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Meneses DG, Dos Santos FR, Botelho AJ, Bispo LM, Matos CG, Propheta VGS, Rodrigues AF, Oliveira GU, da Silva AM, Gurgel RQ. Diagnosis of cystic fibrosis: a high heterogeneity of symptoms and genotypes in a Brazil population. BMC Pediatr 2024; 24:422. [PMID: 38956483 PMCID: PMC11218259 DOI: 10.1186/s12887-024-04891-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
INTRODUCTION In highly multiracial populations with inadequate newborn screening, knowledge of the various phenotypic presentations of Cystic Fibrosis (CF) can help reach an early diagnosis. This study aims to describe phenotypes and genotypes at the time of CF diagnosis in a state in the Northeast Region of Brazil. METHODS Retrospective cross-sectional study. Clinical data were extracted from the medical records of CF patients. Clinical, laboratory, and genotypic characteristics were described for patients admitted to a tertiary referral center between 2007 and 2021. RESULTS Fifty-eight (58) patients were included in the study, 53.5% of whom were diagnosed through clinical suspicion. The median age at diagnosis was 4.7 months (IQR: 1.5-14.8 months). Five patients had false-negative results in the newborn screening. Faltering growth was the most frequent clinical manifestation. Bronchiectasis and a history of pneumonia predominated in those older than ten, while thinness, underweight, and electrolyte imbalances were more frequent in children under two. Sequencing of the CFTR gene identified 27 genotypes, with at least one class I-III variant in all patients, and nine variants that are rare, previously undescribed, or have uncertain significance (619delA, T12991, K162Q, 3195del6, 1678del > T, 124del123bp, 3121-3113 A > T). The most frequent alleles were p.Phe508del, p.Gly542*, p.Arg334Trp, and p.Ser549Arg. CONCLUSIONS Malnutrition and electrolyte imbalances were the most frequent phenotypes for children < 2 years and were associated with genotypes including 2 class I-III variants. Rare and previously undescribed variants were identified. The p.Gly542*, p.Arg334Trp, and p.Ser549Arg alleles were among the most frequent variants in this population.
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Affiliation(s)
- Daniela Gois Meneses
- Department of Medicine, Federal University of Sergipe, Aracaju, Sergipe, Brazil.
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil.
- Center for Biological and Health Sciences (NPGME), University Hospital, Federal University of Sergipe, Rua Cláudio Batista 505, Palestina, Aracaju, Sergipe, CEP 49060-025, Brazil.
| | - Fábia Regina Dos Santos
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Center for Biological and Health Sciences (NPGME), University Hospital, Federal University of Sergipe, Rua Cláudio Batista 505, Palestina, Aracaju, Sergipe, CEP 49060-025, Brazil
| | - Anne Jardim Botelho
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Center for Biological and Health Sciences (NPGME), University Hospital, Federal University of Sergipe, Rua Cláudio Batista 505, Palestina, Aracaju, Sergipe, CEP 49060-025, Brazil
| | - Luciana Mota Bispo
- Center for Biological and Health Sciences (NPGME), University Hospital, Federal University of Sergipe, Rua Cláudio Batista 505, Palestina, Aracaju, Sergipe, CEP 49060-025, Brazil
| | - Camilla Guerra Matos
- Center for Biological and Health Sciences (NPGME), University Hospital, Federal University of Sergipe, Rua Cláudio Batista 505, Palestina, Aracaju, Sergipe, CEP 49060-025, Brazil
| | - Vynicius Goltran Sobral Propheta
- Center for Biological and Health Sciences (NPGME), University Hospital, Federal University of Sergipe, Rua Cláudio Batista 505, Palestina, Aracaju, Sergipe, CEP 49060-025, Brazil
| | - Alexia Ferreira Rodrigues
- Center for Biological and Health Sciences (NPGME), University Hospital, Federal University of Sergipe, Rua Cláudio Batista 505, Palestina, Aracaju, Sergipe, CEP 49060-025, Brazil
| | - Géssica Uruga Oliveira
- Center for Biological and Health Sciences (NPGME), University Hospital, Federal University of Sergipe, Rua Cláudio Batista 505, Palestina, Aracaju, Sergipe, CEP 49060-025, Brazil
| | - Angela Maria da Silva
- Department of Medicine, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
| | - Ricardo Queiroz Gurgel
- Department of Medicine, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
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Wu M, Davis JD, Zhao C, Daley T, Oliver KE. Racial inequities and rare CFTR variants: Impact on cystic fibrosis diagnosis and treatment. J Clin Transl Endocrinol 2024; 36:100344. [PMID: 38765466 PMCID: PMC11099334 DOI: 10.1016/j.jcte.2024.100344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/21/2024] [Accepted: 04/14/2024] [Indexed: 05/22/2024] Open
Abstract
Cystic fibrosis (CF) has been traditionally viewed as a disease that affects White individuals. However, CF occurs among all races, ethnicities, and geographic ancestries. The disorder results from mutations in the CF transmembrane conductance regulator (CFTR). Varying incidence of CF is reported among Black, Indigenous, and People of Color (BIPOC), who typically exhibit worse clinical outcomes. These populations are more likely to carry rare CFTR variants omitted from newborn screening panels, leading to disparities in care such as delayed diagnosis and treatment. In this study, we present a case-in-point describing an individual of Gambian descent identified with CF. Patient genotype includes a premature termination codon (PTC) (c.2353C>T) and previously undescribed single nucleotide deletion (c.1970delG), arguing against effectiveness of currently available CFTR modulator-based interventions. Strategies for overcoming these two variants will likely include combinations of PTC suppressors, nonsense mediated decay inhibitors, and/or alternative approaches (e.g. gene therapy). Investigations such as the present study establish a foundation from which therapeutic treatments may be developed. Importantly, c.2353C>T and c.1970delG were not detected in the patient by traditional CFTR screening panels, which include an implicit racial and ethnic diagnostic bias as these tests are comprised of mutations largely observed in people of European ancestry. We suggest that next-generation sequencing of CFTR should be utilized to confirm or exclude a CF diagnosis, in order to equitably serve BIPOC individuals. Additional epidemiologic data, basic science investigations, and translational work are imperative for improving understanding of disease prevalence and progression, CFTR variant frequency, genotype-phenotype correlation, pharmacologic responsiveness, and personalized medicine approaches for patients with African ancestry and other historically understudied geographic lineages.
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Affiliation(s)
- Malinda Wu
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Jacob D. Davis
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Conan Zhao
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Tanicia Daley
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
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Chernykh V, Krasovsky S, Solovova O, Adyan T, Stepanova A, Marnat E, Shtaut M, Sedova A, Sorokina T, Beskorovainaya T, Kondratyeva E, Shchagina O, Polyakov A. Pathogenic Variants and Genotypes of the CFTR Gene in Russian Men with Cystic Fibrosis and CBAVD Syndrome. Int J Mol Sci 2023; 24:16287. [PMID: 38003474 PMCID: PMC10671388 DOI: 10.3390/ijms242216287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogenic CFTR variants cause cystic fibrosis (CF), and CF-related disorders (CF-RD), including bilateral aplasia of the vas deferens (CBAVD). The spectrum of clinical manifestations depends on the CFTR genotype. The frequency and spectrum of the CFTR variants vary between populations and clinical groups. CFTR variants and genotypes were analyzed in Russian men with CF (n = 546) and CBAVD syndrome (n = 125). Pathogenic variants were detected in 93.95% and 39.2% of the CF and CBAVD alleles, respectively. The most frequent c.1521_1523del (F508del; p.Phe508del) variant was found in 541 (49.5%) CF alleles. A total of 162 CFTR genotypes were revealed in CF patients, including 152 homozygous and 394 compound-heterozygous. The most common CF-genotype was F508del/F508del (24.9%). Other frequent CF-genotypes were F508del/3849+10kbC>T, F508del/CFTRdele2,3, and F508del/E92K. CF-causing variants and/or 5T allele were found in 88% of CBAVD patients: 5T/CFTRmut (48.0%), CFTRmut/N (17.6%), CFTRmut/CFTRmut (6.4%), 5T/5T (10.4%), 5T/N (5.6%) and N/N (12.0%), with the most common CBAVD-genotype being F508del/5T (29.6%). The allele frequencies of F508del, CFTRdele2,3 394delTT, and 3849+10kbC>T were significantly higher in CF patients. L138ins/L138ins, 2184insA/E92K, and L138ins/N genotypes were found in CBAVD, but not in CF patients. The results indicate certain differences in the frequency of some CFTR variants and genotypes in Russian CF and CBAVD patients.
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Affiliation(s)
- Vyacheslav Chernykh
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
- Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 117997 Moscow, Russia;
| | - Stanislav Krasovsky
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Olga Solovova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Tagui Adyan
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Anna Stepanova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Ekaterina Marnat
- Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 117997 Moscow, Russia;
| | - Maria Shtaut
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Anna Sedova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Tatyana Sorokina
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Tatyana Beskorovainaya
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Elena Kondratyeva
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Olga Shchagina
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
| | - Aleksandr Polyakov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (S.K.); (O.S.); (T.A.); (A.S.); (M.S.); (A.S.); (T.S.); (T.B.); (E.K.); (O.S.); (A.P.)
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Chernykh V, Sorokina T, Sedova A, Shtaut M, Solovova O, Marnat E, Adyan T, Beskorovaynaya T, Stepanova A, Shchagina O, Polyakov A. L138ins Variant of the CFTR Gene in Russian Infertile Men. Genes (Basel) 2023; 14:1407. [PMID: 37510311 PMCID: PMC10379041 DOI: 10.3390/genes14071407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/02/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
(1) Introduction: Pathogenic variants in the CFTR (Cystic Fibrosis Transmembrane conductance Regulator, OMIM: 602421) gene cause Cystic Fibrosis (CF, OMIM: 219700) and CF-related disorders (CF-RD), often accompanied by obstructive azoospermia due to congenital bilateral aplasia of vas deferens (CBAVD, OMIM: 277180) in male patients. The L138ins (c.413_415dup; p. (Leu138dup)) is a mild variant in the CFTR gene that is relatively common among CF-patients in Slavic populations. The frequency of this variant in Russian infertile men has not been sufficiently studied; (2) Materials and Methods: The sample consisted of 6033 Russian infertile men. The patients were tested for 22 common in Russian populations pathogenic variants of the CFTR gene and the IVS9Tn-polymorphic locus of the intron 9. Molecular-genetic studies were performed using amplified fragment length polymorphism (AFLP-PCR), multiplex ligation-dependent probe amplification (MLPA), and nested PCR (for analysis of the IVS9Tn-polymorphic locus); (3) Results: Pathogenic variants in the CFTR were detected in 3.9% of patients. The most frequent variants were F508del and CFTRdele2.3(21kb), accounted for 61.0% and 7.1% of detected variants, respectively. The L138ins variant was detected in 17 (0.28%) individuals: one of them was homozygous, 10 patients were heterozygous, and 6 patients were compound-heterozygous (F508del/L138ins, n = 4; L138ins/N1303K, n = 1; L138ins/5T, n = 1). Two pathogenic CF-causing variants in the CFTR gene were detected in 8 patients, including 7 compound heterozygous (F508del/L138ins, n = 4; F508del/N1303K, n = 1; 2184insA/E92K, n = 1; 3849+10kbC>T/E92K, n = 1) and one homozygous (L138ins/L138ins). The L138ins variant was found in 7 out of 16 (43.75%) chromosomes in six of these patients. The most common pathogenic variant, F508del, was identified in five out of them, in 5 of 16 (31.25%) chromosomes. The allele frequency (AF) of the L138ins variant in the sample has been found to be 0.0014.; (4) Conclusions: The L138ins variant of the CFTR gene is the third most common variant after F508del and CFTRdele2.3(kb) among Russian infertile men.
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Affiliation(s)
- Vyacheslav Chernykh
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
- Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 117997 Moscow, Russia;
| | - Tatyana Sorokina
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
| | - Anna Sedova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
| | - Maria Shtaut
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
| | - Olga Solovova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
| | - Ekaterina Marnat
- Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 117997 Moscow, Russia;
| | - Tagui Adyan
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
| | - Tatyana Beskorovaynaya
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
| | - Anna Stepanova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
| | - Olga Shchagina
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
| | - Aleksandr Polyakov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.S.); (A.S.); (M.S.); (O.S.); (T.A.); (T.B.); (A.S.); (O.S.); (A.P.)
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Hosseini Nami A, Kabiri M, Zafarghandi Motlagh F, Shirzadeh T, Fakhari N, Karimi A, Bagherian H, Jamali M, Younesikhah S, Shadman S, Zeinali R, Zeinali S. Genetic attributes of Iranian cystic fibrosis patients: the diagnostic efficiency of CFTR mutations in over a decade. Front Genet 2023; 14:1140034. [PMID: 37274793 PMCID: PMC10234504 DOI: 10.3389/fgene.2023.1140034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/10/2023] [Indexed: 06/07/2023] Open
Abstract
Objectives: Cystic fibrosis (CF) is the most prevalent autosomal recessive disorder among Caucasians. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause this pathology. We, therefore, aimed to describe the CFTR mutations and their geographical distribution in Iran. Method: The mutation spectrum for 87 families from all Iranian ethnicities was collected using ARMS PCR, Sanger sequencing, and MLPA. Results: Mutations were identified in 95.8% of cases. This dataset revealed that the most frequent mutations in the Iranian population were F508del, c.1000C>T, c.1397C>G, c.1911delG, and c.1393-1G>A. In addition, we found weak evidence for Turkey being the possible geographical pathway for introducing CFTR mutations into Iran by mapping the frequency of CFTR mutations. Conclusion: Our descriptive results will facilitate the genetic detection and prenatal diagnosis of cystic fibrosis within the Iranian population.
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Affiliation(s)
- Amin Hosseini Nami
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Mahboubeh Kabiri
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Tina Shirzadeh
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Negar Fakhari
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Ali Karimi
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Hamideh Bagherian
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Mojdeh Jamali
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Shahrzad Younesikhah
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Sara Shadman
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Razie Zeinali
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Sirous Zeinali
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
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Clinical and Genetic Characterisation of Cystic Fibrosis Patients in Latvia: A Twenty-Five-Year Experience. Diagnostics (Basel) 2022; 12:diagnostics12112893. [PMID: 36428953 PMCID: PMC9689702 DOI: 10.3390/diagnostics12112893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Cystic fibrosis (CF) is the most common life-limiting genetic disorder in European descent populations. It is caused by pathogenic variants in the CFTR gene, and inheritance is autosomal recessive. This study provides an up-to-date, comprehensive estimation of the distribution of CFTR pathogenic variants in Latvia and their phenotypic characteristics. It also reports the first results of the CF newborn screening programme following its implementation in 2019. We analysed the clinical and molecular data of CF patients treated at the only tertiary hospital in Latvia providing specialised healthcare for the disorder. Between 1997 and 2022, 66 CF patients from 62 families were diagnosed based on symptoms or a molecular confirmation (six patients were diagnosed through the CF newborn screening programme). F508del was identified in 70.5% of all CF chromosomes. Known variants were identified in more than one family: dele2,3, R1006H, L1335P, W57R, R553X, 2143delT and 3849+10kb C>T (legacy names used). Furthermore, two novel variants were identified, namely, c.503C>A p.(Ser168Ter) and c.(743+1_744-1)_(1584+1_1585-1)del p.(?). The available follow-up results indicated that Latvian CF patients demonstrated similar tendencies to CF patients worldwide. The oldest age at diagnosis prior to the implementation of the CF newborn screening programme was 14 years. We provide here, for the first time, a comprehensive description of Latvian CF patients. An improvement in the healthcare of CF patients over time, including access to diagnosis, is evident. Two novel CF-causing variants are reported, and F508del is the most frequently occurring variant in the population, thus suggesting that F508del screening should be followed by the testing of the full CFTR gene.
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Reporting Two Novel Mutations in Two Iranian Families with Cystic Fibrosis, Molecular and Bioinformatic Analysis. IRANIAN BIOMEDICAL JOURNAL 2022; 26:398-405. [PMID: 35468710 PMCID: PMC9763878 DOI: 10.52547/ibj.3713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Cystic fibrosis (CF) is the most common heredity disease among the Caucasian population. More than 350 known pathogenic variations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene (NM_000492.4) cause CF. Herein, we report the outcome of our investigation in two unrelated Iranian families with CF patients. Methods We conducted phenotypic examination, segregation, linkage analysis, and CFTR gene sequencing to define causative mutations. Results We found two novel mutations in the present study. The first one was a deletion causing frameshift, c.299delT p.(Leu100Profs*7), and the second one was a missense mutation, c.1857G>T, at nucleotide binding domain 1 of the CFTR protein. Haplotype segregation data supported our new mutation findings. Conclusion Findings of this study expand the spectrum of CFTR pathogenic variations and can improve prenatal diagnosis and genetic counseling for CF.
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Petrova NV, Kashirskaya NY, Vasilyeva TA, Balinova NV, Marakhonov AV, Kondratyeva EI, Zhekaite EK, Voronkova AY, Kutsev SI, Zinchenko RA. High frequency of complex CFTR alleles associated with c.1521_1523delCTT (F508del) in Russian cystic fibrosis patients. BMC Genomics 2022; 23:252. [PMID: 35365085 PMCID: PMC8973895 DOI: 10.1186/s12864-022-08466-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
Cystic fibrosis (CF, MIM# 219,700) is an autosomal recessive disease caused by pathogenic variants within the CFTR gene. It was shown that genetic variants located in cis can affect disease severity or treatment response because of additive or epistatic effects. Studies on the prevalence of complex alleles in Russian CF patients have just begun. Aim To evaluate frequencies and genetic background of complex alleles carrying c.1521_1523delCTT (F508del) and c.1399C>T (L467F), c.2562T>G (T854=) or c.4389G>A (Q1463=) in cis; to determine clinical consequences of complex allele c.[1399C>T;1521_1523delCTT] ([L467;F508del]) in Russian CF patients. Methods Sequencing of coding regions of CFTR gene and analysis of polymorphic markers in CF patients carrying F508del variant. Comparing of clinical features in two groups patients having genotypes [L467F;F508del];[F508del] (group 1) and [F508del];[F508del] (group 2). Results Frequency of [L467F;F508del] allele linked to 2–2–21–6–17–13 haplotype was 4.42%, of [F508del;T854=;Q1463=] allele linked to haplotype 1–2–21–6–17–13 – 2.2% in F508del chromosomes. No differences in disease severity in patients carrying complex allele [L467F;F508del] and patients homozygous for F508del was found. Conclusion The frequency of complex alleles associated with F508del was at least 6.6% in Russian CF patients, which should be taken into account for the decision on optimal treatment options with CFTR modulators.
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Affiliation(s)
- Nika V Petrova
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | | | | | | | - Andrey V Marakhonov
- Research Centre for Medical Genetics, Moscow, Russian Federation. .,Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics, Moskvorechie St., 1, 115522, Moscow, Russian Federation.
| | | | - Elena K Zhekaite
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Anna Y Voronkova
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Sergey I Kutsev
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Rena A Zinchenko
- Research Centre for Medical Genetics, Moscow, Russian Federation.,N.A. Semashko National Research Institute of Public Health, Moscow, Russian Federation
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Cheng H, Yang S, Meng Q, Zheng B, Gu Y, Wang L, Song T, Xu C, Wang G, Han M, Shen L, Ding J, Li H, Ouyang J. Genetic analysis and intracytoplasmic sperm injection outcomes of Chinese patients with congenital bilateral absence of vas deferens. J Assist Reprod Genet 2022; 39:719-728. [PMID: 35119551 PMCID: PMC8995229 DOI: 10.1007/s10815-022-02417-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/27/2022] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Congenital bilateral absence of the vas deferens (CBAVD) is a major cause of obstructive azoospermia and male factor infertility. CBAVD is mainly caused by mutations in the genes encoding CFTR (cystic fibrosis transmembrane conductance regulator) and ADGRG2 (adhesion G protein-coupled receptor G2). This study aimed to describe CFTR and ADGRG2 variations in 46 Chinese CBAVD patients and evaluated sperm retrieval and assisted reproductive technology outcomes. METHODS The CFTR and ADGRG2 genes were sequenced and analyzed by whole-exome sequencing (WES), and variations were identified by Sanger sequencing. Bioinformatic analysis was performed. We retrospectively reviewed the outcomes of patients undergoing sperm retrieval surgery and intracytoplasmic sperm injection (ICSI). RESULTS In total, 35 of 46 (76.09%) patients carried at least one variation in CFTR, but no copy number variants or ADGRG2 variations were found. In addition to the IVS9-5 T allele, there were 27 CFTR variations, of which 4 variations were novel and predicted to be damaging by bioinformatics. Spermatozoa were successfully retrachieved in 46 patients, and 39 of the patients had their own offspring through ICSI. CONCLUSION There are no obvious hotspot CFTR mutations in Chinese CBAVD patients besides the IVS9-5 T allele. Therefore, WES might be the best detection method, and genetic counseling should be different from that provided to Caucasian populations. After proper counseling, all patients can undergo sperm retrieval from their epididymis or testis, and most of them can have their own children through ICSI.
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Affiliation(s)
- Hongbo Cheng
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 Jiangsu China ,Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Shenmin Yang
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Qingxia Meng
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Bo Zheng
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yidong Gu
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Luyun Wang
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Tao Song
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu China
| | - Chunlu Xu
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu China
| | - Gaigai Wang
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Mutian Han
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Liyan Shen
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jie Ding
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Hong Li
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.
| | - Jun Ouyang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China.
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10
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Alibakhshi R, Mohammadi A, Khamooshian S, Kazeminia M, Moradi K. CFTR gene mutation spectrum among 735 Iranian patients with cystic fibrosis: A comprehensive systematic review. Pediatr Pulmonol 2021; 56:3644-3656. [PMID: 34525262 DOI: 10.1002/ppul.25647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/06/2021] [Accepted: 08/25/2021] [Indexed: 01/17/2023]
Abstract
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.
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Affiliation(s)
- Reza Alibakhshi
- Department of Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Aboozar Mohammadi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sahand Khamooshian
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Kazeminia
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Keivan Moradi
- Department of Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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11
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Cantú-Reyna C, Galindo-Ramírez R, Vázquez-Cantú M, Haddad-Talancón L, García-Muñoz W. Frequency of allele variations in the CFTR gene in a Mexican population. BMC Med Genomics 2021; 14:262. [PMID: 34740355 PMCID: PMC8569977 DOI: 10.1186/s12920-021-01111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/27/2021] [Indexed: 11/21/2022] Open
Abstract
Background Cystic fibrosis (CF) is an autosomal recessive disorder caused by pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The CF variants incidence is highly variable and even undetermined in some countries like Mexico. Methods In this study, the allele frequencies of 361 variants in the CFTR gene were investigated in 1455 Mexicans without a CF or CFTR-related disorders (CFTR-RD) diagnosis. We also performed a statistical comparative analysis against allele frequencies of different populations to measure genetic differences in the prevalence of CFTR variants. Results In the vast majority of cases, the allele frequencies of this cohort were comparable to those found in other populations. However, some variants displayed significant differences in their allele frequencies when compared with European and African populations. Conclusions This study provides information about CFTR variants to predict the prevalence of CF in Mexico and uncover other unknown but frequent pathogenic variants in the country. Additionally, other CFTR-RD variants have also been studied using population data of the same CFTR variants. Studies like this could help develop a regional molecular diagnostic screen to optimize the medical care of CF patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01111-w.
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Affiliation(s)
- Consuelo Cantú-Reyna
- Laboratorio de genética humana, Código 46, S.A de C.V, Camelias 3-Int 10, Los Tabachines, C.P. 62498, Cuernavaca Morelos, Mexico.,Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Monterrey, Nuevo León, Mexico
| | - Roberto Galindo-Ramírez
- Laboratorio de genética humana, Código 46, S.A de C.V, Camelias 3-Int 10, Los Tabachines, C.P. 62498, Cuernavaca Morelos, Mexico
| | - Mercedes Vázquez-Cantú
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Monterrey, Nuevo León, Mexico
| | - Lorenza Haddad-Talancón
- Laboratorio de genética humana, Código 46, S.A de C.V, Camelias 3-Int 10, Los Tabachines, C.P. 62498, Cuernavaca Morelos, Mexico
| | - Willebaldo García-Muñoz
- Laboratorio de genética humana, Código 46, S.A de C.V, Camelias 3-Int 10, Los Tabachines, C.P. 62498, Cuernavaca Morelos, Mexico.
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12
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Ramensky VE, Ershova AI, Zaicenoka M, Kiseleva AV, Zharikova AA, Vyatkin YV, Sotnikova EA, Efimova IA, Divashuk MG, Kurilova OV, Skirko OP, Muromtseva GA, Belova OA, Rachkova SA, Pokrovskaya MS, Shalnova SA, Meshkov AN, Drapkina OM. Targeted Sequencing of 242 Clinically Important Genes in the Russian Population From the Ivanovo Region. Front Genet 2021; 12:709419. [PMID: 34691145 PMCID: PMC8529250 DOI: 10.3389/fgene.2021.709419] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/31/2021] [Indexed: 12/16/2022] Open
Abstract
We performed a targeted sequencing of 242 clinically important genes mostly associated with cardiovascular diseases in a representative population sample of 1,658 individuals from the Ivanovo region northeast of Moscow. Approximately 11% of 11,876 detected variants were not found in the Single Nucleotide Polymorphism Database (dbSNP) or reported earlier in the Russian population. Most novel variants were singletons and doubletons in our sample, and virtually no novel alleles presumably specific for the Russian population were able to reach the frequencies above 0.1-0.2%. The overwhelming majority (99.3%) of variants detected in this study in three or more copies were shared with other populations. We found two dominant and seven recessive known pathogenic variants with allele frequencies significantly increased compared to those in the gnomAD non-Finnish Europeans. Of the 242 targeted genes, 28 were in the list of 59 genes for which the American College of Medical Genetics and Genomics (ACMG) recommended the reporting of incidental findings. Based on the number of variants detected in the sequenced subset of ACMG59 genes, we approximated the prevalence of known pathogenic and novel or rare protein-truncating variants in the complete set of ACMG59 genes in the Ivanovo population at 1.4 and 2.8%, respectively. We analyzed the available clinical data and observed the incomplete penetrance of known pathogenic variants in the 28 ACMG59 genes: only 1 individual out of 12 with such variants had the phenotype most likely related to the variant. When known pathogenic and novel or rare protein-truncating variants were considered together, the overall rate of confirmed phenotypes was about 19%, with maximum in the subset of novel protein-truncating variants. We report three novel protein truncating variants in APOB and one in MYH7 observed in individuals with hypobetalipoproteinemia and hypertrophic cardiomyopathy, respectively. Our results provide a valuable reference for the clinical interpretation of gene sequencing in Russian and other populations.
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Affiliation(s)
- Vasily E Ramensky
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra I Ershova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Marija Zaicenoka
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
| | - Anna V Kiseleva
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Anastasia A Zharikova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri V Vyatkin
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Evgeniia A Sotnikova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Irina A Efimova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Mikhail G Divashuk
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Olga V Kurilova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Olga P Skirko
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Galina A Muromtseva
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | | | | | - Maria S Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Svetlana A Shalnova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Alexey N Meshkov
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Oxana M Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
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13
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Petrova N, Balinova N, Marakhonov A, Vasilyeva T, Kashirskaya N, Galkina V, Ginter E, Kutsev S, Zinchenko R. Ethnic Differences in the Frequency of CFTR Gene Mutations in Populations of the European and North Caucasian Part of the Russian Federation. Front Genet 2021; 12:678374. [PMID: 34220950 PMCID: PMC8242336 DOI: 10.3389/fgene.2021.678374] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Nika Petrova
- Research Centre for Medical Genetics, Moscow, Russia
| | | | | | | | | | | | | | - Sergey Kutsev
- Research Centre for Medical Genetics, Moscow, Russia
| | - Rena Zinchenko
- Research Centre for Medical Genetics, Moscow, Russia
- N.A. Semashko National Research Institute of Public Health, Moscow, Russia
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14
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Petrova NV, Marakhonov AV, Balinova NV, Abrukova AV, Konovalov FA, Kutsev SI, Zinchenko RA. Genetic Variant c.245A>G (p.Asn82Ser) in GIPC3 Gene Is a Frequent Cause of Hereditary Nonsyndromic Sensorineural Hearing Loss in Chuvash Population. Genes (Basel) 2021; 12:820. [PMID: 34071867 PMCID: PMC8226456 DOI: 10.3390/genes12060820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 11/05/2022] Open
Abstract
Hereditary nonsyndromic sensorineural hearing loss is a disease in which hearing loss occurs due to damage to the organ of the inner ear, the auditory nerve, or the center in the brain that is responsible for the perception of sound, characterized by wide locus and allelic heterogeneity and different types of inheritance. Given the diversity of population of the Russian Federation, it seems necessary to study the ethnic characteristics of the molecular causes of the disease. The aim is to study the molecular and genetic causes of hereditary sensorineural hearing loss in Chuvash, the fifth largest ethnic group in Russia. DNA samples of 26 patients from 21 unrelated Chuvash families from the Republic of Chuvashia, in whom the diagnosis of hereditary sensorineural hearing loss had been established, were analyzed using a combination of targeted Sanger sequencing, multiplex ligase-dependent probe amplification, and whole exome sequencing. The homozygous variant NM_133261.3(GIPC3):c.245A>G (p.Asn82Ser) is the major molecular cause of hereditary sensorineural hearing loss in 23% of Chuvash patients (OMIM #601869). Its frequency was 25% in patients and 1.1% in healthy Chuvash population. Genotyping of the NM_133261.3(GIPC3):c.245A>G (p.Asn82Ser) variant in five neighboring populations from the Volga-Ural region (Russian, Udmurt, Mary, Tatar, Bushkir) found no evidence that this variant is common in those populations.
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Affiliation(s)
- Nika V. Petrova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
| | - Andrey V. Marakhonov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
| | - Natalia V. Balinova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
| | - Anna V. Abrukova
- Presidential Perinatal Center of the Public Health Ministry of Chuvashia, Genetic Counseling Department, 428018 Cheboksary, Russia;
| | | | - Sergey I. Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
| | - Rena A. Zinchenko
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
- N.A. Semashko National Research Institute of Public Health, 105064 Moscow, Russia
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15
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Current Status of Genetic Diagnosis Laboratories and Frequency of Genetic Variants Associated with Cystic Fibrosis through a Newborn-Screening Program in Turkey. Genes (Basel) 2021; 12:genes12020206. [PMID: 33572515 PMCID: PMC7910984 DOI: 10.3390/genes12020206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/15/2022] Open
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.
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16
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Petrova NV, Kashirskaya NY, Krasovskiy SA, Amelina EL, Kondratyeva EI, Marakhonov AV, Vasilyeva TA, Voronkova AY, Sherman VD, Ginter EK, Kutsev SI, Zinchenko RA. Clinical Presentation of the c.3844T>C (p.Trp1282Arg, W1282R) Variant in Russian Cystic Fibrosis Patients. Genes (Basel) 2020; 11:E1137. [PMID: 32992607 PMCID: PMC7600230 DOI: 10.3390/genes11101137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/12/2020] [Accepted: 09/23/2020] [Indexed: 11/25/2022] Open
Abstract
The goal was to study the phenotypic manifestations of c.3844T>C (p.Trp1282Arg, W1282R) variant, a CF-causing mutation, in patients from the Russian Federation. Clinical manifestations and complications (the age at CF diagnosis, sweat test, pancreatic status, lung function, microbial infection, body mass index (BMI), the presence of meconium ileus (MI), diabetes, and severe liver disease) were compared in four groups: group 1-patients carrying c.3844T>C and severe class I or II variant in trans; group 2-3849+10kbC>T/F508del patients; group 3-F508del/F508del patients; and group 4-patients with W1282R and "mild" variant in trans. Based on the analyses, W1282R with class I or II variant in trans appears to cause at least as severe CF symptoms as F508del homozygotes as reflected in the early age of diagnosis, high sweat chloride concentration, insufficient pancreatic function, and low lung function, in contrast to 3849+10kbC-T/F508del compound heterozygotes having milder clinical phenotypes. The W1282R pathogenic variant is seemed to lead to severe disease phenotype with pancreatic insufficiency similarly to the F508del homozygous genotype.
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Affiliation(s)
- Nika V. Petrova
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
| | - Nataliya Y. Kashirskaya
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
| | - Stanislav A. Krasovskiy
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
- Pulmonology Research Institute under FMBA of Russia, Orekhoviy boulevard, 28, 115682 Moscow, Russia;
| | - Elena L. Amelina
- Pulmonology Research Institute under FMBA of Russia, Orekhoviy boulevard, 28, 115682 Moscow, Russia;
| | - Elena I. Kondratyeva
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
| | - Andrey V. Marakhonov
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
| | - Tatyana A. Vasilyeva
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
| | - Anna Y. Voronkova
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
| | - Victoria D. Sherman
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
| | - Evgeny K. Ginter
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
| | - Sergey I. Kutsev
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
| | - Rena A. Zinchenko
- Research Centre for Medical Genetics, Russian Federation, Moskvorechie St., 1, 115522 Moscow, Russia; (N.V.P.); (S.A.K.); (E.I.K.); (A.V.M.); (T.A.V.); (A.Y.V.); (V.D.S.); (E.K.G.); (S.I.K.); (R.A.Z.)
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