Novel mutations and deletions in cystic fibrosis in a tertiary cystic fibrosis center in Istanbul

Population Characteristics of the Spectrum and Frequencies of CFTR Gene Mutations in Patients with Cystic Fibrosis from the Republic of Bashkortostan (Russia)

BACKGROUND/OBJECTIVES

Cystic fibrosis (CF) is one of the most common autosomal-recessive disorders worldwide. The incidence of CF depends on the prevalence of cystic fibrosis transmembrane conductance regulator gene (CFTR) mutations in the population, which is determined by genetic diversity and ethnicity.

METHODS

The search for the causes of mutations in the transmembrane conductance regulator gene (CFTR) was carried out using targeted next-generation sequencing (NGS) on the Illumina platform in patients with cystic fibrosis from the Republic of Bashkortostan (Russia), taking into account the ethnic structure of the sample.

RESULTS

A total of 35 distinct causal variants were found in 139 cases from 129 families. Five (F508del, E92K, 3849+10kbC>T, CFTRdele2.3, L138ins) explain 78.7% of identified CF causal alleles. Variants N13103K and 394delTT were found in four families each. Variants 2143delT, S1196X, W1282X, Y84X, G194R, and 1525-1G>A, as well as the two previously described complex alleles-c. [S466X; R1070Q] and str.[G509D;E217G]-were found in two or three families each. Twenty additional variants occurred only once. Variant c.3883_3888dup has not been described previously. Thus, regional and ethnic features were identified in the spectrum of frequencies of pathogenic variants of the CFTR gene in the three major sub-groups of patients-Russians, Tatars, and Bashkirs.

CONCLUSIONS

Taking into account these results, highlighting the genetic specificity of the region, a more efficient search for CFTR mutations in patients can be performed. In particular it is possible to choose certain test kits for quick and effective genetic screening before use of NGS sequencing.

Exploring Turkey's mosaic of novel variants and complex alleles in cystic fibrosis genetics

BACKGROUNDS

Genetic variants in CF transmembrane conductance regulator (CFTR) gene causes cystic fibrosis (CF), a prevalent autosomal recessive disorder. More than 2000 variants in CFTR have been described as disease causative. This study aims to delineate the genotypic and phenotypic landscape of CF among people with CF (pwCF) followed at the largest CF center in Turkey.

METHODS

We conducted a descriptive and retrospective analysis of 481 patients registered with the European CF Society Patient Registry and followed at Marmara University Selim Çöremen CF Center from 2015 onwards. Comprehensive CFTR analysis was utilized for genetic diagnosis. Besides the whole cohort, novel variants and complex alleles were also described.

RESULTS

Our cohort exhibited a broad spectrum of CFTR variants, with 136 different variants detected, indicating substantial genetic diversity. The F508del variant was less prevalent in our cohort compared to US and European averages, which could reflect unique genetic and demographic characteristics of the Turkish population. Additionally, we identified nine novel variants in 12 alleles, which enhances the understanding of CF's genetic complexity in this region, and complex alleles in 32 pwCF.

CONCLUSION

Our research underscores the heterogeneity of CFTR variants in Turkey and highlights the necessity for extensive genetic profiling particularly for diverse populations to provide effective personalized treatment strategies. It is crucial to understand the full spectrum of CFTR variants with the advent of CFTR modulators.

Beyond the 10%: Unraveling the genetic diversity in Turkish cystic fibrosis patients not eligible for CFTR modulators

BACKGROUND

Cystic fibrosis (CF) is an autosomal recessive disease caused by variants of CFTR gene. Over 2000 variants have been identified, and new drugs called CFTR modulators have been developed to target specific defects in the CFTR protein. However, these drugs are only suitable for patients with certain variants of CFTR, and eligibility rates vary depending on race and geographical region. This study aimed to reveal the detailed genotype and clinical characteristics of people with CF (pwCF) at our center in Turkey, a developing country, who are not eligible for CFTR modulators.

METHODS

A total of 445 pwCF followed up at Marmara University were reviewed retrospectively. Variants of the patients ineligible to CFTR modulators were classified based on American College of Medical Genetics guidelines, CFTR classification, the change in the encoded protein, and the variant type.

RESULTS

The study revealed that 139 (31.2%) patients weren't eligible for CFTR modulators. There were 60 different variants in the 276 alleles, as two were missing. The majority of patients had missense or nonsense variants, and that the most common variant was c.1545_1546del, which can be said unique to this geography.

CONCLUSION

The study highlights the importance of detecting the variants of ineligible patients in detail to guide future approaches for more targeted and effective interventions in CF care. Testing the effectiveness of CFTR modulators for rare or newly occurring variants is crucial to ensure equal access for pwCF to these therapies from different racial backgrounds and ethnic minorities.

Exploring the diversity of CFTR gene mutations in cystic fibrosis individuals of South Asia

OBJECTIVE

Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CFTR gene. This study aimed to identify the spectrum of CFTR variants reported in individuals with CF from South Asia (ISA).

DATA SOURCES AND STUDY SELECTION

We conducted a PubMed search for CFTR variants reported in ISA. Full text of original articles and case reports was read to compile data on reported variants. To gather additional data, we independently cross-referenced each variant with the CFTR Mutation Database and ClinVar.

RESULTS

Our investigation identified a total of 92 CFTR variants reported across 30 articles. The most frequently tested, and reported variant was ΔF508 with a global frequency of 69.74%. Notably, we found 14 pathogenic CFTR mutations shared among ISA, originating from more than one South Asian country: ΔF508, 1525-1 G > A, G542X, S549N, R117H, S549R, R709X, V456A, Y569D, L1077P, 1161delC, 1898 + 1 G > T, G551D, and 2184insA.

CONCLUSION

In summary, the higher prevalence of consanguinity and the limited availability of CF diagnostic resources in South Asia considerably contribute to the prevalence of genetic disorders like CF. The spectrum of CFTR mutations exhibits noticeable variations within South Asian and other populations. The inclusion of current study-enlisted CFTR gene variants is highly recommended for CF disease genetic testing in South Asia which may aid in achieving a precise diagnosis, enhancing disease management, and discovering drugs for currently untreatable genetic variants. It is also imperative to conduct a comprehensive study in this region, especially in previously unexplored countries such as Nepal, Bhutan, Maldives, and Bangladesh.

Cystic fibrosis year in review 2019: Section 3 multisystem-based care and research

During the year 2019, numerous research studies and other reports were published that are interesting and instructive to professionals who care for people with cystic fibrosis (CF) and their families.  This report is the third of 3 CF year in review articles and focuses on the multisystem manifestations of CF care. Previous articles have addressed cystic fibrosis transmembrane regulator modulators and reports on CF pulmonary disease and airway infections. It is an exciting time to be involved in care and research that aims to improve care for people with CF and their families.

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

Here, we describe a cystic fibrosis (CF) family with affected siblings, two of whom have a combination of I1234V and 1677delTA variants with classic CF features, the third child with a combination of I1234V and L997F variants with atypical CF, and the apparently healthy mother with a combination of 1677delTA and L997F alleles. Interestingly, the sibling with I1234V and L997F variants had normal sweat test results and had a much milder phenotype than the other two siblings with I1234V and 1677delTA variants, suggesting that this combination is causative for atypical CF. The fact that their mother with the combination of 1677delTA and L997F appears to be healthy suggests that the L997F variant causes different phenotypes in different allele combinations. The current cases show that there is a genotype-phenotype correlation in this disease and underline the importance of genotyping individuals with suspected CF to allow prediction of disease severity and effective treatment.

Pancreatic Insufficiency in a Child with p.Gly542* and c.2657+5G>A Heterozygote CFTR: A Case Report

Cystic fibrosis is a monogenic and autosomal recessive disease. It is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator gene responsible for encoding the CFTR protein. Involvement of the gastrointestinal and respiratory systems is the main clinical manifestation. In this case, we report a heterozygous CFTR patient harboring class I (p.Gly542*) and class V (c.2657+5G>A) mutations. The importance of this case report lies in the clinical features because the patient, aged 3 years, presented with early exocrine pancreatic insufficiency, which can be considered atypical, as most individuals with this genotype are pancreatic sufficient or develop pancreatic insufficiency later in life. This report aims at presenting the tests requested that contributed to the patient's diagnosis, as well as at understanding the association between these mutations and their phenotypic presentation. Interpretation of the genotype-phenotype relationship represents a challenge, as genetic analysis alone is not sufficient to clearly predict severity of the disease. This is because the significant phenotypic heterogeneity existing among patients with the same genotype may exert socioeconomic and sociocultural influences, or by the action of CFTR modifiers, such as environmental and modifying genes, which can alter the protein's function and exert an impact on the individual's phenotype.

CFTR gene mutation spectrum among 735 Iranian patients with cystic fibrosis: A comprehensive systematic review

In this study, the spectrum and frequency of cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations previously reported among Iranian cystic fibrosis (CF) patients have been reviewed and discussed. Using the keywords of Cystic Fibrosis, CF, CFTR, and Iran, along with their Persian equivalents, a comprehensive search was performed on the online databases. After applying the inclusion and exclusion criteria, 16 articles with an overall sample of 735 Iranian patients with CF, were included in this systematic review. A total of 101 different CFTR gene variants had been reported. The mutation of p.Phe508del (c.1521_1523delCTT) (21.22%) was the most frequent one among Iranian patients with CF. In conclusion, due to the fact that in many provinces of Iran no specific study has been done so far, it seems that the CFTR gene mutation spectrum in patients with CF from Iran is much wider.

Cumulative Antimicrobial Susceptibility Data of Pseudomonas Aeruginosa Isolates from Cystic Fibrosis Patients: 4-Year Experience

Objective Pseudomonas aeruginosa is the most important cause of lung infection among cystic fibrosis (CF) patients, and to reduce the severity of the infection, facility-specific cumulative antibiograms could help clinicians in empirical treatment.

Methods Respiratory samples of CF patients between January 2015 and December 2018 were scanned through Laboratory Operating System retrospectively. Demographical data of patients, culture results, and antibiotic susceptibilities are recorded using Microsoft Excel 2010. Cumulative antibiogram data were obtained according to the CLSI M39A4 document.

Results The number of registered patients increased in 4 years from 154 to 253. The mean age of patients varied from 9 to 11.7 (range, 2–42). The ratio of patients with a positive culture for P. aeruginosa increased from 32 to 40%, and the mean patients' age decreased from 16.6 to 11.1 (p <0.05). A total number of 4,146 respiratory samples were analyzed. Sputum samples consisted of 42.5% (n: 1,767) of the samples with a 58.4% isolation rate of P. aeruginosa (n: 1,034). A notable increase of resistance was seen almost all antimicrobials tested by years. The ratio of multidrug-resistant (MDR) P. aeruginosa was 4.1, 10.2, 4.5, and 8.6% in 2015, 2016, 2017, and 2018.

Conclusion Antimicrobial resistance is a challenging problem in CF patients, and surveillance should be done regularly.

Ethnic Differences in the Frequency of CFTR Gene Mutations in Populations of the European and North Caucasian Part of the Russian Federation

Cystic fibrosis (CF) is a common monogenic disease caused by pathogenic variants in the CFTR gene. The distribution and frequency of CFTR variants vary in different countries and ethnic groups. The spectrum of pathogenic variants of the CFTR gene was previously studied in more than 1,500 CF patients from different regions of the European and North Caucasian region of Russia and the spectrum of the most frequent pathogenic variants of the CFTR gene and ethnic features of their distribution were determined. To assess the population frequency of CFTR gene mutations some of the common variants were analyzed in the samples of healthy unrelated individuals from the populations of the European part of the Russian Federation: 1,324 Russians from four European regions (Pskov, Tver, Rostov, and Kirov regions), representatives of five indigenous ethnic groups of the Volga-Ural region [Mari (n = 505), Udmurts (n = 613), Chuvash (n = 780), Tatars (n = 704), Bashkirs (n = 517)], and six ethnic groups of the North Caucasus [Karachay (n = 324), Nogais (n = 118), Circassians (n = 102), Abazins (n = 128), Ossetians (n = 310), and Chechens (n = 100)]. The frequency of common CFTR mutations was established in studied ethnic groups. The frequency of F508del mutation in Russians was found to be 0.0056 on average, varying between four regions, from 0.0027 in the Pskov region to 0.0069 in the Rostov region. Three variants W1282X, 1677delTA, and F508del were identified in the samples from the North Caucasian populations: in Karachay, the frequency of W1282X mutation was 0.0092, 1677delTA mutation - 0.0032; W1282X mutation in the Nogais sample - 0.0127, the frequency of F508del mutations was 0.0098 and 1677delTA - 0.0098 in Circassians; in Abazins F508del (0.0039), W1282X (0.0039) and 1677delTA (0.0117) mutations were found. In the indigenous peoples of the Volga-Ural region, the maximum frequency of the F508del mutation was detected in the Tatar population (0.099), while this mutation was never detected in the Mari and Bashkir populations. The E92K variant was found in Chuvash and Tatar populations. Thus, interethnic differences in the spectra of CFTR gene variants were shown both in CF patients and in healthy population of the European and North Caucasian part of Russia.

Analysis of rearrangements of the CFTR gene in patients from Turkey with CFTR-related disorders: frequent exon 2 deletion

Cystic fibrosis is a hereditary disease that mostly affects the sweat glands, respiratory system, digestive system, and reproductive system. Many and various types of mutations have been reported in CFTR in different ethnicities and countries/regions. Analysis of CFTR gene rearrangements is recommended in patients with unidentified mutated alleles in CFTR sequencing analysis. We collected MLPA analyses of 527 patients from Turkey who had at least one unidentified mutation in CFTR sequence analysis. Heterozygous/homozygous deletions were detected in the CFTR gene in 49 individuals (9.2%) from 35 families. Twelve different single/multi exon deletions were demonstrated, two of which were not previously reported in the literature. Mutations have previously reported in patients from various regions including Asia, Europe, and Africa, and Turkey is located at a crossroads between them. The most frequent mutation was the exon 2 deletion, accounting for 60%. Moreover, patients with exon 2 deletions, were especially originated from northern Turkey. This finding is valuable in leading and shaping planned screening programs in Turkey. Our study, the most comprehensive study for rearrangement analysis in patients from Tukey, revealed a candidate hotspot region of patients suspected of having CFTR-related disorders from Turkey.

Cystic fibrosis in Turkey: First data from the national registry

BACKGROUND

Cystic fibrosis (CF) care has been implemented in Turkey for a long time; however, there had been no patient registry. For this purpose, the Turkish National CF Registry was established. We present the first results of registry using data collected in 2017.

METHODS

The data were collected using a data-entry software system, which was accessed from the internet. Demographic and annually recorded data consisted of 15 and 79 variables, respectively.

RESULTS

There were 1170 patients registered from 23 centers; the estimated coverage rate was 30%. The median age at diagnosis was 1.7 years (median current age: 7.3 years); 51 (4.6%) patients were aged over 18 years. Among 293 patients who were under 3 years of age, 240 patients (81.9%) were diagnosed through newborn screening. Meconium ileus was detected in 65 (5.5%) patients. Genotyping was performed in 978 (87.4%) patients and 246 (25.2%) patients' mutations were unidentified. The most common mutation was deltaF508 with an allelic frequency of 28%, followed by N1303K (4.9%). The median FEV1% predicted was 86. Chronic colonization with Pseudomonas aeruginosa was seen in 245 patients. The most common complication was pseudo-Bartter syndrome in 120 patients. The median age of death was 13.5 years in a total of 15 patients.

CONCLUSIONS

Low coverage rate, lack of genotyping, unidentified mutations, and missing data of lung functions are some of our greatest challenges. Including data of all centers and reducing missing data will provide more accurate data and help to improve the CF care in Turkey in the future.