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Orlova M, Gundorova P, Kadnikova V, Polyakov A. Spectrum of pathogenic variants and high prevalence of pathogenic BBS7 variants in Russian patients with Bardet-Biedl syndrome. Front Genet 2024; 15:1419025. [PMID: 39092430 PMCID: PMC11291329 DOI: 10.3389/fgene.2024.1419025] [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: 04/17/2024] [Accepted: 06/05/2024] [Indexed: 08/04/2024] Open
Abstract
Introduction Bardet-Biedl syndrome is a rare condition characterized by obesity, retinitis pigmentosa, polydactyly, development delay, and structural kidney anomalies. This syndrome has an autosomal recessive type of inheritance. For the first time, molecular genetic testing has been provided for a large cohort of Russian patients with Bardet-Biedl syndrome. Materials and methods Genetic testing was provided to 61 unrelated patients using an MPS panel that includes coding regions and intronic areas of all genes (n = 21) currently associated with Bardet-Biedl syndrome. Results The diagnosis was confirmed for 41% of the patients (n = 25). Disease-causing variants were observed in BBS1, BBS4, BBS7, TTC8, BBS9, BBS10, BBS12, and MKKS genes. In most cases, pathogenic and likely pathogenic variants were localized in BBS1, BBS10, and BBS7 genes; recurrent variants were also observed in these genes. Discussion The frequency of pathogenic and likely pathogenic variants in the BBS1 and BBS10 genes among Russian patients matches the research data in other countries. The frequency of pathogenic variants in the BBS7 gene is about 1.5%-2% of patients with Bardet-Biedl syndrome, while in the cohort of Russian patients, the fraction is 24%. In addition, the recurrent pathogenic variant c.1967_1968delinsC was detected in the BBS7 gene. The higher frequency of this variant in the Russian population, as well as the lack of association of this pathogenic variant with Bardet-Biedl syndrome in other populations, suggests that the variant c.1967_1968delinsC in the BBS7 gene is major and has a founder effect in the Russian population. Results provided in this article show the significant role of pathogenic variants in the BBS7 gene for patients with Bardet-Biedl syndrome in the Russian population.
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Affiliation(s)
- M. Orlova
- DNA-diagnostics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - P. Gundorova
- University Children’s Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - V. Kadnikova
- DNA-diagnostics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - A. Polyakov
- DNA-diagnostics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
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Niederlova V, Modrak M, Tsyklauri O, Huranova M, Stepanek O. Meta-analysis of genotype-phenotype associations in Bardet-Biedl syndrome uncovers differences among causative genes. Hum Mutat 2019; 40:2068-2087. [PMID: 31283077 DOI: 10.1002/humu.23862] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/17/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022]
Abstract
Bardet-Biedl syndrome (BBS) is a recessive genetic disease causing multiple organ anomalies. Most patients carry mutations in genes encoding for the subunits of the BBSome, an octameric ciliary transport complex, or accessory proteins involved in the BBSome assembly or function. BBS proteins have been extensively studied using in vitro, cellular, and animal models. However, the molecular functions of particular BBS proteins and the etiology of the BBS symptoms are still largely elusive. In this study, we applied a meta-analysis approach to study the genotype-phenotype association in humans using our database of all reported BBS patients. The analysis revealed that the identity of the causative gene and the character of the mutation partially predict the clinical outcome of the disease. Besides their potential use for clinical prognosis, our analysis revealed functional differences of particular BBS genes in humans. Core BBSome subunits BBS2, BBS7, and BBS9 manifest as more critical for the function and development of kidneys than peripheral subunits BBS1, BBS4, and BBS8/TTC8, suggesting that incomplete BBSome retains residual function at least in the kidney.
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Affiliation(s)
- Veronika Niederlova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Modrak
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Oksana Tsyklauri
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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Exome-based search for recurrent disease-causing alleles in Russian population. Eur J Med Genet 2019; 62:103656. [DOI: 10.1016/j.ejmg.2019.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/12/2019] [Accepted: 04/21/2019] [Indexed: 11/18/2022]
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Shen T, Gao JM, Shou T, Li L, Zhang JP, Zhao Q, Yan XM. Identification of a homozygous BBS7 frameshift mutation in two (related) Chinese Miao families with Bardet-Biedl Syndrome. J Chin Med Assoc 2019; 82:110-114. [PMID: 30839500 DOI: 10.1097/jcma.0000000000000011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Bardet-Biedl Syndrome (BBS) is a genetically heterogeneous autosomal recessive disorder with a wide spectrum of clinical features. To date, mutations in 21 different genes (BBS1-21) have been identified as causing isolated or complex BBS phenotypes. In this report, we present three Chinese Miao ethnic patients who were diagnosed with BBS on the basis of characteristic clinical features and investigated the exsome of these patients. METHODS To evaluate disease genes, the Agilent SureSelect system and Illumina HiSeq 2000 platform for whole exome enrichment and sequencing (WES) were used on the proband and her mother. Variants that fit a recessive model of inheritance only were compared and filtered using public databases. Variants detected by exome sequencing were validated by Sanger sequencing. A total of 981 phenotypically normal subjects were enrolled as control data set. RESULTS A frameshift homozygous germline mutation in BBS7 was detected by WES and identified by Sanger sequencing in affected individuals. This mutation was predicted to result in premature termination of exon5 (c.389_390delAC, p.Asn130ThrfsX3; RefSeq NM_176824.2) and lead to a 133 amino acid truncated protein. The inheritance patterns in the families are consistent with autosomal recessive inheritance, and no such homozygous mutation was found in the other 981 controls. CONCLUSION This mutation has not yet been described in any reported literature, and this is the first report on BBS7 mutation in Chinese Miao families with BBS phenotypes.
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Affiliation(s)
- Tao Shen
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Jian-Mei Gao
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Tao Shou
- Oncology Department, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Li Li
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Jin-Ping Zhang
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Qian Zhao
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Xin-Min Yan
- Institute of Basic and Clinical Medicine, Key laboratory of Clinical Virology, Key Laboratory for Birth Defects and Genetic Diseases, the First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
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Genetics of body fat mass and related traits in a pig population selected for leanness. Sci Rep 2017; 7:9118. [PMID: 28831160 PMCID: PMC5567295 DOI: 10.1038/s41598-017-08961-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/17/2017] [Indexed: 12/21/2022] Open
Abstract
Obesity is characterized as the excessive accumulation of body fat and has a complex genetic foundation in humans including monogenic high-risk mutations and polygenic contributions. Domestic pigs represent a valuable model on an obesity-promoting high-caloric diet while constantly evaluated for body characteristics. As such, we investigated the genetics of obesity-related traits, comprising subcutaneous fat thickness, lean mass percentage, and growth rate, in a pig population. We conducted genome-wide association analyses using an integrative approach of single-marker regression models and multi-marker Bayesian analyses. Thus, we identified 30 genomic regions distributed over 14 different chromosomes contributing to the variation in obesity-related traits. In these regions, we validated the association of four candidate genes that are functionally connected to the regulation of appetite, processes of adipogenesis, and extracellular matrix formation. Our findings revealed fundamental genetic factors which deserves closer attention regarding their roles in the etiology of obesity.
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Qi Z, Shen Y, Fu Q, Li W, Yang W, Xu W, Chu P, Zhang Y, Wang H. Whole-exome sequencing identified compound heterozygous variants in MMKS in a Chinese pedigree with Bardet-Biedl syndrome. SCIENCE CHINA-LIFE SCIENCES 2017. [PMID: 28624958 DOI: 10.1007/s11427-017-9085-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bardet-Biedl syndrome (BBS) is a genetically heterogeneous disorder characterized by retinal dystrophy, polydactyly, obesity, developmental delay, and renal defects. At least 21 candidate BBS-associated genes (BBS1-19, NPHP1, and IFT172) have previously been identified, and all of them play important roles in ciliary function. Here, we collected a BBS pedigree with four members and performed whole-exome sequencing on the proband. The variants were analyzed and evaluated to confirm their pathogenicity. We found compound heterozygous variants (c.1192C>T, p.Q398* and c.1175C>T, p.T392M) in MKKS in both the siblings, and these were likely to be pathogenic variants. We also found a missense variant (c.2029G>C, p.E677Q) in NPHP1 and a missense variant (c.2470C>T, p.R824C) in BBS9 in the proband only, which are variants of uncertain significance. The compound heterozygous variants were probably responsible for the BBS phenotype in this Chinese pedigree and the missense mutations in NPHP1 and BBS9 might contribute to the mutation load.
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Affiliation(s)
- Zhan Qi
- Beijing Key Laboratory for Genetics of Birth Defects, Key Laboratory of Major Diseases in Children of Ministry of Education, Center for Medical Genetics, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Ying Shen
- Beijing Key Laboratory for Chronic Renal Disease and Blood Purification, Key Laboratory of Major Diseases in Children of Ministry of Education; Nephrology Department, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Qian Fu
- Beijing Key Laboratory for Chronic Renal Disease and Blood Purification, Key Laboratory of Major Diseases in Children of Ministry of Education; Nephrology Department, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Key Laboratory of Major Diseases in Children of Ministry of Education, Center for Medical Genetics, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wei Yang
- Beijing Key Laboratory for Genetics of Birth Defects, Key Laboratory of Major Diseases in Children of Ministry of Education, Center for Medical Genetics, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wenshan Xu
- Beijing Key Laboratory for Genetics of Birth Defects, Key Laboratory of Major Diseases in Children of Ministry of Education, Center for Medical Genetics, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Ping Chu
- Beijing Key Laboratory for Pediatric Disease of Otolaryngology, Head and Neck Surgery, Key Laboratory of Major Diseases in Children of Ministry of Education; Beijing Pediatric Research Institute; Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Yaxin Zhang
- School of Pediatrics, Capital Medical University, Beijing, 100069, China
| | - Hui Wang
- Beijing Key Laboratory for Chronic Renal Disease and Blood Purification, Key Laboratory of Major Diseases in Children of Ministry of Education; Nephrology Department, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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Abstract
Bardet-Biedl syndrome (BBS) is a rare autosomal recessive genetic disorder. It is characterized by heterogeneous clinical manifestations including primary features of the disease (rod-cone dystrophy, polydactyly, obesity, genital abnormalities, renal defects, and learning difficulties) and secondary BBS characteristics (developmental delay, speech deficit, brachydactyly or syndactyly, dental defects, ataxia or poor coordination, olfactory deficit, diabetes mellitus, congenital heart disease, etc.); most of these symptoms may not be present at birth but appear and progressively worsen during the first and second decades of life. At least 20 BBS genes have already been identified, and all of them are involved in primary cilia functioning. Genetic diagnosis of BBS is complicated due to lack of gene-specific disease symptoms; however, it is gradually becoming more accessible with the invention of multigene sequencing technologies. Clinical management of BBS is largely limited to a symptomatic treatment. Mouse experiments demonstrate that the most debilitating complication of BBS, blindness, can be rescued by topical gene therapy. There is a published case report describing the delay of BBS symptoms by nutritional compensation of the disease-related biochemical deficiencies. Progress in DNA testing technologies is likely to rapidly resolve all limitations in BBS diagnosis; however, much slower improvement is expected with regard to BBS treatment.
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Affiliation(s)
- Evgeny N Suspitsin
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia; St. Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Evgeny N Imyanitov
- N.N. Petrov Institute of Oncology, St. Petersburg, Russia; St. Petersburg Pediatric Medical University, St. Petersburg, Russia; I.I. Mechnikov North-Western Medical University, St. Petersburg, Russia; St. Petersburg State University, St. Petersburg, Russia
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Chiang J(PW, Gorin MB. Challenges confronting precision medicine in the context of inherited retinal disorders. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1152159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Sokolenko AP, Suspitsin EN, Kuligina ES, Bizin IV, Frishman D, Imyanitov EN. Identification of novel hereditary cancer genes by whole exome sequencing. Cancer Lett 2015; 369:274-88. [PMID: 26427841 DOI: 10.1016/j.canlet.2015.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 02/09/2023]
Abstract
Whole exome sequencing (WES) provides a powerful tool for medical genetic research. Several dozens of WES studies involving patients with hereditary cancer syndromes have already been reported. WES led to breakthrough in understanding of the genetic basis of some exceptionally rare syndromes; for example, identification of germ-line SMARCA4 mutations in patients with ovarian hypercalcemic small cell carcinomas indeed explains a noticeable share of familial aggregation of this disease. However, studies on common cancer types turned out to be more difficult. In particular, there is almost a dozen of reports describing WES analysis of breast cancer patients, but none of them yet succeeded to reveal a gene responsible for the significant share of missing heritability. Virtually all components of WES studies require substantial improvement, e.g. technical performance of WES, interpretation of WES results, mode of patient selection, etc. Most of contemporary investigations focus on genes with autosomal dominant mechanism of inheritance; however, recessive and oligogenic models of transmission of cancer susceptibility also need to be considered. It is expected that the list of medically relevant tumor-predisposing genes will be rapidly expanding in the next few years.
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Affiliation(s)
- Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny N Suspitsin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Ekatherina Sh Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
| | - Ilya V Bizin
- Laboratory of Bioinformatics, RASA Research Center, St.-Petersburg State Polytechnical University, St.-Petersburg 195251, Russia
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, TU Muenchen, Freising 85354, Germany; Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Neuherberg 85764, Germany
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia; Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg 191015, Russia; Department of Oncology, St.-Petersburg State University, St.-Petersburg 199034, Russia.
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