF testing leads to fewer CF-affected births. It is difficult to assess whether this means the test is valuable, since patients may not value TOP primarily in terms of maternal or fetal health outcomes, psychological or otherwise. The value of testing should arguably be measured in terms of improving patient autonomy rather than health.

Universal strategy for preimplantation genetic testing for cystic fibrosis based on next-generation sequencing.

We developed and applied a universal strategy for preimplantation genetic testing for all cystic fibrosis gene mutations (PGT-CF) based on next-generation sequencing (NGS). A molecular protocol was designed to diagnose all CF mutations at preimplantation stage. The detection of CF mutations was performed by direct gene sequencing and linkage strategy testing 38 specific SNPs located upstream and inside the gene for PGT-CF. Seventeen couples at risk of CF transmission decided to undergo PGT-CF. Trophectoderm cell biopsies were performed on days 5-6 blastocysts. PGT for aneuploidy (PGT-A) was performed from the same samples. Tested embryos were transferred on further natural cycles. PGT was performed on 109 embryos. Fifteen CF mutations were tested. PGT-CF and PGT-A were conclusive for, respectively, 92.7% and 95.3% of the samples. A mean of 24.1 SNPs was informative per couple. After single embryo transfer on natural cycle, 81.3% of the transferred tested embryos implanted. The present protocol based on the entire CFTR gene sequencingtogether with informative SNPs outside and inside the gene can be applied to diagnose all CF mutations at preimplantation stage.

Universal strategy for preimplantation genetic testing for cystic fibrosis based on next generation sequencing

PurposeWe developed and applied a universal strategy for preimplantation genetic testing for all cystic fibrosis gene mutations (PGT-CF) based on next-generation sequencing (NGS).MethodsA molecular protocol was designed to diagnose all CF mutations at preimplantation stage. The detection of CF mutations was performed by direct gene sequencing and linkage strategy testing 38 specific SNPs located upstream and inside the gene for PGT-CF. Seventeen couples at risk of CF transmission decided to undergo PGT-CF. Trophectoderm cell biopsies were performed on day 5–6 blastocysts. PGT for aneuploidy (PGT-A) was performed from the same samples. Tested embryos were transferred on further natural cycles.ResultsPGT was performed on 109 embryos. Fifteen CF mutations were tested. PGT-CF and PGT-A were conclusive for respectively 92.7% and 95.3% of the samples. A mean of 24.1 SNPs was informative per couple. After a single embryo transfer on natural cycle, 81.3% of the transferred tested embryos were implanted.ConclusionsThe present protocol based on the entire CFTR gene together with informative SNPs outside and inside the gene can be applied to diagnose all CF mutations at preimplantation stage.

Microarray analysis in pregnancies with isolated echogenic bowel

IntroductionFetal echogenic bowel is a frequent sonographic finding, demonstrated in about 1% of pregnancies. The advised evaluation of fetal echogenic bowel includes maternal serology, genetic testing for cystic fibrosis, detailed sonographic anatomic survey, and invasive prenatal testing for fetal chromosomal aberrations. The objective of our study was to evaluate the risk for clinically significant chromosomal microarray analysis (CMA) findings in pregnancies with isolated echogenic bowel. MethodsData from all CMA analyses performed due to isolated echogenic bowel reported to the Israeli Ministry of Health between January 2013 and September 2016 were retrospectively obtained. Risk estimation was performed comparing the rate of abnormal microarray findings to the control population, based on a systematic review of 9272 pregnancies and a large local cohort of 5541 fetuses with normal ultrasound, undergoing CMA testing due to maternal request. ResultsOf 103 CMA analyses performed due to isolated echogenic bowel, two (1.94%) pathogenic findings were detected (47,XYY and 16p11.2 duplication). This risk was not significantly elevated compared to the control groups. In addition, three variants of unknown significance were demonstrated. ConclusionsTo our best knowledge, our study is the first report describing the rate of clinically significant copy number variants in pregnancies with isolated echogenic bowel. According to our results, it seems that pregnancies with isolated echogenic bowel do not have an increased risk for abnormal CMA compared to fetuses with no evidence of sonographic anomalies. Our findings suggest that the consideration to perform CMA analysis in such pregnancies should not differ from any pregnancy with normal ultrasound.

19 Genetic testing for cystic fibrosis in Bosnia and Herzegovina

19 Genetic testing for cystic fibrosis in Bosnia and Herzegovina

Validation of a semiconductor next-generation sequencing assay for the clinical genetic screening of CFTR.

Genetic testing for cystic fibrosis and CFTR-related disorders mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the CFTR gene. We have explored a more efficient genetic screening strategy based on next-generation sequencing (NGS) of the CFTR gene. We validated this approach in a cohort of 177 patients with previously known CFTR mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq™ CFTR panel. The DNA libraries were pooled, barcoded, and sequenced using an Ion Torrent PGM sequencer. The combination of different robust bioinformatics tools allowed us to detect previously known pathogenic mutations and polymorphisms in the 177 samples, without detecting spurious pathogenic calls. In summary, the assay achieves a sensitivity of 94.45% (95% CI: 92% to 96.9%), with a specificity of detecting nonvariant sites from the CFTR reference sequence of 100% (95% CI: 100% to 100%), a positive predictive value of 100% (95% CI: 100% to 100%), and a negative predictive value of 99.99% (95% CI: 99.99% to 100%). In addition, we describe the observed allelic frequencies of 94 unique definitely and likely pathogenic, uncertain, and neutral CFTR variants, some of them not previously annotated in the public databases. Strikingly, a seven exon spanning deletion as well as several more technically challenging variants such as pathogenic poly-thymidine-guanine and poly-thymidine (poly-TG-T) tracts were also detected. Targeted NGS is ready to substitute classical molecular methods to perform genetic testing on the CFTR gene.

Molecular genetic testing for cystic fibrosis: laboratory performance on the College of American Pathologists external proficiency surveys.

Molecular testing for cystic fibrosis mutations is widespread and routine in reproductive decision making and diagnosis. Our objective was to assess the level of performance of laboratories for this test. The College of American Pathologists administers external proficiency testing with multiple DNA samples distributed biannually. RESULTS are analyzed, reviewed, and graded by the joint College of American Pathologists/American College of Medical Genetics and Genomics Biochemical and Molecular Genetics Committee. Assessment is based on genotype and associated clinical interpretation. Overall, 357 clinical laboratories participated in the proficiency testing survey between 2003 and 2013 (322 in the United States and 35 international). In 2013, US participants reported performing nearly 120,000 tests monthly. Analytical sensitivity and specificity of US laboratories were 98.8% (95% confidence interval: 98.4-99.1%) and 99.6% (95% confidence interval: 99.4-99.7%), respectively. Analytical sensitivity improved between 2003 and 2008 (from 97.9 to 99.3%; P = 0.007) and remained steady thereafter. Clinical interpretation matched the intended response for 98.8, 86.0, and 91.0% of challenges with no, one, or two mutations, respectively. International laboratories performed similarly. Laboratory testing for cystic fibrosis in the United States has improved since 2003, and these data demonstrate a high level of quality. Neither the number of samples tested nor test methodology affected performance.

Genetic testing of sperm donors for cystic fibrosis and spinal muscular atrophy: evaluation of clinical utility

ObjectiveTo evaluate the clinical utility of genetic testing for cystic fibrosis (CF) and spinal muscular atrophy (SMA) in sperm donors. Study designWe studied the results of the genetic tests for CF and SMA applied to 372 sperm donor candidates. The CF carrier screening test analysed 32 mutations on the CFTR gene. Regarding SMA, the carrier test studied possible deletions of SMN1/2 by Multiplex Ligation-dependent Probe Amplification (MLPA) methodology. ResultsThe carrier frequency obtained was greater for SMA than for CF. After adjusting the results obtained for the sensitivity of the tests, and taking into account the prevalence of female carriers in our population, the probability of transmission of the disease to the child from a donor with a negative genetic test was about five times lower in the case of SMA than in CF, although this difference was not statistically significant. The number of donors needed to screen (NNS) to avoid the occurrence of a child being affected by CF and SMA in our population was similar in both cases (1591 vs. 1536). ConclusionsThis study demonstrates the need to include SMA among the diseases for which genetic screening is performed in the process of sperm donor selection. We believe that testing donors for SMA is as important and as useful as doing so for CF.

Patient and Family Issues Regarding Genetic Testing for Cystic Fibrosis

Cystic fibrosis (CF) is a potentially life-shortening autosomal recessive genetic condition resulting in chronic progressive respiratory involvement, malnutrition, electrolyte imbalance, and male infertility It is the most common autosomal inherited condition in the white population, and its presence is recorded with varying prevalence across ethnicities. Since the 1989 discovery of the genetic variant F508del, the most common cystic fibrosis transmembrane conductance regulator (CFTR) mutation, more than 1900 CF mutations have been identified. The 1997 National Institutes of Health (NIH) Consensus Statement on Cystic Fibrosis, along with 2001 and 2005 recommendations from the American College of Obstetricians and Gynecologists (ACOG), provide the basis for population CF carrier screening in the prenatal setting. Recommendations for newborn screening (NBS) for cystic fibrosis were released in 2004, with NBS programs in the United States initiated thereafter. With the wide variety of CFTR mutations and mutation combinations, there is not a clear understanding of the genotype-phenotype correlations or of the anticipated clinical trajectory for an individual who has identified CFTR mutations. This ambiguity creates challenges for patients and families in decision making related to CFTR carrier screening during the prenatal period, understanding the results of newborn screening for CF, or coping with the new genetic knowledge obtained. This literature review examines research regarding genetic testing for CF as it related to population screening. Patient and family issues from both the prenatal period and newborn testing are reviewed. Opportunities for future nursing research and implication for nursing practice are discussed.

Impact of gene patents and licensing practices on access to genetic testing for cystic fibrosis

Cystic fibrosis is one of the most commonly tested autosomal recessive disorders in the United States. Clinical cystic fibrosis is associated with mutations in the CFTR gene, of which the most common mutation among Caucasians, ΔF508, was identified in 1989. The University of Michigan, Johns Hopkins University, and the Hospital for Sick Children, where much of the initial research occurred, hold key patents on cystic fibrosis genetic sequences, mutations, and methods for detecting them. Several patents, including the one that covers detection of the ΔF508 mutation, are jointly held by the University of Michigan and the Hospital for Sick Children in Toronto, with Michigan administering patent licensing in the United States. The University of Michigan broadly licenses the ΔF508 patent for genetic testing with >60 providers of genetic testing to date. Genetic testing is now used in newborn screening, diagnosis, and for carrier screening. Interviews with key researchers and intellectual property managers, a survey of laboratories' prices for cystic fibrosis genetic testing, a review of literature on cystic fibrosis tests' cost-effectiveness, and a review of the developing market for cystic fibrosis testing provide no evidence that patents have significantly hindered access to genetic tests for cystic fibrosis or prevented financially cost-effective screening. Current licensing practices for cystic fibrosis genetic testing seem to facilitate both academic research and commercial testing. More than 1000 different CFTR mutations have been identified, and research continues to determine their clinical significance. Patents have been nonexclusively licensed for diagnostic use and have been variably licensed for gene transfer and other therapeutic applications. The Cystic Fibrosis Foundation has been engaged in licensing decisions, making cystic fibrosis a model of collaborative and cooperative patenting and licensing practice.

Development of Genomic Reference Materials for Cystic Fibrosis Genetic Testing

The number of different laboratories that perform genetic testing for cystic fibrosis is increasing. However, there are a limited number of quality control and other reference materials available, none of which cover all of the alleles included in commercially available reagents or platforms. The alleles in many publicly available cell lines that could serve as reference materials have neither been confirmed nor characterized. The Centers for Disease Control and Prevention-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the genetic testing community as well as Coriell Cell Repositories, have characterized an extended panel of publicly available genomic DNA samples that could serve as reference materials for cystic fibrosis testing. Six cell lines [containing the following mutations: E60X (c.178G>T), 444delA (c.312delA), G178R (c.532G>C), 1812-1G>A (c.1680-1G>A), P574H (c.1721C>A), Y1092X (c.3277C>A), and M1101K (c.3302T>A)] were selected from those existing at Coriell, and seven [containing the following mutations: R75X (c.223C>T), R347H (c.1040G>A), 3876delA (c.3744delA), S549R (c.1646A>C), S549N (c.1647G>A), 3905insT (c.3773_3774insT), and I507V (c.1519A>G)] were created. The alleles in these materials were confirmed by testing in six different volunteer laboratories. These genomic DNA reference materials will be useful for quality assurance, proficiency testing, test development, and research and should help to assure the accuracy of cystic fibrosis genetic testing in the future. The reference materials described in this study are all currently available from Coriell Cell Repositories.

Cystic fibrosis and intrauterine death

Fetal death is not commonly associated with cystic fibrosis (CF). We report a case of late intrauterine death attributed to cardiovascular failure and shock consequent to malrotation and intestinal volvulus in a fetus affected with CF. An argument is made that CF promoted this deleterious incident. Whole blood or cell-rich tissue specimens should be preserved and genetic testing for CF considered in stillbirths with intestinal complications.

Pediatric cystic fibrosis: Evaluating costs and genetic testing

The purpose of this article is to present a systematic, critical review of literature and data sources pertaining to pediatric cystic fibrosis, emphasizing and evaluating factors of costs and genetic testing. Cystic fibrosis is the most common fatal genetic disease in the United States. Therefore, its cause, prevalence, cost, and prevention make it important for review. Furthermore, the recent National Institutes of Health Consensus Statement on Genetic Testing for Cystic Fibrosis, the laboratory standards and guidelines published by the American College of Medical Genetics, the American College of Obstetricians and Gynecologists, and the National Human Genome Research Institute, and the increasing interest in genetic testing make it timely to discuss this major pediatric health topic. A broad educational effort, particularly among health care professionals, and genetic screening are advocated.

Genetic testing and quality control in diagnostic laboratories.

To evaluate the quality of genetic testing for cystic fibrosis, 136, 145 and 159 laboratories participated in a European study in 1996, 1997 and 1998, respectively. We sent six purified DNA samples carrying the more common CFTR mutations with the request to test them using routine protocols. A panel of experts reviewed the results together with the raw data.

Genetic Testing for Cystic Fibrosis

To provide health care providers, patients, and the general public with a responsible assessment of the optimal practices for genetic testing for cystic fibrosis (CF).A non-Federal, nonadvocate, 14-member panel representing the fields of genetics, obstetrics, internal medicine, nursing, social work, epidemiology, pediatrics, psychiatry, genetic counseling, bioethics, health economics, health services research, law, and the public. In addition, 21 experts from these same fields presented data to the panel and a conference audience of 500.The literature was searched through Medline, and an extensive bibliography of references was provided to the panel and the conference audience. Experts prepared abstracts with relevant citations from the literature. Scientific evidence was given precedence over clinical anecdotal experience.The panel, answering predefined questions, developed its conclusions based on the scientific evidence presented in open forum and the scientific literature. The panel composed a draft statement that was read in its entirety and circulated to the experts and the audience for comment. Thereafter, the panel resolved conflicting recommendations and released a revised statement at the end of the conference. The panel finalized the revisions within a few weeks after the conference.

Update and Review: Cystic Fibrosis.

Cystic fibrosis (CF) is one of the most commonly inherited recessive disorders in U.S. Caucasians, with a carrier frequency of approximately 1 in 29. Genetic counseling and CF mutation analysis has traditionally been offered to the affected patient and his/her extended family, in keeping with policy statements from professional organizations (ASHG, NSGC, ACOG). The target population for CF testing and counseling may be evolving after the release of the 1997 National Institutes of Health Consensus Statement, Genetic Testing for Cystic Fibrosis, which recommends that CF screening be offered to all preconceptional and pregnant couples. Genetic counseling for CF is complicated by reports of polymorphisms in the CF gene that are associated with symptoms that do not meet the diagnostic criteria for CF, such as bilateral congenital absence of the vas deferens, bronchiectasis, and idiopathic pancreatitis. To aid genetic counselors with these issues, this review explores the symptoms of CF, patient management, gene function, genetics, genotype/phenotype correlation, and genetic counseling issues.

12. Quality control in genetic testing for cystic fibrosis: There is room for further improvement

12. Quality control in genetic testing for cystic fibrosis: There is room for further improvement