Current Status of Genetic Diagnosis Laboratories and Frequency of Genetic Variants Associated with Cystic Fibrosis through a Newborn-Screening Program in Turkey

Abstract

Background: Cystic fibrosis (CF) is the most common worldwide, life-shortening multisystem hereditary disease, with an autosomal recessive inheritance pattern caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The national newborn screening (NBS) program for CF has been initiated in Turkey since 2015. If the immunoreactive trypsinogen (IRT) is elevated (higher than 70 μg/L in the second control) and confirmed by sweat test or clinical findings, genetic testing is performed. The aims of this study are to emphasize the effect of NBS on the status of genetic diagnosis centers with the increasing numbers of molecular testing methods, and to determine the numbers and types of CFTR mutations in Turkey. Methods: The next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) results of 1595 newborns, who were referred to Cukurova University Adana Genetic Diseases Diagnosis and Treatment Center (AGENTEM) for molecular genetic testing, were evaluated with positive CF NBS program results since 2017. Results: According to the results; 560 (35.1%) of the 1595 patients carried at least 1 (one) CF-related variant, while 1035 patients (64.9%) had no mutation. Compound heterozygosity for two mutations was the most common in patients, while two detected variants were homozygote in 14 patients. A total of 161 variants were detected in 561 patients with mutations. Fifteen novel variants that have not been previously reported were found. Moreover, p.L997F was identified as the most frequent pathogenic mutation that might affect the IRT measurements used for the NBS. The distribution of mutation frequencies in our study showed a difference from those previously reported; for example, the well-known p.F508del was the third most common (n = 42 alleles), rather than the first. The most striking finding is that 313 cases had a pathogenic variant together with the V470M variant, which might have a cumulative effect on CF perpetuation. Conclusion: This study is the first to determine the mutational spectrum of CFTR in correlation with the NBS program in the Turkish population. NBS for CF raises issues regarding screening in diverse populations, both medical and non-medical benefits, and carrier identification. Through the lens of NBS, we focused on the integrated diagnostic algorithms and their effect on the results of genetic testing.

Clinical findings of patients with cystic fibrosis according to newborn screening results

“…The second patient was diagnosed with growth retardation, pancreatic insufficiency, recurrent pneumonia, and chronic S. aureus infection at the age of three. In the study by Bozdogan et al ., F508del was detected in 5.9% of the patients with positive NBS in Turkey 30 . In our study, 91% of all patients with homozygous F508del mutations were patients with positive NBS.…”

“…In the study by Bozdogan et al, F508del was detected in 5.9% of the patients with positive NBS in Turkey. 30 In our study, 91% of all patients with homozygous F508del mutations were patients with positive NBS. Severe mutation frequency was higher in NBS positive patients.…”

Genotype-phenotype correlations of cystic fibrosis in siblings compound heterozygotes for rare variant combinations: Review of literature and case report

“…In a recent study, Atag and colleagues [ 21 ] genotyped 150 CF patients in Turkey who were diagnosed based on two positive sweat chloride tests and the presence of typical pulmonary and gastrointestinal symptoms. None of these patients had the L997F variant, while other Turkish authors [ 22 ] have genotyped 1595 NBS-positive infants since 2017. Interestingly, the second most common allele in this cohort was L997F (after the V470M allele, which is classified as a polymorphism according to the ACMG).…”

Variability of Clinical Presentation in Patients Heterozygous for the F508del Cystic Fibrosis Variant: A Series of Three Cases and a Review of the Literature

“…D1152H is one of the variants frequently encountered in patients with CFTR-RD [ 4 ]. Variant V470M has been found to affect protein maturity [ 16 ] but is largely considered benign on its own, acting mainly to affect the penetrance of other variants [ 16 , 17 ].…”