Are p.I148T, p.R74W and p.D1270N cystic fibrosis causing mutations ?

BACKGROUND: To contribute further to the classification of three CFTR amino acid changes (p.I148T, p.R74W and p.D1270N) either as CF or CBAVD-causing mutations or as neutral variations. METHODS: The CFTR genes from individuals who carried at least one of these changes were extensively scanned by a well established DGGE assay followed by direct sequencing and familial segregation analysis of mutations and polymorphisms. RESULTS: Four CF patients (out of 1238) originally identified as carrying the p.I148T mutation in trans with a CF mutation had a second mutation (c.3199del6 or a novel mutation c.3395insA) on the p.I148T allele. We demonstrate here that the deletion c.3199del6 can also be associated with CF without p.I148T. Three CBAVD patients originally identified with the complex allele p.R74W-p.D1270N were also carrying p.V201M on this allele, by contrast with non CF or asymptomatic individuals including the mother of a CF child, who were carrying p.R74W-p.D1270N alone. CONCLUSION: These findings question p.I148T or p.R74W-p.D1270N as causing by themselves CF or CBAVD and emphazises the necessity to perform a complete scanning of CFTR genes and to assign the parental alleles when novel missense mutations are identified

Ranking insertion, deletion and nonsense mutations based on their effect on genetic information

<p>Abstract</p> <p>Background</p> <p>Genetic variations contribute to normal phenotypic differences as well as diseases, and new sequencing technologies are greatly increasing the capacity to identify these variations. Given the large number of variations now being discovered, computational methods to prioritize the functional importance of genetic variations are of growing interest. Thus far, the focus of computational tools has been mainly on the prediction of the effects of amino acid changing single nucleotide polymorphisms (SNPs) and little attention has been paid to indels or nonsense SNPs that result in premature stop codons.</p> <p>Results</p> <p>We propose computational methods to rank insertion-deletion mutations in the coding as well as non-coding regions and nonsense mutations. We rank these variations by measuring the extent of their effect on biological function, based on the assumption that evolutionary conservation reflects function. Using sequence data from budding yeast and human, we show that variations which that we predict to have larger effects segregate at significantly lower allele frequencies, and occur less frequently than expected by chance, indicating stronger purifying selection. Furthermore, we find that insertions, deletions and premature stop codons associated with disease in the human have significantly larger predicted effects than those not associated with disease. Interestingly, the large-effect mutations associated with disease show a similar distribution of predicted effects to that expected for completely random mutations.</p> <p>Conclusions</p> <p>This demonstrates that the evolutionary conservation context of the sequences that harbour insertions, deletions and nonsense mutations can be used to predict and rank the effects of the mutations.</p

Asthma and COPD in cystic fibrosis intron-8 5T carriers. A population-based study

BACKGROUND: Carriers of cystic fibrosis intron-8 5T alleles with high exon-9 skipping could have increased annual lung function decline and increased risk for asthma or chronic obstructive pulmonary disease (COPD). METHODS: We genotyped 9131 individuals from the adult Danish population for cystic fibrosis 5T, 7T, 9T, and F508del alleles, and examined associations between 11 different genotype combinations, and annual FEV(1 )decline and risk of asthma or COPD. RESULTS: 5T heterozygotes vs. 7T homozygous controls had no increase in annual FEV(1 )decline, self-reported asthma, spirometry-defined COPD, or incidence of hospitalization from asthma or COPD. In 5T/7T heterozygotes vs. 7T homozygous controls we had 90% power to detect an increase in FEV(1 )decline of 8 ml, an odds ratio for self-reported asthma and spirometry-defined COPD of 1.9 and 1.7, and a hazard ratio for asthma and COPD hospitalization of 1.8 and 1.6, respectively. Both 5T homozygotes identified in the study showed evidence of asthma, while none of four 5T/F508del compound heterozygotes had severe pulmonary disease. 7T/9T individuals had annual decline in FEV(1 )of 19 ml compared with 21 ml in 7T homozygous controls (t-test:P = 0.03). 6.7% of 7T homozygotes without an F508del allele in the cystic fibrosis transmembrane conductance regulator gene reported asthma vs. 11% of 7T/9T individuals with an F508del allele (χ(2):P = 0.01) and 40% of 7T homozygotes with an F508del allele (P = 0.04). 7T homozygotes with vs. without an F508del allele also had higher incidence of asthma hospitalization (log-rank:P = 0.003); unadjusted and adjusted equivalent hazard ratios for asthma hospitalization were 11 (95%CI:1.5–78) and 6.3 (0.84–47) in 7T homozygotes with vs. without an F508del allele. CONCLUSION: Polythymidine 5T heterozygosity is not associated with pulmonary dysfunction or disease in the adult Caucasian population. Furthermore, our results support that F508del heterozygosity is associated with increased asthma risk independently of the 5T allele

Population variation of common cystic fibrosis mutations

Since the identification of the gene and the major mutation responsible for cystic fibrosis (CF) in 1989, more than 400 presumed mutations and about 90 DNA sequence variations have been identified in the cystic fibrosis transmembrane conductance regulator (CFTR) gene in the past 4 years. A list of CFTR mutations can be found in an earlier report in this journal (Tsui, 1992). While ∆F508 appears to be common in all study populations its relative frequency varies among different geographic locations (CF Genetic Analysis Consortium, 1990). The distribution of other CF mutations has also been found to be heterogeneous among different populations. In fact, most of the described mutations have only been detected in the original reported cases. To obtain a better understanding of the distribution of the relatively common mutations in the world population, CF mutation screening data were collected for the 30 most common mutations from members of the CF Genetic Analysis Consortium in October 1993. The list of mutations was chosen according to an earlier compilation completed in May 1992 (unpublished data). As the updated test results show, there were only 19 mutations, each detected on 50 or more chromosomes. The center-by-center distribution for 24 of the more commons mutations is shown in Table 1 and the distribution by continent is summarized in Table 2. Two of the previously surveyed mutations, namely, Y122X and 3905insT, are included in Table 3. The three other mutations that were surveyed but not reported here are Q493X, S549R (T→G), and 3849 + 4A→G (≤20 chromosomes each; actual numbers available from L. C. Tsui). Since the broad survey could have missed some of the mutations that are present in substantial proportion (i.e. ≥1%) in some study populations, members of the Consortium were also asked to submit data for such unique mutations not listed in Tables 1 and 2. The results are displayed in Table 3. Most notably, 394delTT is a mutation that was not included in the previous survey but detected on more than 50 chromosomes. It is important to note that the frequencies reported here are the best estimate provided by each participating group. The investigators (up to 3 listed per group) responsible for each data set are shown in the respective tables as contributors to this report. Although an effort has been made to minimize the redundant data, there may be a slight overlap of samples. Moreover, the data presented here are essentially derived from testing CF patients; the frequencies shown may not reflect the true proportion of these mutations in the respective populations due to possible sampling bias. Some of the data have appeared in previous reports. Because of the large number of entries, however, references are only cited for the original mutation descriptions. In conclusion, this report has compiled population data to document that there is a striking difference in the distribution of CFTR mutations in different populations; the overall detection rate for the 24 most common mutations surveyed varies from 50% to 97% (Tables 1,2). This information is important when designing strategies for DNA testing of cystic fibrosis