Targeted sequencing reveals complex, phenotype-correlated genotypes in cystic fibrosis

Abstract

BackgroundCystic fibrosis (CF) is one of the most common life-threatening genetic disorders. Around 2000 variants in the CFTR gene have been identified, with some proportion known to be pathogenic and 300 disease-causing mutations have been characterized in detail by CFTR2 database, which complicates its analysis with conventional methods.MethodsWe conducted next-generation sequencing (NGS) in a cohort of 89 adult patients negative for p.Phe508del homozygosity. Complete clinical and demographic information were available for 84 patients.ResultsBy combining MLPA with NGS, we identified disease-causing alleles in all the CF patients. Importantly, in 10% of cases, standard bioinformatics pipelines were inefficient in identifying causative mutations. Class IV-V mutations were observed in 38 (45%) cases, predominantly ones with pancreatic sufficient CF disease; rest of the patients had Class I-III mutations. Diabetes was seen only in patients homozygous for class I-III mutations. We found that 12% of the patients were heterozygous for more than two pathogenic CFTR mutations. Two patients were observed with p.[Arg1070Gln, Ser466*] complex allele which was associated with milder pulmonary obstructions (FVC 107 and 109% versus 67%, CI 95%: 63-72%; FEV 90 and 111% versus 47%, CI 95%: 37-48%). For the first time p.[Phe508del, Leu467Phe] complex allele was reported, observed in four patients (5%).ConclusionNGS can be a more information-gaining technology compared to standard methods. Combined with its equivalent diagnostic performance, it can therefore be implemented in the clinical practice, although careful validation is still required.Electronic supplementary materialThe online version of this article (10.1186/s12920-018-0328-z) contains supplementary material, which is available to authorized users.

Novel, rare and common pathogenic variants in the CFTR gene screened by high-throughput sequencing technology and predicted by in silico tools

“…Lately, screening CFTR variants has been crucial for genetic counseling, for greater understanding of CF and its diversity/variability and, possibly, for the use of precision medicine 11 . Accordingly, high-throughput sequencing has represented a major breakthrough in CF diagnosis, due to increased information output during CFTR sequencing, enabling quick and efficient genotypic identification ( CFTR variant) with full gene screening, when associated with the identification of deletions and insertions, for example, using MLPA (multiplex ligation-dependent probe amplification) 12,13 . Thus, high-throughput sequencing is one method to determine CFTR variability with the aim at encouraging the use of precision medicine, observing its original description: “ an emerging approach for disease treatment and prevention that takes into account individual variability in genes , environment , and lifestyle for each person ” (Genetics Home Reference, U.S. National Library of Medicine).…”

Cystic fibrosis and congenital adrenal hyperplasia: A rare occurrence with diagnostic dilemmas, similarities and contradictions

“…This mutation is a class V mutation which normal CFTR protein is created and moved to the cell surface but in insuf icient quantities. Classes IV, V mutations cause a reduction in function and have a milder effect in opposition to classes I, II, and III mutations that generally lead to complete loss of function and a more severe disease [19]. The causes of the false negative results on sweat test are indicated as technical reasons, speci ic mutations, hypohydrotic ectodermal dysplasia, inadequate sweat collection, mineralocorticoid treatment, young age, edema, hypoproteinemia and penicillin treatment [1].…”

Should isolated Pseudo‐Bartter syndrome be considered a CFTR‐related disorder of infancy?

“…These data suggest that L467F could be a rare polymorphism or acts as a variant with very mild effect on gene/protein function. A recently published paper reports the identification of the novel complex allele F508del;L467F in four adult patients from Russia …”