A new approach for identifying non-pathogenic mutations. An analysis of the cystic fibrosis transmembrane regulator gene in normal individuals

Abstract

Given q as the global frequency of the alleles causing a disease, any allele with a frequency higher than q minus the cumulative frequency of the previously known disease-causing mutations (threshold) cannot be the cause of that disease. This principle was applied to the analysis of cystic fibrosis transmembrane conductance regulator (CFTR) mutations in order to decide whether they are the cause of cystic fibrosis. A total of 191 DNA samples from random individuals from Italy, France, and Spain were investigated by DGGE (denaturing gradient gel electrophoresis) analysis of all the coding and proximal non-coding regions of the gene. The mutations detected by DGGE were identified by sequencing. The sample size was sufficient to select essentially all mutations with a frequency of at least 0.01. A total of 46 mutations was detected, 20 of which were missense mutations. Four

A large-scale study of the random variability of a coding sequence: a study on the CFTR gene

“…Preliminary results on a subset of 400 individuals, and details on the method, are in Bombieri et al 13 The sample All the individuals studied (present investigation and previous data 13 ) come from six geographical areas, namely, Northern Italy (Verona), Central Italy (Rome), Southern France (Montpellier), Northern France (Brest), the Czech Republic (Prague) and Spain (Barcelona). All individuals gave their informed consent.…”

Best practice guidelines for molecular genetic diagnosis of cystic fibrosis and CFTR-related disorders – updated European recommendations

“…68 Novel sequence changes may be subjected to the analysis by computer algorithms to assist in determining their potential pathogenicity. Such programmes include SIFT, 69 Polyphen, 70 and Splice site prediction.…”

Haplotype block structure study of the CFTR gene. Most variants are associated with the M470 allele in several European populations

“…In that study, 10 certainly non-CF-causing alleles were classified. 2 Present paper reports eight further certainly not fully penetrant CF-causing alleles identified through this purely statistical approach. However, the most interesting finding concerned the very different patterns of variability found on the CFTR genes carrying the M470 or the V470 allele.…”

“…1 For many of the several hundreds CFTR variants reported, it is not known whether they are or not CFcausing and this may produce difficulties for genetic counselling. Besides the obvious criteria to identify with certainty the CF-causing mutations (eg frameshift and termination mutations), a purely statistical approach to identify not fully penetrant CF-causing mutations has been proposed by Bombieri et al 2 It is based on the consideration that every CFTR variant with a frequency certainly higher than the cumulative frequency of the not unambiguously identified CF-causing alleles cannot be a fully penetrant CF-causing allele. It was applied to a random sample of 191 Europeans ( ¼ 382 genes), a population where the cumulative frequency of the not unambiguously identified CF-causing alleles is 0.004 (the difference between 0.02, the total frequency of the CF-causing alleles, and 0.016, the total frequency of the well identified CFcausing alleles: WHO Report 3 ).…”