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

• Published in: BMC medical genomics Vol. 11; no. Suppl 1; p. 13
• Main Authors: Ivanov, Maxim, Matsvay, Alina, Glazova, Olga, Krasovskiy, Stanislav, Usacheva, Mariya, Amelina, Elena, Chernyak, Aleksandr, Ivanov, Mikhail, Musienko, Sergey, Prodanov, Timofey, Kovalenko, Sergey, Baranova, Ancha, Khafizov, Kamil
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 13-02-2018; BioMed Central; BMC
• Subjects: Adult; Analysis; Biomarkers - analysis; CFTR cystic fibrosis; Cohort Studies; Cystic fibrosis; Cystic Fibrosis - genetics; Cystic Fibrosis - pathology; Cystic Fibrosis Transmembrane Conductance Regulator - deficiency; Cystic Fibrosis Transmembrane Conductance Regulator - genetics; DNA sequencing; Female; Genetic aspects; Genetic Association Studies; Genotypes; High-Throughput Nucleotide Sequencing - methods; Humans; Male; Middle Aged; Mutation; NGS next generation sequencing; Young Adult; NGS next generation sequencing; CFTR cystic fibrosis
• ISSN: 1755-8794; 1755-8794
• DOI: 10.1186/s12920-018-0328-z

Cystic 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.
We 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.
By 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%).
NGS 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.