Identification of mutations in exons 1 through 8 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene

A cystic fibrosis patient homozygous for 621 + 1G-->T mutation has a severe pulmonary disease, mild pancreatic insufficiency and a gastro-esophageal reflux

A cystic fibrosis patient homozygous for 621 + 1G-->T mutation of the CFTR gene has been identified during a molecular screening program of Polish CF families. The patient is currently a 21-year-old female with severe pulmonary involvement, mild pancreatic insufficiency and complicated gastroesophageal reflux.

Determination of cystic fibrosis carrier frequency for Zuni native Americans of New Mexico

The Zuni native Americans of the Southwest have an incidence of cystic fibrosis of approximately one in 333 or seven and one-half times that found for Caucasians. Earlier studies indicated that dF508 was not among the cystic fibrosis mutations causing this disease. Through a collaborative study the R1162X mutation was found on 12 out of 12 cystic fibrosis chromosomes from six Zuni patients. Because of the relative high incidence of cystic fibrosis, we undertook a study to determine the carrier frequency of the R1162X mutation among randomly sampled individuals. We found the carrier frequency in the general population for the R1162X to be 6.7%, a very significant number when compared with the carrier frequency for all cystic fibrosis mutations in the Caucasian population of approximately 4%.

Haplotype analysis of 94 cystic fibrosis mutations with seven polymorphic CFTR DNA markers

We have analyzed 416 normal and 467 chromosomes carrying 94 different cystic fibrosis (CF) mutations with polymorphic genetic markers J44, IVS6aGATT, IVS8CA, T854, IVS17BTA, IVS17BCA, and TUB20. The number of mutations found with each haplotype is proportional to its frequency among normal chromosomes, suggesting that there is no preferential haplotype in which mutations arise and thus excluding possible selection for specific haplotypes. While many common mutations in the worldwide CF population showed absence of haplotype variation, indicating their recent origins, some mutations were associated with more than one haplotype. The most common CF mutations, delta F508, G542X, and N1303K, showed the highest number of slippage events at microsatellites, suggesting that they are the most ancient CF mutations. Recurrence was probably the case for 9 CF mutations (R117H, H199Y, R347YH, R347P, L558S, 2184insA, 3272-26A-->G, R1162X, and 3849 + 10kbC-->T). This analysis of 94 CF mutations should facilitate mutation screening and provides useful data for studies on population genetics of CF.

Mutation characterization of CFTR gene in 206 Northern Irish CF families: thirty mutations, including two novel, account for approximately 94% of CF chromosomes

A variety of mutation detection techniques, including restriction endonuclease digestion, allele specific oligonucleotides, and automated fluorescent sequencing, were used in the identification of 15 CFTR mutations representing 86.7% of CF chromosomes in 206 Northern Irish cystic fibrosis (CF) families. A systematic analysis of the 27 exons and intron/exon boundaries of the CFTR gene was performed using denaturing gradient gel electrophoresis (DGGE) in an attempt to characterise the 55 unknown CF mutations in 51 patients. Twenty different mutations were detected by DGGE on 30 chromosomes accounting for a further 7.3% of CF alleles. Fifteen of these mutations had not previously been found in Northern Ireland, and two are novel, M1I(G > T) and V562L. In total, 30 CFTR mutations account for 93.9% of the 412 Northern Irish CF chromosomes tested. The three major CF mutations in Northern Ireland are delta F508, G551D, and R117H with respective frequencies of 68.0%, 5.1%, and 4.1%. The efficacy of the DGGE technique was proven by the detection of 77 out of 77 control variants from all the CFTR exons. DGGE is a highly efficient and sensitive method for mutation screening especially in large genes where the mutation spectrum is known to be heterogeneous.

Fluorescent multiplex microsatellites used to define haplotypes associated with 75 CFTR mutations from the UK on 437 CF chromosomes

The cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene contains three highly informative microsatellites: IVS8CA, IVS17bTA, and IVS17bCA. Their analysis improves prenatal/ carrier diagnosis and generates haplotypes from CF chromosomes that are strongly associated with specific mutations. Microsatellite haplotypes were defined for 75 CFTR mutations carried on 437 CF chromosomes (220 for delta F508, 217 for other mutations) from Northern Ireland and three English regions: the North-West, East Anglia, and the South. Fluorescently labelled microsatellites were amplified in a triplex PCR reaction and typed using an ABI 373A fluorescent fragment analyser. These mutations cover all the common and most of the rare CF defects found in the UK, and their corresponding haplotypes and geographic region are tabulated here. Ancient mutations, delta F508, G542X, N1303K, were associated with several related haplotypes due to slippage during replication, whereas other common mutations were associated with the one respective haplotype (e.g., G551D and R560T with 16-7-17, R117H with 16-30-13, 621 + 1G > T with 21-31-13, 3659delC with 16-35-13). This simple, fast, and automated method for fluorescent typing of these haplotypes will help to direct mutation screening for uncharacterised CF chromosomes.

Correlation of sweat chloride concentration with classes of the cystic fibrosis transmembrane conductance regulator gene mutations

OBJECTIVE

To compare differences in epithelial chloride conductance according to class of mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene.

METHODS

We evaluated the relationship between the functional classes of CFTR mutations and chloride conductance using the first diagnostic sweat chloride concentration in a large cystic fibrosis (CF) population.

RESULTS

There was no difference in sweat chloride value value between classes of CFTR mutations that produce no protein (class I), fail to reach the apical membrane because of defective processing (class II), or produce protein that fails to respond to cyclic adenosine monophosphate (class III). Those mutations that produce a cyclic adenosine monophosphate-responsive channel with reduced conductance (class IV) were associated with a significantly lower, intermediate sweat chloride value. However, patients with the mutations that cause reduced synthesis or partially defective processing of normal CFTR (class V) had sweat chloride concentrations similar to those in classes I to III.

CONCLUSION

Studies of differences in chloride conductance between functional classes of CFTR mutations provide insight into phenotypic expression of the disease.

Search for mutations in pancreatic sufficient cystic fibrosis Italian patients: detection of 90% of molecular defects and identification of three novel mutations

A cohort of 31 cystic fibrosis patients showing pancreatic sufficiency and bearing an unidentified mutation on at least one chromosome was analyzed through denaturing gradient gel electrophoresis of the whole coding region of the cystic fibrosis transmembrane conductance regulator gene, including intron-exon boundaries. Three new and 19 previously described mutations were detected. The combination of these with known mutations detected by other methods, allowed the characterization of mutations on 56/62 (90.3%) chromosomes. Among those identified, 17 can be considered responsible for pancreatic sufficiency, since they were found in patients carrying a severe mutation on the other chromosome. Among these presumed mild mutations, eight were detected more than once, R352Q being the most frequent in this sample (4.83%). Intragenic microsatellite analysis revealed that the six chromosomes still bearing unidentified mutations are associated with five different haplotypes. This may indicate that these chromosomes bear different mutations, rarely occurring among cystic fibrosis patients, further underlying the molecular heterogeneity of the genetic defects present in patients having pancreatic sufficiency.

Highly variable incidence of cystic fibrosis and different mutation distribution among different Jewish ethnic groups in Israel

The incidence of cystic fibrosis (CF) and the frequency of disease-causing mutations varies among different ethnic and geographic populations. The Jewish population around the world is comprised of two major ethnic groups; Ashkenazi and non-Ashkenazi. The latter is further classified according to country of origin. In this study, we analyzed the incidence of CF and the distribution of CF mutations in the general Jewish population in Israel and in most of the Jewish ethnic subgroups. The disease frequency varies considerably among the latter. Among Ashkenazi Jews, the frequency of CF is 1:3300, which is similar to the frequency in most Caucasian populations. Among non-Ashkenazi Jews, the disease occurs at a similar frequency among Jews from Libya (1:2700), Georgia (1:2700), Greece and Bulgaria (1:2400), but is rare in Jews from Yemen (1:8800), Morocco (1:15000), Iraq (1:32000), and Iran (1:39000). So far, only 12 mutations have been identified in Israeli Jews, and this enables the identification of 91% of the CF chromosomes in the entire Jewish CF population. However, in each Jewish ethnic group, the disease is caused by a different repertoire of mutations. The frequency of identified mutations is high in Ashkenazi Jews (95%), and in Jews originating from Tunisia (100%), Libya (91%), Turkey (90%), and Georgia (88%). However, a lower frequency of mutations can be identified in Moroccan (85%), Egyptian (50%), and Yemenite (0%) Jews. For genetic counseling of a Jewish individual, it is necessary to calculate the residual risk according to ethnic origin. Carrier screening of healthy Jewish individuals is currently feasible for Ashkenazi Tunisian, Libyan, Turkish, and Georgian Jews. These results provide the required information for genetic counseling of Jewish CF families and screening programs of Jewish populations worldwide.

Frequency of common cystic fibrosis gene mutations in chronic bronchitis patients

It has been suggested that the delta F508 deletion, the most common mutation in the cystic fibrosis (CF) gene, might be linked to chronic bronchial hypersecretion. We investigated whether such an association could be found in chronic bronchitis, since chronic bronchial hypersecretion is an important and specific element of chronic bronchitis. We screened 100 patients hospitalized for chronic bronchitis with six of the most frequently occurring CF gene mutations: delta F508, R553X, G542X, G551D, N1303K, and 621-1G-->T. Only one patient affected by chronic bronchitis and diffuse bronchiectasis was heterozygous for the deletion delta F508; no other mutations were found. This is not significantly different from the expected frequency of CF carriers in northern Europe, which is 1 in 25. Thus, no association between the most commonly occurring cystic fibrosis genes and chronic bronchitis is likely to exist and routine screening of patients without further signs of cystic fibrosis would seem to be of no benefit in northern Europe.

Skipping of exon 12 as a consequence of a point mutation (1898 + 5G-->T) in the cystic fibrosis transmembrane conductance regulator gene found in a consanguineous Chinese family

A point mutation (1898 + 5G-->T) located five base pairs downstream from the donor splice site in intron 12 of the CFTR gene has been identified in a consanguineous CF patient of Chinese origin. To determine if this nucleotide substitution could affect mRNA splicing, PCR analysis was performed with RNA isolated from the lymphoblastoid cell line of the mother of the deceased patient. While exon 12-minus transcript was detected in this sample, it was also found in individuals without 1898 + 5G-->T, albeit in a smaller proportion. Using a sequence polymorphism associated with each of the two alleles in the mother, however, we showed that mutant transcript was almost exclusively produced by the 1898 + 5G-->T allele. Skipping of exon 12 would result in the deletion of 29 amino acids from the first nucleotide binding domain of CFTR, rendering the protein non-functional. The possibility of a low level (< or = 2.5%) of normal transcript from the mutant allele cannot be excluded and it may explain the pancreatic sufficient phenotype of the patient. The 1898 + 5G-->T mutation was found in two other CF patients of Chinese origin, but it was not detected in 192 CF chromosomes of Caucasian origin and 30 other chromosomes from Chinese individuals without a family history of CF.

Antenatal screening for carriers of cystic fibrosis: randomised trial of stepwise v couple screening

OBJECTIVE

To perform a rigorous comparative evaluation of stepwise and couple approaches to antenatal carrier screening for cystic fibrosis.

DESIGN

Pragmatic randomised trial.

SETTING

Hospital antenatal clinic serving a regional population.

SUBJECTS

2002 women (couples) attending for booking antenatal visit at less than 17 weeks' gestation with no family history of cystic fibrosis.

INTERVENTIONS

Offering counselling and carrier testing for cystic fibrosis, either to women in the first instance (stepwise) or to couples (couple screening).

MAIN OUTCOME MEASURES

Uptake rates; anxiety; knowledge of cystic fibrosis and carrier status (both partners); attitudes to health, pregnancy, the baby, and screening (both partners); and uptake of carrier testing by relatives.

RESULTS

Uptake of screening was the same for both approaches (90%). After delivery most women remembered test results and their meaning, but 53/253 (21%) of those with negative results of couple testing had forgotten that repeat testing would be advisable if they had a pregnancy with a new partner. With stepwise screening women identified as carriers had high levels of anxiety when results were received (mean anxiety score 52.3). This dissipated with a reassuring partner's result (carriers' mean anxiety score 36.1) to levels similar to those receiving negative results from couple screening. Of those receiving negative results, women who had stepwise screening were significantly less anxious than those who had couple screening (mean score with result 32.1 v 35.4, 95% confidence interval for difference -4.7 to -2.1).

CONCLUSIONS

Couple screening allows carriers to avoid transient high levels of anxiety, but is associated with more anxiety and false reassurance among most screenees who will test negative. Stepwise screening gives carriers and their relatives genetic information and is, in our opinion, the better method.

Mild cystic fibrosis disease in three Mexican delta-F508/G551S compound heterozygous siblings

We describe three delta-F508/G551S compound heterozygous siblings with a mild CF phenotype, characterized by mild chronic pulmonary disease, pancreatic sufficiency and increased sweat chloride levels. PCR-mediated site-directed mutagenesis detected the delta-F508 mutation on one allele, and the G551S mutation was detected by SSCP and sequence analysis of exon 11. Two previously described sisters who were homozygous for the G551S mutation had a very mild phenotype with normal sweat chloride concentrations. In our patients the mild phenotype resulted from the combined effect of the mild G551S allele with the severe delta-F508 allele.

Common CFTR mutations are not likely to predispose to chronic bronchitis in northern Germany

The frequency of six common mutations in the cystic fibrosis transmembrane conductance regulator gene was studied in 100 patients hospitalized with chronic bronchitis. Only one patient with chronic bronchitis and diffuse bronchiectasis was heterozygous for the common delta F508 mutation. R553X, G542X, G551D, N1303K and 621 + 1G-->T were not detected. This result is not significantly different from the frequency of cystic fibrosis carriers in Northern Europe. Predisposition of heterozygotes for chronic bronchitis is therefore unlikely.

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.

Identification of six mutations (R31L, 441delA, 681delC, 1461ins4, W1089R, E1104X) in the cystic fibrosis transmembrane conductance regulator (CFTR) gene

Six new mutations have been identified in the CFTR gene. These mutations, representing three different categories--missense (R31L, W1098R), nonsense (E1104X), and frameshift (441delA, 681delC, 1461ins4)--are located in exons 2, 4, 5, 9, and 17b of the gene and presumed to cause cystic fibrosis (CF) in patients. All these mutations are probably rare in the population, as no additional examples were found for any of them in a cohort of 545 CF patients. Our study also revealed a benign sequence variation (3499 + 45T-->C) in intron 17b.

Cystic fibrosis mutation analysis: report from 22 U.K. regional genetics laboratories

We have collated the results of cystic fibrosis (CF) mutation analysis conducted in 22 laboratories in the United Kingdom. A total of 9,807 CF chromosomes have been analysed, demonstrating 56 different mutations so far observed and accounting for 86% of CF genes in the native Caucasian population of the United Kingdom. delta F508 is the most common at 75.3% of CF mutations (range 56.5-83.7%), followed by G551D (3.08%; range 0.71-7.60%), G542X (1.68%; range 0.85-3.66%), 621 + 1 (G > T) (0.93%; range 0.41-3.16%), 1717-1(G > A) (0.57%; range 0.17-1.14%), 1898 + 1)(G > A) (0.46%), R117H (0.46%), N1303K (0.46%), and R553X (0.46%). The data show a clear geographical variation in the distribution of some of the mutations, most notably a marked regional variation in the distribution of 621 + 1 (G > T) and 1989 + 1(G > A), which are both apparently more frequent in Wales. R560T and R117H appear to be more frequent in Ireland and Scotland, and G551D more frequent in Scotland. In summary, these data illustrate that the mutations present within a particular population need to be defined in order to provide meaningful carrier screening and testing for rare mutations in affected individuals. Furthermore, it is apparent that the ethnic origin of a patient, even within a small country such as the United Kingdom, should be taken into account.

Mutation heterogeneity of cystic fibrosis in France: screening by denaturing gradient gel electrophoresis using psoralen-modified oligonucleotide

In order to establish counseling guidelines and aid carrier risk assessment, we sought to establish the frequencies of cystic fibrosis (CF) mutations that are present in CF families living in the Ile de France region, a region notable for its ethnic heterogeneity. We studied 470 CF chromosomes in which we identified more than 90% of the CF mutations. We systematically screened 21 exons and the adjacent sequences of the CF transmembrane conductance regulator (CFTR) gene by denaturing gradient gel electrophoresis using chemical clamps. We detected 41 different CF mutations located in 14 exons. One of these mutations had not been previously described. Given the heterogeneity of these mutations, population screening does not appear to be readily feasible in our population.

Cystic fibrosis and congenital agenesis of the vas deferens, antisperm antibodies and CF-genotype

Antisperm antibodies are formed as a result of vasal and epididymal obstruction. Fourteen males of different ages (pre-, peri- and post-pubertal) with bilateral congenital vasal agenesis and epididymal obstruction secondary to cystic fibrosis (CF), and seven men with congenital bilateral aplasia of the vas deferens (CBAVD) were evaluated with regard to both the presence and levels of serum antisperm antibodies, and the CF-genotype. While IgA and IgG were not detected among pre- and peri-pubertal CF patients, 4 out of 10 (40%) exhibited IgM binding to sperm tail-tip. Post-pubertal CF patients showed high antisperm antibody (ASA) levels in 3 of the 4 males (75%) evaluated for the three isotypes assayed. ASA were found in 5 of 7 CBAVD patients (71%); IgG (n = 3) and IgM (n = 4) were found to be the predominant isotypes bound to sperm tail-tip. CF-genotype analysis revealed two pre-pubertal patients with the DeltaF508/DeltaF508 CF-genotype and a positive ASA response, thus suggesting an earlier or more severe blockage. In addition, the two CBAVD patients found to have a ?/? CF-genotype on the initial screening did not have ASA. The altered antigenicity of sperm associated with initiation of spermatogenesis appears to modify the antisperm antibody isotypes. Further studies on a larger number of patients may allow for a better understanding of the ASA response, as well as a better understanding of a possible phenotype/genotype association between the CF-genotype and the immunologic response.

A cluster of cystic fibrosis mutations in exon 17b of the CFTR gene: a site for rare mutations

Intensive screening has improved our understanding of the profile of mutations in the CFTR gene in which more than 400 mutations have been detected to date. In collaboration with several European laboratories we are involved in such analysis. We have identified 14 new mutations in exon 17b of CFTR, having analysed 780 CF chromosomes, and have compared the frequency of mutations in this exon with that of other regions of the CFTR gene. The results obtained indicate an accumulation of mutations, not only in regions encoding the two nucleotide binding folds, but also in those encoding transmembrane domains of the CFTR gene, in particular exon 17b.

Evaluation of laboratory methods for cystic fibrosis carrier screening: reliability, sensitivity, specificity, and costs

We report a comparative evaluation of three different laboratory methods for screening large numbers of mouthwash DNA samples for common cystic fibrosis mutations. Sensitivity, specificity, and costs of ARMS (allele refractory mutation detection system), dot blotting, and a deletion/digest/PAGE method (multiplex PCR of exons 10 and 11, digest with HincII followed by polyacrylamide gel electrophoresis (PAGE)) were assessed. ARMS was the most reliable and sensitive method and so was considered more suitable than the cheaper deletion/digest/PAGE. As well as being less reliable than ARMS, the dot blotting method assessed was considerably more costly. ARMS was the best laboratory method for CF screening tested.

Unexpected inactivation of acceptor consensus splice sequence by a -3 C to T transition in intron 2 of the CFTR gene

Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). Analysis of DNA from a pancreatic sufficient patient by means of denaturing gradient gel electrophoresis (DGGE) and subsequent DNA sequencing led to the identification of a novel potential splice mutation and a novel missense mutation in the CFTR gene. One C to T substitution (297-3C-->T) was found at the splice acceptor site of intron 2 and a T to C substitution at 1213 was found in exon 7. To determine the effect of the potential splicing mutation on the patient's CFTR transcripts and by taking advantage of the "illegitimate" transcription phenomenon, RNA from EBV-lymphoblastoid cells was reverse transcribed and amplified by the polymerase chain reaction (PCR). Direct sequencing of the PCR product revealed that the transcript from the chromosome with the 297-3C-->T mutation exhibited the skipping of exon 3.

The adolescent growth spurt in children with cystic fibrosis

The adolescent spurt in 230 children with cystic fibrosis (CF) treated at the Cleveland CF centre in northeastern Ohio was compared to that found in normal children from the Fels Longitudinal Growth Study in southwestern Ohio. The Preece-Baines Model 1 (PB1) growth equation was applied to longitudinal height data from both samples to describe a large number of data points for each child in terms of a few biologically meaningful parameters, such as age, height, and velocity at the take-off and peak of the adolescent growth spurt. The growth spurt is delayed by an average of 0.8 years and is about 1 cm/year slower at its peak in CF patients compared to the normal controls. This delay should be considered when comparing clinical growth measurements of adolescent CF patients with normal standards. Peak velocity is lower than expected, even for late-maturing normal children, and height at take-off, peak velocity, and adulthood is significantly reduced, especially in boys. These findings are consistent with the clinical impression that the growth spurt is delayed and attenuated in CF patients, particularly those with poor pulmonary function. Girls homozygous for the delta F508 mutation have significantly more growth retardation than those with other CF mutations.

Organization of the human CD40L gene: implications for molecular defects in X chromosome-linked hyper-IgM syndrome and prenatal diagnosis

Recently, CD40L has been identified as the gene responsible for X chromosome-linked hyper-IgM syndrome (HIGM1). CD40L on activated T cells from HIGM1 patients fails to bind B-cell CD40 molecules, and subsequent analysis of CD40L transcripts by reverse transcription PCR demonstrated coding region mutations in these patients. This approach, however, is of limited use for prenatal diagnosis of HIGM1 in the early-gestation fetus. In this report, we have defined the genomic structure of the CD40L gene, which is composed of five exons and four intervening introns. With this information, we have defined at the genomic level the CD40L gene abnormalities for three previously described HIGM1 patients who demonstrated clustered deletions in the CD40L coding region. These different deletions arose from three distinct mechanisms, including (i) a splice donor mutation with exon skipping, (ii) a splice acceptor mutation with utilization of a cryptic splice site, and (iii) a deletion/insertion event with the creation of a new splice acceptor site. In addition, we have performed prenatal evaluation of an 11-week-old fetus at risk for HIGM1. CD40L genomic clones provide a starting point for further studies of the genetic elements that control CD40L expression. Our knowledge of the CD40L gene structure will prove useful for the identification of additional mutations in HIGM1 and for performing genetic counseling about this disease.

Development of RNA-SSCP protocols for the identification and screening of CFTR mutations: identification of two new mutations

A strategy is described that allows a rapid and accurate identification and screening of cystic fibrosis gene mutations. It consists of setting up and developing RNA single strand conformation polymorphism (rSSCP) protocols, a technique based on the large repertoire of secondary structure of single-stranded RNA. By incorporating the T7 phage promoter sequence into PCR primers, it is possible to carry out rSSCP and compare it to standard single-strand conformation polymorphism (SSCP). Several parallel tests indicate that rSSCP detects a higher fraction of single base changes, and is less time consuming than SSCP since it requires only one fairly short electrophoretic run. Using this technique we were able to identify two new splicing mutations in introns 5 (711 + 5G-->A) and 10 (1717-8G-->A) of the CFTR gene.

Identification of rare and novel mutations in the CFTR genes of CF patients in southern England

Cystic fibrosis patients referred to two genetics centres in southern England and not found to carry common CF-associated mutations in one or both of their CFTR genes have been subjected to an extensive mutation search. The whole of the coding region of the CFTR gene, all intron-exon boundaries and 5' and 3' untranslated regions have been examined by a combination of single stranded conformational polymorphism analysis and chemical mismatch detection; 48 chromosomes with rare mutations have been identified, including 7 novel mutations, 182delT in exon 1, G27X in exon 2, Q151X in exon 4, Q220X in exon 6a, Q525X in exon 10, 3041delG in exon 16, and 4271delC in exon 23.

Screening for CF mutations in adult cystic fibrosis patients with a directed and optimized SSCP strategy

Twenty adolescent and adult cystic fibrosis (CF) patients have been studied for the presence of mutations in the CFTR gene. Mutations other than deltaF508 have been detected by comparison to the single-stranded conformation polymorphism (SSCP) pattern of known mutations in eight exons, in which 80% of the more common mutations are present. Each mutation was confirmed by direct sequencing. For each of the analyzed exons, optimal SSCP conditions have been determined that allow all available known mutations in that exon to be distinguished from each other. This approach allowed mutations to be defined in 75% of the non deltaF508 alleles and 92% of all CF alleles in this cohort.

Analysis of the CFTR gene in the Spanish population: SSCP-screening for 60 known mutations and identification of four new mutations (Q30X, A120T, 1812-1 G-->A, and 3667del4)

In order to determine the spectrum of CF mutations in the Spanish population, we have analysed 40 unrelated Spanish CF patients, with at least one chromosome negative for mutations delta F508, G542X, and N1303K. Exons 1-7,10-14a,15,16,17b,18-21 of the CFTR gene were studied by Single Strand Conformation Polymorphism (SSCP) analysis, using 60 known CF mutations as controls. SSCP screening allowed us to detect 28 different mutations in 52 CF chromosomes, and to identify four new mutations (Q30X in exon 2, A120T in exon 4, 1812-1G-->A in intron 11 and and 3667del4 in exon 19). Further analysis of the four new mutations in a total of 950 Spanish CF chromosomes showed a final frequency of 0.4%, 0.1%, 0.1%, and 0.1% for 1812-1G-->A,Q30X, A120T, and 3667del4, respectively. No mutations were detected in exons 1, 3, 14a, 16, and 18. We have also detected 10 intragenic polymorphisms and DNA sequence variants and have analysed their frequencies in our population. The total of 28 mutations identified in the 80 CF chromosomes highlight the molecular heterogeneity of CF in the Spanish population.

Rapid detection of single nucleotide deletions: application to the beta 6 (-A) mutation of the beta-globin gene and to cystic fibrosis

The formation of heteroduplexes from the amplified products of homologous alleles has been shown to be useful in the identification of heterozygotes carrying deletion or insertion mutations. Here, we describe an improved procedure that allows the detection of single base pair (bp) deletions on nondenaturing polyacrylamide gels. Carriers for a common Mediterranean beta-thalassemic mutation, beta6 (-A), could be easily detected by use of this method, as could carriers of a 1-bp deletion in the cystic fibrosis gene.

A mutation in CFTR produces different phenotypes depending on chromosomal background

Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene but the association between mutation (genotype) and disease presentation (phenotype) is not straightforward. We have been investigating whether variants in the CFTR gene that alter splicing efficiency of exon 9 can affect the phenotype produced by a mutation. A missense mutation, R117H, which has been observed in three phenotypes, was found to occur on two chromosome backgrounds with intron 8 variants that have profoundly different effects upon splicing efficiency. A close association is shown between chromosome background of the R117H mutation and phenotype. These findings demonstrate that the genetic context in which a mutation occurs can play a significant role in determining the type of illness produced.

Cystic fibrosis transmembrane conductance regulator splice variants are not conserved and fail to produce chloride channels

In the human CFTR only the rare exon 4- splice variant is conserved in mice. We have discovered two novel murine variants, exon 5- and exon 11b+. The exon 5- variant represents up to 40% of mRNA in all CFTR-expressing tissues and leaves the reading frame intact. The exon 11b+ variant inserts a novel exon between exons 11 and 12 with expression restricted to the testis. Two variants of 11b have been found and both introduce premature stop codons. When we expressed human CFTR variants lacking either exon 5 or exon 9 in HeLa cells, they failed to generate cAMP-mediated chloride transport, due to defective intracellular processing. The lack of conservation of splice variants between species and the inability of the more abundant splice variants to generate protein that is correctly processed argue against a physiological role and may simply represent aberrant splicing that is tolerated by the cell and organism.

Genotype analysis in cystic fibrosis in relation to the occurrence of diabetes mellitus

Carbohydrate intolerance and frank diabetes mellitus (DM) are recognised features of cystic fibrosis (CF), but their cause has not been established. Damage to the islet cells due to pancreatic fibrosis is the most common explanation. The relationship between the genotype and the occurrence of diabetes mellitus has been examined in 21 cystic fibrosis patients attending our out-patient chest clinics. DNA samples were tested for the presence of the most common mutation (delta F508) and the results related to the degree of carbohydrate intolerance. We found that in CF patients over 18 years of age diabetes is more frequent among those homozygous for the delta F508 allele than the heterozygotes (P < 0.05). Those homozygous for delta F508 were diagnosed as CF at an earlier age than the heterozygotes (P < 0.05). Both the mean age and the female/male ratio were similar in the diabetic and non-diabetic groups. The prevalence of the delta F508 allele was similar to that expected in a random sample of East Anglian cystic fibrosis patients. These data suggest that the occurrence of diabetes mellitus in patients with cystic fibrosis is related to the genotype, which could be secondary to the way the genetic factors influence the degree of pancreatic disease and its rate of progression.

A novel mutation in exon 3 of the CFTR gene

We have screened the 27 exons of the cystic fibrosis transmembrane conductance regulator gene in 87 non-delta F508 chromosomes of Breton origin using the combined techniques of denaturing gradient gel electrophoresis and direct sequencing. By this process, we have detected a new missense mutation, G91R, which results in an arginine for glycine at codon 91. Three affected patients with a delta F508/G91R genotype are pancreatic sufficient. Such observations could facilitate a better understanding of the functional importance of different regions of the encoded product and of the pathogenesis of the disease.

Single-stranded conformation polymorphism analysis of the CFTR gene in Slovenian cystic fibrosis patients: detection of mutations and sequence variations

Cystic fibrosis (CF) mutations have been identified in Slovenian CF patients using single-stranded conformation polymorphism (SSCP) analysis. The entire coding region and all of the splice junction sites were screened in 24 patients. By varying the electrophoretic conditions and composition of the gel, 16 different nucleotide changes have been observed in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Three newly described mutations and four previously reported mutations were found. In addition two new polymorphisms have been identified. Of 35 non-delta F508 chromosomes examined, mutations were detected on 25.7%, raising the proportion of Slovenian CF alleles characterized to 67.5%. Because of the high sensitivity of the SSCP technique most of the remaining uncharacterized CF mutations probably lie in large introns, promoter sequences, or putative regulatory regions not yet analyzed.

Mutation analysis of 184 cystic fibrosis families in Wales

We describe a molecular analysis of 184 cystic fibrosis (CF) families in Wales. To determine accurate frequency data for the CF mutations in the Welsh population, families with at least three Welsh grandparents were strictly regarded as Welsh. Of these 74 families, we have identified approximately 90% of mutations causing CF, with delta F508 accounting for 71.8% and 621 + 1G greater than T 6.7%. We observed a significant difference between the Welsh and Scottish frequencies of 621 + 1G greater than T. To allow the rapid and efficient screening for the more common mutations we modified a multiplex used by Watson et al enabling the detection of delta F508, G551D, and R553X simultaneously with 621 + 1G greater than T. In parallel to this system we ran the Cellmark Diagnostics ARMS multiplex kit, which detects delta F508, 621 + 1G greater than T, G551D, and G542X. RFLP analysis of the 184 families shows that the delta F508 chromosomes are almost exclusively found on the B haplotype (XV2c 1, KM19 2); the other CF mutations have more heterogeneous backgrounds. Strong haplotype correlations exist between the markers XV2c, KM19, D9, and G2 and the other CF mutations. Haplotype data suggest that there are at least seven mutations that remain to be identified in these families.

The spectrum of cystic fibrosis mutations

Although the major mutation causing cystic fibrosis accounts for almost 70% of mutant chromosomes screened, almost 300 sequence alterations have been identified in the gene during the past two and a half years. At least 230 of these mutations are probably associated with disease. This rapid accumulation of data is in part due to the highly coordinated effort by members of the Cystic Fibrosis Genetic Analysis Consortium. The information is not only essential to genetic diagnosis, but also will aid in understanding the structure and function of the protein, and possibly in correlating genotype with phenotype.

A termination mutation (2143delT) in the CFTR gene of German cystic fibrosis patients

German patients with cystic fibrosis (CF) were screened for molecular lesions in exon 13 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene by single strand conformation polymorphism (SSCP) and chemical cleavage of mismatch analyses. Direct sequencing of four samples that displayed the same SSCP pattern and that were susceptible to cleavage of hetero-duplexes by osmium tetroxide revealed, in all cases, a deletion of a single T residue at nucleotide position 2143 within codon 671 of the CFTR gene. As a result, leucine codon 671 is changed into a termination codon. In total, the 2143delT mutation was confirmed in 6 out of 271 German non-delta F508 CF chromosomes by artificial restriction fragment length polymorphism analysis, indicating that this frameshift mutation accounts for about 2% of German non-delta F508 mutations. The 6 pancreas insufficient patients who are compound heterozygous for 2143-delT suffer from the typical features of pulmonary and gastrointestinal CF disease. The 2143delT mutation completes the panel of the more frequent CFTR mutations that reside on the "delta F508 haplotype" and that contribute to its overpresentation among German non-delta F508 alleles that are associated with severe forms of disease.

Incidence and expression of the N1303K mutation of the cystic fibrosis (CFTR) gene

The N1303K mutation was identified in the second nucleotide binding fold of the cystic fibrosis (CF) gene last year. We have gathered data from laboratories throughout Europe and the United States of America in order to estimate its frequency and to attempt to characterise the clinical manifestations of this mutation. N1303K, identified on 216 of nearly 15,000 CF chromosomes tested, accounts for 1.5% of all CF chromosomes. The frequency of the N1303K allele varies significantly between countries and ethnic groups, being more common in Southern than in Northern Europe. This variation is independent of the delta F508 allele. It was not found on UK Asian, American Black or Australian chromosomes. N1303K is associated with four different linked marker haplotypes for the polymorphic markers XV-2c, KM.19 and pMP6d-9. Ten patients are homozygous for this mutation, whereas 106 of the remainder carry one of 12 known CF mutations in the other CF allele. We classify N1303K as a "severe" mutation with respect to the pancreas, but can find no correlation between this mutation, in either the homozygous or heterozygous state, and the severity of lung disease.

Molecular characterization of cystic fibrosis: 16 novel mutations identified by analysis of the whole cystic fibrosis conductance transmembrane regulator (CFTR) coding regions and splice site junctions

The spectrum of cystic fibrosis (CF) mutations was determined in 105 patients by using denaturing gradient gel electrophoresis to screen the entire coding regions and adjacent cystic fibrosis transmembrane conductance regulator (CFTR) gene sequences. The nucleotide substitutions detected included 16 novel mutations, 11 previously described defects, and 11 nucleotide sequence polymorphisms. Among the novel mutations, 6 were of the missense type, 4 were nonsense mutations, 4 were frameshift defects, and 2 affected mRNA splicing. The mutations involved all the CFTR domains, including the R domain. Of the 61 non-delta F508 CF chromosomes studied, mutations were found on 36 (59%), raising the proportion of CF alleles characterized in our patient cohort to 88%. Given the efficacy of the screening method used, the remaining uncharacterized mutations probably lie in DNA sequences outside the regions studied, e.g., upstream-promoter sequences, the large introns, or putative regulatory regions. Our results further document the highly heterogeneous nature of CF mutations and provide the information required for DNA-based genetic testing.

Detection of over 98% cystic fibrosis mutations in a Celtic population

We have conducted a large systematic study of 365 cystic fibrosis (CF) chromosomes in a Celtic population from Brittany, France, in which we have been able to identify more than 98% of the cystic fibrosis gene mutations. We detected 19 different CFTR mutations located in 9 exons. Eleven of these mutations have not been described previously and nine of them are presented in this study. The denaturing gradient gel electrophoresis strategy we have used, can be applied to other populations suggesting that population screening for CF on a large scale might be possible.

Genetic analysis of cystic fibrosis in Denmark. Implications for genetic counselling, carrier diagnosis and prenatal diagnosis

Cystic fibrosis is the most common, severe, inherited disease in the Caucasian population. As a consequence, the demand for genetic counselling of patients with cystic fibrosis and their families is large. In Denmark the incidence of cystic fibrosis is 1:4700, which is quite low compared to other European countries. We have investigated 268 Danish cystic fibrosis patients with respect to DNA markers (haplotypes) and the most common mutation delta F508. The delta F508 mutation is found on 88% of all cystic fibrosis chromosomes, the highest frequency reported so far. This had had an important impact on genetic counselling, prenatal diagnosis and eventually population screening. In the Danish population 78% of all couples at risk will be informative for delta F508 and will be identifiable by simple screening methods.

Intra- and extragenic marker haplotypes of CFTR mutations in cystic fibrosis families

In order to facilitate the screening for the less common mutations in the cystic fibrosis (CF) gene viz., the CF transmembrane conductance regulator gene (CFTR), marker haplotypes were determined for German non-CF (N) and CF chromosomes by polymerase chain reaction analysis of four polymorphisms upstream of the CF gene (XV-2c, KM.19, MP6-D9, J44) and six intragenic polymorphisms (GATT, TUB9, M470V, T854T, TUB18, TUB20) that span the CFTR gene from exon 6 through exon 21. Novel informative sequence variants of CFTR were detected in front of exons 10 (1525-61 A or G), 19 (3601-65 C or A), and 21 (4006-200 A or G). The CF locus exhibits strong long-range marker-marker linkage disequilibrium with breakpoints of recombination between XV-2c and KM.19, and between exons 10 and 19 of CFTR. Marker alleles of GATT-TUB9 and TUB18-TUB20 were found to be in absolute linkage disequilibrium. Four major haplotypes encompass more than 90% of German N and CF chromosomes. Fifteen CFTR mutations detected on 421 out of 500 CF chromosomes were each identified on one of these four predominant 7-marker haplotypes. Whereas all analysed delta F508 chromosomes carried the same KM.19-D9-J44-GATT-TUB9-M470V-T854T haplotype, another frequent mutation in Germany, R553X, was identified on two different major haplotypes. Hence, a priori haplotyping cannot exclude a particular CF mutation, but in combination with population genetic data, enables mutations to be ranked by decreasing probability.