Mutation analysis for heterozygote detection and the prenatal diagnosis of cystic fibrosis

Stoichiometric approach to quantitative analysis of biomolecules: the case of nucleic acids

Majority of protocols for quantitative analysis of biomarkers (including nucleic acids) require calibrations and target standards. In this work, we developed a principle for quantitative analysis that eliminates the need for a standard of a target molecule. The approach is based on stoichiometric reporting. While stoichiometry is a simple and robust analytical platform, its utility toward the analysis of biomolecules is very limited due to the lack of general methodologies for detecting the equivalence point. In this work, we engineer a new target/probe-binding model that enables detecting the equivalence point while maintaining an appropriate level of specificity. We establish the probe design principles through theoretical simulations and experimental confirmation. Further, we demonstrate the utility of the stoichiometric analysis via a proof-of-concept system based on oligonucleotide hybridization. Overall, the approach that requires neither standard nor calibration yields quantitative results with an adequate accuracy (> 90-110%) and a high specificity. The principles established in our work are very general and can extend beyond oligonucleotide targets toward quantitative analysis of many other biomolecules such as antibodies and proteins.

Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry

Objective

Chromovert® Technology is presented as a new cell engineering technology to detect and purify living cells based on gene expression.

Methods

The technology utilizes fluorogenic oligonucleotide signaling probes and flow cytometry to detect and isolate individual living cells expressing one or more transfected or endogenously-expressed genes.

Results

Results for production of cell lines expressing a diversity of ion channel and membrane proteins are presented, including heteromultimeric epithelial sodium channel (αβγ-ENaC), sodium voltage-gated ion channel 1.7 (NaV1.7-αβ1β2), four unique γ-aminobutyric acid A (GABA_A) receptor ion channel subunit combinations α1β3γ2s, α2β3γ2s, α3β3γ2s and α5β3γ2s, cystic fibrosis conductance regulator (CFTR), CFTR-Δ508 and two G-protein coupled receptors (GPCRs) without reliance on leader sequences and/or chaperones. In addition, three novel plasmid-encoded sequences used to introduce 3′ untranslated RNA sequence tags in mRNA expression products and differentially-detectable fluorogenic probes directed to each are described. The tags and corresponding fluorogenic signaling probes streamline the process by enabling the multiplexed detection and isolation of cells expressing one or more genes without the need for gene-specific probes.

Conclusions

Chromovert technology is provided as a research tool for use to enrich and isolate cells engineered to express one or more desired genes.

Electronic health record phenotypes associated with genetically regulated expression of CFTR and application to cystic fibrosis

PURPOSE

The increasing use of electronic health records (EHRs) and biobanks offers unique opportunities to study Mendelian diseases. We described a novel approach to summarize clinical manifestations from patient EHRs into phenotypic evidence for cystic fibrosis (CF) with potential to alert unrecognized patients of the disease.

METHODS

We estimated genetically predicted expression (GReX) of cystic fibrosis transmembrane conductance regulator (CFTR) and tested for association with clinical diagnoses in the Vanderbilt University biobank (N = 9142 persons of European descent with 71 cases of CF). The top associated EHR phenotypes were assessed in combination as a phenotype risk score (PheRS) for discriminating CF case status in an additional 2.8 million patients from Vanderbilt University Medical Center (VUMC) and 125,305 adult patients including 25,314 CF cases from MarketScan, an independent external cohort.

RESULTS

GReX of CFTR was associated with EHR phenotypes consistent with CF. PheRS constructed using the EHR phenotypes and weights discovered by the genetic associations improved discriminative power for CF over the initially proposed PheRS in both VUMC and MarketScan.

CONCLUSION

Our study demonstrates the power of EHRs for clinical description of CF and the benefits of using a genetics-informed weighing scheme in construction of a phenotype risk score. This research may find broad applications for phenomic studies of Mendelian disease genes.

Fenretinide favorably affects mucins (MUC5AC/MUC5B) and fatty acid imbalance in a manner mimicking CFTR-induced correction

Cystic fibrosis (CF) is the most common genetic disease in Caucasians. CF is manifested by abnormal accumulation of mucus in the lungs, which serves as fertile ground for the growth of microorganisms leading to recurrent infections and ultimately, lung failure. Mucus in CF patients consists of DNA from dead neutrophils as well as mucins produced by goblet cells. MUC5AC mucin leads to pathological plugging of the airways whereas MUC5B has a protective role against bacterial infection. Therefore, decreasing the level of MUC5AC while maintaining MUC5B intact would in principle be a desirable mucoregulatory treatment outcome. Fenretinide prevented the lipopolysaccharide-induced increase of MUC5AC gene expression, without affecting the level of MUC5B, in a lung goblet cell line. Additionally, fenretinide treatment reversed the pro-inflammatory imbalance of fatty acids by increasing docosahexaenoic acid and decreasing the levels of arachidonic acid in a lung epithelial cell line and primary leukocytes derived from CF patients. Furthermore, for the first time we also demonstrate the effect of fenretinide on multiple unsaturated fatty acids, as well as differential effects on the levels of long- compared to very-long-chain saturated fatty acids which are important substrates of complex phospholipids. Finally, we demonstrate that pre-treating mice with fenretinide in a chronic model of P. aeruginosa lung infection efficiently decreases the accumulation of mucus. These findings suggest that fenretinide may offer a new approach to therapeutic modulation of pathological mucus production in CF.

Biochemistry of very-long-chain and long-chain ceramides in cystic fibrosis and other diseases: The importance of side chain

Ceramides, the principal building blocks of all sphingolipids, have attracted the attention of many scientists around the world interested in developing treatments for cystic fibrosis, the most common genetic disease of Caucasians. Many years of fruitful research in this field have produced some fundamentally important, yet controversial results. Here, we aimed to summarize the current knowledge on the role of long- and very-long- chain ceramides, the most abundant species of ceramides in animal cells, in cystic fibrosis and other diseases. We also aim to explain the importance of the length of their side chain in the context of stability of transmembrane proteins through a concise synthesis of their biophysical chemistry, cell biology, and physiology. This review also addresses several remaining riddles in this field. Finally, we discuss the technical challenges associated with the analysis and quantification of ceramides. We provide the evaluation of the antibodies used for ceramide quantification and we demonstrate their lack of specificity. Results and discussion presented here will be of interest to anyone studying these enigmatic lipids.

Biochemistry of very-long-chain and long-chain ceramides in cystic fibrosis and other diseases: The importance of side chain

Ceramides, the principal building blocks of all sphingolipids, have attracted the attention of many scientists around the world interested in developing treatments for cystic fibrosis, the most common genetic disease of Caucasians. Many years of fruitful research in this field have produced some fundamentally important, yet controversial results. Here, we aimed to summarize the current knowledge on the role of long- and very-long- chain ceramides, the most abundant species of ceramides in animal cells, in cystic fibrosis and other diseases. We also aim to explain the importance of the length of their side chain in the context of stability of transmembrane proteins through a concise synthesis of their biophysical chemistry, cell biology, and physiology. This review also addresses several remaining riddles in this field. Finally, we discuss the technical challenges associated with the analysis and quantification of ceramides. We provide the evaluation of the antibodies used for ceramide quantification and we demonstrate their lack of specificity. Results and discussion presented here will be of interest to anyone studying these enigmatic lipids.

Mortality Due to Cystic Fibrosis over a 36-Year Period in Spain: Time Trends and Geographic Variations

The aim of this study is to analyze population-based mortality attributed to cystic fibrosis (CF) over 36 years in Spain. CF deaths were obtained from the National Statistics Institute, using codes 277.0 from the International Classification of Diseases (ICD) ninth revision (ICD9-CM) and E84 from the tenth revision (ICD10) to determine the underlying cause of death. We calculated age-specific and age-adjusted mortality rates, and time trends were assessed using joinpoint regression. The geographic analysis by district was performed by standardized mortality ratios (SMRs) and smoothed-SMRs. A total of 1002 deaths due to CF were identified (50.5% women). Age-adjusted mortality rates fell by −0.95% per year between 1981 and 2016. The average age of death from CF increased due to the annual fall in the mortality of under-25s (−3.77% males, −2.37% females) and an increase in over-75s (3.49%). We identified districts with higher than expected death risks in the south (Andalusia), the Mediterranean coast (Murcia, Valencia, Catalonia), the West (Extremadura), and the Canary Islands. In conclusion, in this study we monitored the population-based mortality attributed to CF over a long period and found geographic differences in the risk of dying from this disease. These findings complement the information provided in other studies and registries and will be useful for health planning.

Perspectives in Pediatric Pathology, Chapter 22. Testicular Involvement in Systemic Diseases

Normal testicular physiology requires appropriate function of endocrine glands and other tissues. Testicular lesions have been described in disorders involving the hypothalamus-hypophysis, thyroid glands, adrenal glands, pancreas, liver, kidney, and gastrointestinal tract. Testicular abnormalities can also associate with chronic anemia, obesity, and neoplasia. Although many of the disorders that affect the above-mentioned glands and tissues are congenital, acquired lesions may result in hypogonadism in children and adolescents.

The Italian External Quality Control Programme for cystic fibrosis molecular diagnosis: 4 years of activity

BACKGROUND

The Italian External Quality Control Programme for cystic fibrosis molecular diagnosis started in 2001; public laboratories distributed throughout Italy participated on a voluntary basis.

METHODS

The Italian Public Health Institute (Istituto Superiore di Sanità) sent six validated DNA samples to participating laboratories: technical and clinical information was provided for each sample. Laboratories were required to analyse all six samples. For each sample the laboratories had to provide the results (including raw data) and a report of molecular analysis within 2 months using current methods and nomenclature. Raw data and reports were evaluated by a Steering Committee and their comments were sent to each laboratory.

RESULTS

Genotyping results indicated a general good level of quality for all laboratories, i.e., approximately 1% of alleles were incorrectly assigned each year due to analytical (45%) and misinterpretation (45%) errors. During the first 2 years, more than 70% of laboratories did not test for some regional Italian mutations. Commercial kits for reverse dot-blot and oligonucleotide ligation assay PCR were used to detect mutations by 52.8% and 29.5%, respectively, of the participating laboratories. Reporting of results was still inadequate; in 2004 a model for the written report was introduced, but not all laboratories used it.

CONCLUSIONS

Our data show that few genotyping errors were made by laboratories and were principally due to misinterpretation and analytical reasons. However, reports are still inadequate and it will be interesting to evaluate the introduction of the reporting model in future years.

Light and alcohol evoked electro-oculograms in cystic fibrosis

Cystic fibrosis (CF) is caused by a defect in the cystic fibrosis transmembrane conductance regulator (CFTR) which is a chloride channel. CFTR is expressed in the retinal pigment epithelium (RPE) where it is believed to be important in generating the fast oscillations (FOs) and potentially contributing to the light-electro-oculogram (EOG). The role of CFTR in the alcohol-EOG is unknown. We recruited six individuals with CF (three homozygotes for Delta508 and three heterozygous for Delta508) and recorded the light- and alcohol-EOGs as well as the FOs and compared them to a control group. The results showed that in the CF group the amplitude of the alcohol- and light-EOGs were normal. However, the time to peak of the light- and alcohol-rises were significantly faster than in the control group. We conclude that CFTR is not primarily responsible for the alcohol- or light-rises but is involved in altering the timing of these responses. The FOs showed differences between the homozygotes, heterozygotes and the controls. The amplitudes were significantly higher and the time to the dark troughs were significantly slower in the heterozygote group compared to both controls and the homozygotes. In contrast, the homozygotes did not differ in either amplitude or the timing of the FOs compared to the controls.

Surgical management of pulmonary and gastrointestinal complications in children with cystic fibrosis

PURPOSE OF REVIEW

Cystic fibrosis is a common disorder, affecting as many as 1:2500 Caucasian live births. Despite improved medical management, disease-specific complications are common and are responsible for substantial morbidity and ultimately mortality. Both pulmonary and gastrointestinal complications of cystic fibrosis are well known; however, the complications requiring surgical intervention in the pediatric population are infrequent. We provide a detailed review of the cystic fibrosis-associated pulmonary and gastrointestinal complications and potential surgical options for management in children with cystic fibrosis.

RECENT FINDINGS

Recent operative approaches are described that include application of minimally invasive surgical techniques primarily for intrathoracic disease. Novel medical therapies are also presented. Finally an attempt is made to put in perspective those surgical care advances that have had a benefit on disease outcomes.

SUMMARY

This report will provide the physician caring for the child with cystic fibrosis an understanding of those disease complications that will require surgical consultation and potential operative intervention.

The electro-oculogram

The retinal pigment epithelium (RPE) lying distal to the retina regulates the extracellular environment and provides metabolic support to the outer retina. RPE abnormalities are closely associated with retinal death and it has been claimed several of the most important diseases causing blindness are degenerations of the RPE. Therefore, the study of the RPE is important in Ophthalmology. Although visualisation of the RPE is part of clinical investigations, there are a limited number of methods which have been used to investigate RPE function. One of the most important is a study of the current generated by the RPE. In this it is similar to other secretory epithelia. The RPE current is large and varies as retinal activity alters. It is also affected by drugs and disease. The RPE currents can be studied in cell culture, in animal experimentation but also in clinical situations. The object of this review is to summarise this work, to relate it to the molecular membrane mechanisms of the RPE and to possible mechanisms of disease states.

Cystic fibrosis in Korean children:a case report identified by a quantitative pilocarpine iontophoresis sweat test and genetic analysis

Cystic fibrosis (CF) is inherited as an autosomal recessive trait, and the mutations in cystic fibrosis transmembrane conductance regulator (CFTR) gene contributes to the CF syndrome. Although CF is common in Caucasians, it is known to be rare in Asians. Recently, we experienced two cases of CF in Korean children. The patients were girls with chronic productive cough since early infancy. Chest computed tomography showed the diffuse bronchiectasis in both lungs, and their diagnosis was confirmed by the repeated analysis of a quantitative pilocarpine iontophoresis test (QPIT). The sweat chloride concentrations of the first patient were 108.1 mM/L and 96.7 mM/L. The genetic analysis revealed that she was the compound heterozygote of Q1291X and IVS8 T5-M470V. In the second case, the sweat chloride concentrations were 95.0 mM/L and 77.5 mM/L. Although we performed a comprehensive search for the coding regions and exon-intron splicing junctions of CFTR gene, no obvious disease-related mutations were detected in the second case. To our knowledge, this is the first report of CF in Korean children identified by a QPIT and genetic analysis. The possibility of CF should be suspected in those patients with chronic respiratory symptoms even in Korea.

Current challenges in cystic fibrosis screening

CONTENT

This article gives an overview of the symptoms and mutations associated with classic and atypical cystic fibrosis (CF). Current testing methods for mutation detection in CF are discussed.

OBJECTIVES

Review testing for CF, including American College of Medical Genetics and American College of Obstetrics and Gynecology guidelines and recommendations regarding population screening for CF. Describe symptomatic and mutational differences between patients with classic CF and atypical CF, including monosymptomatic conditions such as congenital bilateral absence of the vas deferens, idiopathic pancreatitis, and chronic sinusitis. Explain the concern about predicting the phenotypic expression of the condition from the genotype. Discuss the challenges of CF testing, including the preanalytic, analytic, and postanalytic phases. List the current methods for detecting CF transmembrane conductance regulator gene mutations, specifying the advantages and disadvantages of each. Describe the basic patient information necessary for laboratories to provide accurate risk assessments, such as ethnicity and family history, and reasons for the test being conducted (carrier or affected status).

RESULTS

The technical challenges of detecting the 25 recommended mutations are being met by commercially available reagents. Challenges remain for the preanalytic and postanalytic phases. Only with accurate patient information can laboratories provide specific risk reductions on the basis of a negative genetic test result.

CONCLUSION

As health care providers become better informed about the recommendations for CF testing and laboratories continue to increase the sensitivities of their assays, patients will benefit from increased screening efficiency and accuracy. This will allow affected individuals to receive prompt and effective treatment and carriers to enjoy an expanded number of reproductive options.

Genetic diseases in adults

Genetic diseases that do not primarily affect the genitourinary tract may have urologic manifestations. These urologic manifestations range from benign and malignant renal disease to infertility. Thus, the practicing urologist may be involved in the care of these patients and should have knowledge of these diseases. Continued improvements in the diagnosis and treatment of these genetic diseases will likely result in improved survival and will increase the number of patients who may develop urologic manifestations of these diseases.

Clinical and genetic features of patients with congenital unilateral absence of the vas deferens

OBJECTIVES

To review the clinical and genetic findings in men with congenital unilateral absence of the vas deferens (CUAVD). CUAVD is important because of its association with renal anomalies and cystic fibrosis transmembrane conductance regulator gene mutations.

METHODS

A retrospective review of two urologic practices, both with subspecialty interest in male infertility, was performed. Renal imaging and cystic fibrosis (CF) testing were recommended to all men found to have CUAVD.

RESULTS

Fifteen men with CUAVD were identified. Only the 12 men with sufficient clinical data were selected for this study. Three patients had CF mutations, and all had obstruction of the contralateral vas deferens in either the pelvis or retroperitoneum. One patient had obstruction of the contralateral pelvic vas deferens and was negative for all CF mutations tested. Four patients (33%) had renal agenesis. Three patients had ipsilateral renal agenesis, and one had contralateral renal agenesis. No patient with CF mutations had renal agenesis. One had polycystic kidney disease, which was considered an incidental finding.

CONCLUSIONS

Patients with CUAVD may have CF mutations and renal agenesis. Renal ultrasonography and CF testing are therefore recommended for these patients. Patients of reproductive age found to have CUAVD should be counseled about the potential risk of transmission of renal anomalies and CF mutations.

Primer on medical genomics part I: History of genetics and sequencing of the human genome

In comparison with most other disciplines of science, the field of genetics is still in its youth. The majority of scientific work in genetics has been done in the past 150 years. The successful preliminary sequencing of the human genome was announced in 2001. Nonetheless, interest in heredity and in other concepts within the field of genetics has existed since the beginning of humanity. This article provides an account of the history of genetics, spanning from humankind's initial attempts to understand and influence heredity, to the early scientific work in the field of genetics, and subsequently to the advancements in modern genetics. Additionally, the Human Genome Project is summarized, from inception to publication of the 'first draft" of the human genome sequence.

Cystic fibrosis transmembrane conductance regulator gene mutations: do they play a role in the aetiology of allergic bronchopulmonary aspergillosis?

BACKGROUND

Previous work suggests that cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations may be implicated in the aetiology of allergic bronchopulmonary aspergilosis (ABPA).

OBJECTIVE

To compare the frequency of CF gene mutations in asthmatics with ABPA of varying severity with asthmatics who were skin prick test (SPT)-positive to Aspergillus fumigatus (Af) without evidence of ABPA and asthmatics SPT-negative to Af.

METHODS

Thirty-one Caucasian patients with ABPA were identified, together with asthmatics SPT positive to Af without evidence of ABPA (n = 23) and SPT negative to Af (n = 28). Genomic DNA was tested for 16 CF mutations accounting for approximately 85% of CF alleles in Caucasian New Zealanders.

RESULTS

Four (12.9%) ABPA patients were found to be carriers of a CF mutation (DeltaF508 n = 3, R117H n = 1), one (4.3%) asthmatic SPT positive to Af without ABPA (DeltaF508), and one (3.6%) asthmatic SPT negative to Af (R117H). All patients with a CF mutation had normal sweat chloride (< 40 mM). There was no significant difference between the frequency of CF mutations in the ABPA patients and asthmatics without ABPA. However, the frequency of CF mutations in the ABPA patients was significantly different (P = 0.0125) to the expected carrier rate in the general population.

CONCLUSION

These results lend further support to a possible link between CF mutations and ABPA.

Cystic fibrosis mutation testing in Italy

In Italy, Cystic fibrosis (CF) mutation frequency differences have been observed in different regions. In the northeastern Veneto and Trentino Alto Adige regions, a complete cystic fibrosis transmembrane conductance regulator (CFTR) gene screening in CF patients detected through a newborn screening program has identified about 90% of the mutations. In these two regions, the current detection rate using a CF screening panel containing the 16 most common mutations is 86.6%. CF mutations in some other Italian regions have not been so thoroughly analysed. Available data indicate that a more general national screening panel comprising 31 mutations may detect about 75% of all CF mutations in Italy.

A simple method for screening bacterial colonies for mutagenized sites in plasmid DNA

Because of the multiple-step process that is involved in the detection of mutagenized restriction enzyme sites in plasmid DNA, a simple and accurate method was developed to analyse the plasmid DNA of site-directed mutagenesis experiments from bacterial colonies. The desired mutated part is located between the Eco RI restriction site on pUC19. Two mutagenic primers were designed to replace only one nucleotide on segments A and B of the bi-segmented genome of infectious bursal disease virus (IBDV). Two restriction sites were created for those mutations in each segment, Fsp I and Dra I, respectively. Following a protocol from the site-directed mutagenesis kit, the mutated plasmids were used to transform, and were propagated and maintained in DH5 alpha competent cells. Colonies were picked from the master plate, and used as DNA template for PCR. The PCR technique included the design of two pairs of primers, one for each segment, which were to amplify a region up to 1000 bp. Samples were pre-incubated for 3 min at 94 degrees C to induce bacterial lysis before starting the nucleic acid amplification. The PCR products 918 bp from segment A and 650 bp from segment B were digested with Fsp I and Dra I at 37 degrees C for 1 h. Products were resolved on 0.9% agarose gel which contained ethidium bromide. This method is simpler, faster and more accurate than the traditional method of mini-prep plasmid isolation and colony blot hybridization to identify the mutated plasmids.

Effect of meconium ileus on the clinical prognosis of patients with cystic fibrosis

The objective of the present study was to determine the possible prognostic factors which may explain the difference in the survival of patients with cystic fibrosis (CF) with and without meconium ileus. Over a period of 20 years, 127 patients with CF, whose diagnosis was confirmed by typical clinical characteristics and altered sweat chloride levels, were studied retrospectively. The patients were divided into two groups: group 1 consisted of patients who presented CF and meconium ileus (N = 9), and group 2 consisted of patients with CF without meconium ileus (N = 118). The characteristics studied were based on data obtained upon admission of the patients using a specific protocol. Demographic, clinical, nutritional and laboratory data were obtained. The genotype was determined in 106 patients by PCR. Survival was analyzed using the Kaplan-Meier method. The median follow-up period was 44 months. A statistically significant difference was observed between the groups studied regarding the following variables: age at diagnosis and weight and height z scores. The presence of meconium ileus was associated with an earlier diagnosis; these patients had greater deficits in height and weight at the time of diagnosis and at the end of the study. The estimated probability of survival for patients with CF without meconium ileus was 62 +/- 14% and for those with meconium ileus 32 +/- 18%. Patients with CF and meconium ileus presented a poor nutritional status at diagnosis and a lower survival rate compared to the general CF population.

Prevalence of cystic fibrosis mutations in Israeli Jews

The aim of this study was to evaluate the screening policies of cystic fibrosis (CF) in the Jewish population. The prevalence of mutations that account for CF in Israel have been defined in the past by determining the frequency of CF mutations in affected individuals. This study is a population-based study and is, therefore, different from previous patient-based studies. We found that the CF mutations D1152H, W1089X, and 405 + IG-->A were present in some ethnic groups in which no CF patients carrying these mutations were reported. These facts necessitate a reevaluation of the screening policy regarding the ethnic groups in Israel. We studied 9,430 healthy Jewish Israeli individuals of 36 countries of origin. The prevalence of CF mutations was 1:19, 1:19, 1:28, and 1:42 for the Ashkenazi, Sephardi, North African, and Eastern Jews, respectively. CF mutations were identified in 374 (4.0%) individuals. These included 173 (46.3%) carriers of the W1282X mutation; 110 (29.4%) found to carry delF508; 23 (6.1%) who carried G542X; 22 (5.9%) who carried 3849 + 10Kb (C-->T; 20 (5.3%) who carried D1152H; 10 (2.7%) who carried N1303K; 11 (2.9%) who carried 405 + IG-->A; 4 (1.1%) who carried W1089X; and one (0.3%) who carried S549R. No carriers were detected for the 1717-1G-->A, G85E, and T360K mutations, which were tested for in 7,383, 1,558, and 41 individuals, respectively.

Molecular analysis in Brazilian cystic fibrosis patients reveals five novel mutations

We have performed molecular genetic analyses on 160 Brazilian patients diagnosed with cystic fibrosis (CF). Screening of mutations in 320 CF chromosomes was performed through single strand conformation polymorphism (SSCP) and heteroduplex analyses assay followed by DNA sequencing of the 27 exons and exon/intron boundaries of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The frequency of CFTR variants of T-tract length of intron 8 (IVS8 Tn) was also investigated. This analysis enabled the detection of 232/320 CF mutations (72.2%) and complete genotyping of 61% of the patients. The deltaF508 mutation was found in 48.4% of the alleles. Another fifteen mutations (previously reported) were detected: G542X, R1162X, N1303K, R334W, W1282X, G58E, L206W, R553X, 621+1G-->T, V232D, 1717-1G-->A, 2347 delG, R851L, 2789+5G-->A, and W1089X. Five novel mutations were identified, V201M (exon 6a), Y275X (exon 6b), 2686 insT (exon 14a), 3171 delC (exon 17a), and 3617 delGA (exon 19). These results contribute to the molecular characterization of CF in the Brazilian population. In addition, the identification of the novel mutation Y275X allowed prenatal diagnosis in a high-risk fetus.

Seminal plasma characteristics as indicators of cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in men with obstructive azoospermia

OBJECTIVE

To determine the prognostic value of seminal plasma volume, pH, fructose, and alpha-glucosidase for the detection of cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations.

DESIGN

Retrospective data analysis.

SETTING

University infertility clinic (referral center).

PATIENT(S)

Fifty-nine men with obstructive azoospermia.

INTERVENTION(S)

Semen analysis including seminal plasma volume, pH, fructose, alpha-glucosidase, molecular genetic diagnosis of CFTR mutations and FSH measurement.

MAIN OUTCOME MEASURE(S)

Sensitivity and specificity of seminal plasma markers for the detection of CFTR mutations.

RESULT(S)

A CFTR mutation was detected in 26 of 59 patients with obstructive azoospermia. Patients carrying a mutation had significantly lower seminal plasma volume (mean +/- SEM: 1.5 +/- 1.4 mL vs. 2.8 +/- 2.2 mL), lower pH levels (25th percentile, median, 75th percentile: 6.5, 6.8, 7.5 vs. 7.7, 7. 9, 7.9) and lower fructose content (1.0, 1.1, 3.7 vs. 5.8, 20.0, 83. 0 micromol/ejaculate) than those without mutations. Diagnostic efficacy for detection of mutations was best (pH 81.4%, fructose 81. 8%) at a cutoff level for pH of 7.4 and fructose of 2 micromol/ejaculate.

CONCLUSION(S)

Seminal plasma markers provide an effective, noninvasive method to predict CFTR mutations in men with obstructive azoospermia.

Reproductive health in women with cystic fibrosis

The life expectancy of women with cystic fibrosis has doubled in the last 20 years. A major implication of this is the advent of previously unseen reproductive health problems. We review the management problems presented by these women throughout their reproductive lives, including pregnancy.

What is a cystic fibrosis diagnosis?

Cystic fibrosis (CF) should be considered in patients with a wide variety of clinical presentations and of diverse racial and ethnic backgrounds. In most cases the diagnosis is suggested by manifestations of chronic sinopulmonary disease and exocrine pancreatic insufficiency, and then confirmed by a positive sweat test result. Patients may, however, present with pancreatic sufficiency or other atypical clinical features, sometimes in association with normal or borderline sweat test results. In such cases, the ability to detect CF mutations and to measure transepithelial bioelectric properties can be diagnostically useful. Mutation analysis can also be used for carrier screening, prenatal diagnosis, and newborn screening.

Prenatal diagnosis of the fetus with cystic fibrosis and meconium ileus

The sonographic finding of hyperechoic or dilated fetal bowel raises suspicion of a number of prenatal disorders including meconium ileus (MI), meconium peritonitis, congenital infection, neoplasm, or chromosomal trisomy. These findings may also represent transient normal variants. The following case report details the evaluation of one pregnancy with abnormal intestinal echogenic findings on serial sonograms (US), to demonstrate inherent diagnostic difficulties in such a case. A diagnostic algorithm is presented to aid in the proper use of US and DNA mutation analysis for cystic fibrosis (CF), so that the cause of an abnormal abdominal US can be established earlier and more accurately than suggested by previous management schemes. Earlier fetal diagnosis may help to anticipate postnatal problems associated with CF/MI, and therefore provide more optimal clinical management of the affected fetus.

Issues in genetic testing for susceptibility to alcoholism: lessons from Alzheimer's disease and Huntington's disease

Evidence from family, twin, and adoption studies suggest a heritable basis for alcoholism. However, alcoholism is likely to be genetically heterogeneous, and any genetic connection is likely to be in the form of genes conferring an increased risk or susceptibility. In this study, we present the evidence for a genetic component for alcoholism, and examine the precedent for genetic testing and screening for genetic susceptibility using Huntington's disease and Alzheimer's disease as examples. Finally, we discuss the preparations that need to be made before taking any findings about the genetics of alcoholism from the research laboratory into the clinic.

Pregnancy in patients with cystic fibrosis

With increasing life span of patients with CF, more women with CF are becoming pregnant and others are seeking information about the risks involved during pregnancy and delivery. A striking limitation of the available information is the lack of large prospective studies of pregnant patients with CF matched for age and disease severity compared with their non-pregnant cohorts. A study investigating the effect of pregnancy on morbidity and mortality is being completed by the Cystic Fibrosis Foundation. We recommend that all women with CF be offered contraceptive measures and counseling on the maternal and fetal risks of pregnancy, including the genetic risks for the child. The issue of who will raise the child in the event of subsequent morbidity or maternal mortality should ideally be prospectively discussed.

Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays

We have combined photochemistry and photolithography with solid-phase DNA synthesis chemistry to form a new technology that makes high density oligonucleotide probe array synthesis possible. Hybridization to these two-dimensional arrays containing hundreds or thousands of oligonucleotide probes provides a powerful DNA sequence analysis tool. Two types of light-generated DNA probe arrays have been used to test for a variety of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. One array, made up of 428 probes, was designed to scan through the length of CFTR exon 11 and identify differences from the wild type reference sequence. The second type of array contained 1480 probes chosen to detect known deletions, insertions, or base substitution mutations. The validity of the probe arrays was established by hybridizing them with fluorescently labeled control oligonucleotide targets. Characterized mutant CFTR genomic DNA samples were then used to further test probe array hybridization specificity. Finally, ten unknown patient samples were genotyped using the CFTR probe array assay. The genotype assignments were identical to those obtained by PCR product restriction fragment analysis. Our results show that light-generated DNA probe arrays are highly effective in analyzing complex mutation and polymorphism patterns in a relatively large gene such as CFTR.

Barriers to carrier testing for adult cystic fibrosis sibs: the importance of not knowing

Early experience in centers offering population screening for cystic fibrosis (CF) has shown that few of the public are taking advantage of the offer [Miller, 1993: New Scientist 139:6]. There is similar low utilization among adult CF sibs [Fanos and Johnson, 1993: Am J Hum Genet 53:A51]. The purpose of this study was to identify factors motivating or interfering with the pursuit of carrier testing in adult CF sibs. Eighty-four adult CF sibs and their spouses, drawn from Children's Hospital, Oakland, CA, and Children's Hospital, Boston, MA, were interviewed for about an hour, and qualitative material was coded on various themes. Structural and psychological barriers to the transmission of genetic information were identified: 1) sibs encountered difficulty in obtaining information concerning availability of testing; 2) parental guilt and blame prevents parents from discussing genetic issues with the sib; 3) sibs rarely discuss testing with each other; 4) the CF patient or parent often has difficulty with the implications of the sib seeking carrier testing; 5) family and individual myths about carrier status influence the sib's decision to seek testing; 6) statistical odds have lost meaning in families where the rare has already occurred; 7) the sib fears loss of interpersonal desirability; and 8) carrier status can serve an important function in binding guilt. Remaining unaware of their carrier status may serve significant psychological functions for individuals at risk.

A mouse model for the delta F508 allele of cystic fibrosis

The most common cause of cystic fibrosis is a mutation that deletes phenylalanine 508 in cystic fibrosis transmembrane conductance regulator (CFTR). The delta F508 protein is misprocessed and degraded rather than traveling to the apical membrane. We used a novel strategy to introduce the delta F508 mutation into the mouse CFTR gene. Affected epithelia from homozygous delta F508 mice lacked CFTR in the apical membrane and were Cl-impermeable. These abnormalities are the same as those observed in patients with delta F508 and suggest that these mice have the same cellular defect. 40% of homozygous delta F508 animals survived into adulthood and displayed several abnormalities found in human disease and in CFTR null mice. These animals should provide an excellent model to investigate pathogenesis and to examine therapies directed at correcting the delta F508 defect.

Protection against bronchial asthma by CFTR delta F508 mutation: a heterozygote advantage in cystic fibrosis

Cystic fibrosis (CF) is a multisystem autosomal recessive disorder caused by mutations of the cystic fibrosis transmembrane regulator (CFTR), a protein that regulates cyclic-AMP-mediated chloride conductance at the apical membrane of secretory epithelia. Mutations in the CFTR gene are common in many populations. In North America, 4-5% of the general population are heterozygous for a CFTR mutation. Although there are over 400 known CFTR mutations, a single mutation, a deletion of the phenylalanine at position 508 (delta F508) in exon 10, accounts for about 70% of all CF chromosomes worldwide. The reasons for the high frequency of the delta F508 CFTR allele--the selective advantage associated with CF heterozygosity--are unknown. Many physiological abnormalities have been observed in CF heterozygotes, although the clinical significance of these observations is unknown. Preliminary unpublished data and anecdotal information from CF families suggested that, remarkably, the delta F508 allele might protect heterozygotes against bronchial asthma prompted us to further investigate this possibility. Here we present evidence that the delta F508 CF allele protects against asthma in childhood and early adult life.

Mutation analysis of Western Australian families affected by cystic fibrosis

OBJECTIVE

To document the results of mutation analysis on 160 individuals with cystic fibrosis and 31 obligate carriers of the cystic fibrosis gene in 191 Western Australian families to facilitate accurate genetic counselling.

METHODS

We tested for 17 mutations of the cystic fibrosis gene by either a variation of the polymerase chain reaction amplification refractory mutation system (PCR-ARMS) or with a series of restriction enzyme cuts and dot blots using chemiluminescent probes.

RESULTS

At least one of the two intragenic mutations causing cystic fibrosis was identified in 98% of affected individuals and both were detected in 68%. The delta F508 deletion occurred in 89.8% of patients: 51% were homozygous for this defect. In carriers, 85% of the mutations were detected with a panel of 16 probes, identifying 17 intragenic defects: the delta F508 deletion occurred in 72.4%. Both cystic fibrosis mutations were detected in 68% of cystic fibrosis families.

CONCLUSIONS

By analysis with 16 intragenic cystic fibrosis genomic probes, we have documented the frequencies of various mutations in the Western Australian population. These data will be useful in accurate genetic counselling for affected families and carrier screening for the general population.

Simultaneous analysis of mutant and normal alleles for multiple cystic fibrosis mutations by the ligase chain reaction

The ligase chain reaction (LCR) involves repetitive cycles of ligation of two adjacent pairs of oligonucleotides to form longer ligated products in a template-dependent manner. This study demonstrates the application of LCR for analysis of multiple small mutations. We adapted the technology for the simultaneous determination of the normal and mutant alleles in a competition format, as well as multiple mutations in a multiplex format. For these purposes, we used mutations causing cystic fibrosis, namely the delta F508, W1282X, and G551D mutations. Blunt ligation was compared to a strategy with a single base gap on one or both strands to be filled by thermostable polymerase prior to ligation. Blunt or gap strategies worked well for detection of the delta F508 mutation. Detection of the W1282X mutation worked well with a blunt strategy when high K+ concentration (180-220 mM) was used to reduce template-independent ligation. For reliable detection of the G551D mutation, we used mismatches in the oligonucleotides 2-5 bp away from the ligation site and hot start of the reaction to achieve allele specificity. Excellent discrimination of mutations was achieved using competitive LCR with six oligonucleotides (two common on one side of the mutation plus two wild type and two mutant on the opposite side with the mutation site at the end adjacent to the common oligonucleotides) and with multiplex-competitive LCR using 12 oligonucleotides to detect both alleles for two mutations in a single tube.(ABSTRACT TRUNCATED AT 250 WORDS)

Diagnostic criteria for cystic fibrosis in men with congenital absence of the vas deferens

The high frequency of cystic fibrosis (CF) mutations in males with absence of vas deferens supported the hypothesis of a primarily genital phenotype of CF disease. To consider the idea of an attenuated form of CF, we investigated 14 men with congenital bilateral aplasia of the vasa deferentia. All patients were consulting for infertility and none was known to have CF. The median age was 30.5 years (range, 20-38 yr). DNA analysis for 22 CF mutations showed at least 1 mutation in 10 patients (71%), whereas the CF carrier frequency is only 4% in the general population. Three compound heterozygotes were identified, all carriers of the R117H mutation. The sweat test was considered positive in 6 patients (43%), and a high frequency of radiologic evidence of sinus disease (8 patients) and of elevated antibodies to Pseudomonas (8 patients) was found. Only 2 patients were free of all these criteria for CF disease. This study strengthens the hypothesis that absence of vas deferens is an attenuated form of CF. We propose a combination of tests including DNA study, computerized tomographic scan of the paranasal sinuses, and testing of anti-Pseudomonas antibodies when the sweat test is inconclusive.