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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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2
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Papingi D, Bierhals T, Volk AE, Kutsche M, Paul K, Herget T. A novel TTC26 variant in a patient with hexadactyly, pituitary stalk interruption, hepatopathy, nephropathy, and bilateral lip-palate cleft: A case report and expansion of the phenotype. Am J Med Genet A 2024; 194:e63515. [PMID: 38135897 DOI: 10.1002/ajmg.a.63515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/29/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023]
Abstract
Biallelic pathogenic variants in the TTC26 gene are known to cause BRENS (biliary, renal, neurological, skeletal) syndrome, an ultra-rare autosomal recessive condition with only few patients published to date. BRENS syndrome is characterized by hexadactyly, severe neonatal cholestasis, and involvement of the brain, heart, and kidney, however the full phenotypic and genotypic spectrum is unknown. Here, we report on a previously undescribed homozygous intronic TTC26 variant (c.1006-5 T > C) in a patient showing some of the known TTC26-associated features like hexadactyly, hypopituitarism, hepatopathy, nephropathy, and congenital heart defect. Moreover, he presented with a suspected unilateral hearing loss and bilateral cleft lip-palate. The variant is considered to affect correct splicing by the loss of the canonical acceptor splice site and activation of a cryptic acceptor splice site. Hereby, our patient represents one additional patient with BRENS syndrome carrying a previously unreported TTC26 variant. Furthermore, we confirm the involvement of the pituitary gland to be a common clinical feature of the syndrome and broaden the clinical spectrum of TTC26 ciliopathy to include facial clefts and a probable hearing involvement.
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Affiliation(s)
- Dzhoy Papingi
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander E Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kevin Paul
- University Children's Hospital, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Bouzidi A, Charoute H, Charif M, Amalou G, Kandil M, Barakat A, Lenaers G. Clinical and genetic spectrums of 413 North African families with inherited retinal dystrophies and optic neuropathies. Orphanet J Rare Dis 2022; 17:197. [PMID: 35551639 PMCID: PMC9097391 DOI: 10.1186/s13023-022-02340-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/26/2022] [Indexed: 11/26/2022] Open
Abstract
Background Inherited retinal dystrophies (IRD) and optic neuropathies (ION) are the two major causes world-wide of early visual impairment, frequently leading to legal blindness. These two groups of pathologies are highly heterogeneous and require combined clinical and molecular diagnoses to be securely identified. Exact epidemiological studies are lacking in North Africa, and genetic studies of IRD and ION individuals are often limited to case reports or to some families that migrated to the rest of the world. In order to improve the knowledge of their clinical and genetic spectrums in North Africa, we reviewed published data, to illustrate the most prevalent pathologies, genes and mutations encountered in this geographical region, extending from Morocco to Egypt, comprising 200 million inhabitants. Main body We compiled data from 413 families with IRD or ION together with their available molecular diagnosis. The proportion of IRD represents 82.8% of index cases, while ION accounted for 17.8%. Non-syndromic IRD were more frequent than syndromic ones, with photoreceptor alterations being the main cause of non-syndromic IRD, represented by retinitis pigmentosa, Leber congenital amaurosis, and cone-rod dystrophies, while ciliopathies constitute the major part of syndromic-IRD, in which the Usher and Bardet Biedl syndromes occupy 41.2% and 31.1%, respectively. We identified 71 ION families, 84.5% with a syndromic presentation, while surprisingly, non-syndromic ION are scarcely reported, with only 11 families with autosomal recessive optic atrophies related to OPA7 and OPA10 variants, or with the mitochondrial related Leber ION. Overall, consanguinity is a major cause of these diseases within North African countries, as 76.1% of IRD and 78.8% of ION investigated families were consanguineous, explaining the high rate of autosomal recessive inheritance pattern compared to the dominant one. In addition, we identified many founder mutations in small endogamous communities. Short conclusion As both IRD and ION diseases constitute a real public health burden, their under-diagnosis in North Africa due to the absence of physicians trained to the identification of inherited ophthalmologic presentations, together with the scarcity of tools for the molecular diagnosis represent major political, economic and health challenges for the future, to first establish accurate clinical diagnoses and then treat patients with the emergent therapies. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02340-7.
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Affiliation(s)
- Aymane Bouzidi
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, CHU d'Angers, CNRS 6015, Université d'Angers, 49933, Angers, France.,Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.,Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaïb Doukkali University, Eljadida, Morocco
| | - Hicham Charoute
- Research Unit of Epidemiology, Biostatistics and Bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Majida Charif
- Genetics, and Immuno-Cell Therapy Team, Mohamed First University, Oujda, Morocco
| | - Ghita Amalou
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, CHU d'Angers, CNRS 6015, Université d'Angers, 49933, Angers, France.,Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.,Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaïb Doukkali University, Eljadida, Morocco
| | - Mostafa Kandil
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaïb Doukkali University, Eljadida, Morocco
| | - Abdelhamid Barakat
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Guy Lenaers
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, CHU d'Angers, CNRS 6015, Université d'Angers, 49933, Angers, France. .,Service de Neurologie, CHU d'Angers, Angers, France.
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4
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Deletion in the Bardet-Biedl Syndrome Gene TTC8 Results in a Syndromic Retinal Degeneration in Dogs. Genes (Basel) 2020; 11:genes11091090. [PMID: 32962042 PMCID: PMC7565673 DOI: 10.3390/genes11091090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
In golden retriever dogs, a 1 bp deletion in the canine TTC8 gene has been shown to cause progressive retinal atrophy (PRA), the canine equivalent of retinitis pigmentosa. In humans, TTC8 is also implicated in Bardet–Biedl syndrome (BBS). To investigate if the affected dogs only exhibit a non-syndromic PRA or develop a syndromic ciliopathy similar to human BBS, we recruited 10 affected dogs to the study. The progression of PRA for two of the dogs was followed for 2 years, and a rigorous clinical characterization allowed a careful comparison with primary and secondary characteristics of human BBS. In addition to PRA, the dogs showed a spectrum of clinical and morphological signs similar to primary and secondary characteristics of human BBS patients, such as obesity, renal anomalies, sperm defects, and anosmia. We used Oxford Nanopore long-read cDNA sequencing to characterize retinal full-length TTC8 transcripts in affected and non-affected dogs, the results of which suggest that three isoforms are transcribed in the retina, and the 1 bp deletion is a loss-of-function mutation, resulting in a canine form of Bardet–Biedl syndrome with heterogeneous clinical signs.
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Jaffal L, Joumaa WH, Assi A, Helou C, Cherfan G, Zibara K, Audo I, Zeitz C, El Shamieh S. Next Generation Sequencing Identifies Five Novel Mutations in Lebanese Patients with Bardet-Biedl and Usher Syndromes. Genes (Basel) 2019; 10:genes10121047. [PMID: 31888296 PMCID: PMC6947157 DOI: 10.3390/genes10121047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 01/15/2023] Open
Abstract
AIM To identify disease-causing mutations in four Lebanese families: three families with Bardet-Biedl and one family with Usher syndrome (BBS and USH respectively), using next generation sequencing (NGS). METHODS We applied targeted NGS in two families and whole exome sequencing (WES) in two other families. Pathogenicity of candidate mutations was evaluated according to frequency, conservation, in silico prediction tools, segregation with disease, and compatibility with inheritance pattern. The presence of pathogenic variants was confirmed via Sanger sequencing followed by segregation analysis. RESULTS Most likely disease-causing mutations were identified in all included patients. In BBS patients, we found (M1): c.2258A > T, p. (Glu753Val) in BBS9, (M2): c.68T > C; p. (Leu23Pro) in ARL6, (M3): c.265_266delTT; p. (Leu89Valfs*11) and (M4): c.880T > G; p. (Tyr294Asp) in BBS12. A previously known variant (M5): c.551A > G; p. (Asp184Ser) was also detected in BBS5. In the USH patient, we found (M6): c.188A > C, p. (Tyr63Ser) in CLRN1. M2, M3, M4, and M6 were novel. All of the candidate mutations were shown to be likely disease-causing through our bioinformatic analysis. They also segregated with the corresponding phenotype in available family members. CONCLUSION This study expanded the mutational spectrum and showed the genetic diversity of BBS and USH. It also spotlighted the efficiency of NGS techniques in revealing mutations underlying clinically and genetically heterogeneous disorders.
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Affiliation(s)
- Lama Jaffal
- Department of Biological and Environmental Sciences, Faculty of Science, Beirut Arab University, Debbieh 1107 2809, Lebanon;
| | - Wissam H Joumaa
- Rammal Hassan Rammal Research Laboratory, Physiotoxicity (PhyTox), Faculty of Sciences, Lebanese University, Nabatieh 1700, Lebanon;
| | - Alexandre Assi
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut 1106, Lebanon; (A.A.); (C.H.); (G.C.)
| | - Charles Helou
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut 1106, Lebanon; (A.A.); (C.H.); (G.C.)
| | - George Cherfan
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut 1106, Lebanon; (A.A.); (C.H.); (G.C.)
| | - Kazem Zibara
- ER045, PRASE, DSST, Lebanese University, Beirut 1700, Lebanon;
- Biology Department, Faculty of Sciences-I, Lebanese University, Beirut 1700, Lebanon
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (I.A.); (C.Z.)
- CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, 75012 Paris, France
- University College London Institute of Ophthalmology, London EC1V 9EL, UK
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (I.A.); (C.Z.)
| | - Said El Shamieh
- Rammal Hassan Rammal Research Laboratory, Physiotoxicity (PhyTox), Faculty of Sciences, Lebanese University, Nabatieh 1700, Lebanon;
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut 1107 2809, Lebanon
- Correspondence:
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6
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Parivesh A, Barseghyan H, Délot E, Vilain E. Translating genomics to the clinical diagnosis of disorders/differences of sex development. Curr Top Dev Biol 2019; 134:317-375. [PMID: 30999980 PMCID: PMC7382024 DOI: 10.1016/bs.ctdb.2019.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The medical and psychosocial challenges faced by patients living with Disorders/Differences of Sex Development (DSD) and their families can be alleviated by a rapid and accurate diagnostic process. Clinical diagnosis of DSD is limited by a lack of standardization of anatomical and endocrine phenotyping and genetic testing, as well as poor genotype/phenotype correlation. Historically, DSD genes have been identified through positional cloning of disease-associated variants segregating in families and validation of candidates in animal and in vitro modeling of variant pathogenicity. Owing to the complexity of conditions grouped under DSD, genome-wide scanning methods are better suited for identifying disease causing gene variant(s) and providing a clinical diagnosis. Here, we review a number of established genomic tools (karyotyping, chromosomal microarrays and exome sequencing) used in clinic for DSD diagnosis, as well as emerging genomic technologies such as whole-genome (short-read) sequencing, long-read sequencing, and optical mapping used for novel DSD gene discovery. These, together with gene expression and epigenetic studies can potentiate the clinical diagnosis of DSD diagnostic rates and enhance the outcomes for patients and families.
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Affiliation(s)
- Abhinav Parivesh
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States; Department of Genomics and Precision Medicine, The George Washington University, Washington, DC, United States
| | - Emmanuèle Délot
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States; Department of Genomics and Precision Medicine, The George Washington University, Washington, DC, United States.
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States; Department of Genomics and Precision Medicine, The George Washington University, Washington, DC, United States.
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7
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Sato S, Morimoto T, Hotta K, Fujikado T, Nishida K. A novel compound heterozygous mutation in TTC8 identified in a Japanese patient. Hum Genome Var 2019; 6:14. [PMID: 30886724 PMCID: PMC6418288 DOI: 10.1038/s41439-019-0045-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 12/24/2018] [Accepted: 01/10/2019] [Indexed: 12/23/2022] Open
Abstract
Bardet-Biedl syndrome (BBS), characterized by rod-cone dystrophy, postaxial polydactyly, central obesity, hypogonadism, renal abnormalities, and mental retardation, is a rare autosomal recessive disorder. To date, 21 causative genes have been reported. Here we describe a Japanese BBS patient with a novel compound heterozygous mutation in TTC8. To the best of our knowledge, this is the first description of a BBS patient with a mutation in the TTC8 gene in Japan.
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Affiliation(s)
- Shigeru Sato
- 1Department of Ophthalmology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takeshi Morimoto
- 1Department of Ophthalmology, Osaka University Graduate School of Medicine, Osaka, Japan.,2Department of Applied Visual Science, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kikuko Hotta
- 3Department of Medical Innovation, Osaka University Hospital, Osaka, Japan
| | - Takashi Fujikado
- 1Department of Ophthalmology, Osaka University Graduate School of Medicine, Osaka, Japan.,2Department of Applied Visual Science, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kohji Nishida
- 1Department of Ophthalmology, Osaka University Graduate School of Medicine, Osaka, Japan
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8
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Sheffield ID, McGee MA, Glenn SJ, Baek DY, Coleman JM, Dorius BK, Williams C, Rose BJ, Sanchez AE, Goodman MA, Daines JM, Eggett DL, Sheffield VC, Suli A, Kooyman DL. Osteoarthritis-Like Changes in Bardet-Biedl Syndrome Mutant Ciliopathy Mice ( Bbs1M390R/M390R): Evidence for a Role of Primary Cilia in Cartilage Homeostasis and Regulation of Inflammation. Front Physiol 2018; 9:708. [PMID: 29971011 PMCID: PMC6018413 DOI: 10.3389/fphys.2018.00708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 05/22/2018] [Indexed: 12/22/2022] Open
Abstract
Osteoarthritis (OA) is a debilitating inflammation related disease characterized by joint pain and effusion, loss of mobility, and deformity that may result in functional joint failure and significant impact on quality of life. Once thought of as a simple “wear and tear” disease, it is now widely recognized that OA has a considerable metabolic component and is related to chronic inflammation. Defects associated with primary cilia have been shown to be cause OA-like changes in Bardet–Biedl mice. We examined the role of dysfunctional primary cilia in OA in mice through the regulation of the previously identified degradative and pro-inflammatory molecular pathways common to OA. We observed an increase in the presence of pro-inflammatory markers TGFβ-1 and HTRA1 as well as cartilage destructive protease MMP-13 but a decrease in DDR-2. We observed a morphological difference in cartilage thickness in Bbs1M390R/M390R mice compared to wild type (WT). We did not observe any difference in OARSI or Mankin scores between WT and Bbs1M390R/M390R mice. Primary cilia appear to be involved in the upregulation of biomarkers, including pro-inflammatory markers common to OA.
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Affiliation(s)
- Isaac D Sheffield
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Mercedes A McGee
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Steven J Glenn
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Da Young Baek
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Joshua M Coleman
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Bradley K Dorius
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Channing Williams
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Brandon J Rose
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Anthony E Sanchez
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Michael A Goodman
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - John M Daines
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Dennis L Eggett
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - Val C Sheffield
- Departments of Pediatrics and Ophthalmology, University of Iowa, Iowa City, IA, United States
| | - Arminda Suli
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
| | - David L Kooyman
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, United States
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9
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Geets E, Meuwissen MEC, Van Hul W. Clinical, molecular genetics and therapeutic aspects of syndromic obesity. Clin Genet 2018; 95:23-40. [PMID: 29700824 DOI: 10.1111/cge.13367] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 12/13/2022]
Abstract
Obesity has become a major health problem worldwide. To date, more than 25 different syndromic forms of obesity are known in which one (monogenic) or multiple (polygenic) genes are involved. This review gives an overview of these forms and focuses more in detail on 6 syndromes: Prader Willi Syndrome and Prader Willi like phenotype, Bardet Biedl Syndrome, Alström Syndrome, Wilms tumor, Aniridia, Genitourinary malformations and mental Retardation syndrome and 16p11.2 (micro)deletions. Years of research provided plenty of information on the molecular genetics of these disorders and the obesity phenotype leading to a more individualized treatment of the symptoms, however, many questions still remain unanswered. As these obesity syndromes have different signs and symptoms in common, it makes it difficult to accurately diagnose patients which may result in inappropriate treatment of the disease. Therefore, the big challenge for clinicians and scientists is to more clearly differentiate all syndromic forms of obesity to provide conclusive genetic explanations and eventually deliver accurate genetic counseling and treatment. In addition, further delineation of the (functions of the) underlying genes with the use of array- or next-generation sequencing-based technology will be helpful to unravel the mechanisms of energy metabolism in the general population.
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Affiliation(s)
- E Geets
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - M E C Meuwissen
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - W Van Hul
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
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10
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Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M, Topper S. Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Genet Med 2017; 19:1105-1117. [PMID: 28492532 PMCID: PMC5632818 DOI: 10.1038/gim.2017.37] [Citation(s) in RCA: 478] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/28/2017] [Indexed: 01/05/2023] Open
Abstract
PurposeThe 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines were a major step toward establishing a common framework for variant classification. In practice, however, several aspects of the guidelines lack specificity, are subject to varied interpretations, or fail to capture relevant aspects of clinical molecular genetics. A simple implementation of the guidelines in their current form is insufficient for consistent and comprehensive variant classification.MethodsWe undertook an iterative process of refining the ACMG-AMP guidelines. We used the guidelines to classify more than 40,000 clinically observed variants, assessed the outcome, and refined the classification criteria to capture exceptions and edge cases. During this process, the criteria evolved through eight major and minor revisions.ResultsOur implementation: (i) separated ambiguous ACMG-AMP criteria into a set of discrete but related rules with refined weights; (ii) grouped certain criteria to protect against the overcounting of conceptually related evidence; and (iii) replaced the "clinical criteria" style of the guidelines with additive, semiquantitative criteria.ConclusionSherloc builds on the strong framework of 33 rules established by the ACMG-AMP guidelines and introduces 108 detailed refinements, which support a more consistent and transparent approach to variant classification.
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Affiliation(s)
- Keith Nykamp
- Invitae Corporation, San Francisco, California, USA
| | | | | | - John Garcia
- Invitae Corporation, San Francisco, California, USA
| | | | - Yuan-Yuan Ho
- Invitae Corporation, San Francisco, California, USA
| | | | - Nila Patil
- Invitae Corporation, San Francisco, California, USA
| | | | | | | | - Scott Topper
- Invitae Corporation, San Francisco, California, USA
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11
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Khan S, Muhammad N, Khan M, Kamal A, Rehman Z, Khan S. Genetics of human Bardet-Biedl syndrome, an updates. Clin Genet 2016; 90:3-15. [DOI: 10.1111/cge.12737] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 12/21/2015] [Accepted: 01/03/2016] [Indexed: 12/22/2022]
Affiliation(s)
- S.A. Khan
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - N. Muhammad
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - M.A. Khan
- Gomal Centre of Biochemistry and Biotechnology; Gomal University; Khyber Pakhtunkhwa Pakistan
- Genomic Core Facility; Interim Translational Research Institute; Doha Qatar
| | - A. Kamal
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - Z.U. Rehman
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - S. Khan
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
- Genomic Core Facility; Interim Translational Research Institute; Doha Qatar
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12
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Alternative Splicing Shapes the Phenotype of a Mutation in BBS8 To Cause Nonsyndromic Retinitis Pigmentosa. Mol Cell Biol 2015; 35:1860-70. [PMID: 25776555 DOI: 10.1128/mcb.00040-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/10/2015] [Indexed: 01/27/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a genetic disorder affecting multiple systems and organs in the body. Several mutations in genes associated with BBS affect only photoreceptor cells and cause nonsyndromic retinitis pigmentosa (RP), raising the issue of why certain mutations manifest as a systemic disorder whereas other changes in the same gene affect only a specific cell type. Here, we show that cell-type-specific alternative splicing is responsible for confining the phenotype of the A-to-G substitution in the 3' splice site of BBS8 exon 2A (IVS1-2A>G mutation) in the BBS8 gene to photoreceptor cells. The IVS1-2A>G mutation leads to missplicing of BBS8 exon 2A, producing a frameshift in the BBS8 reading frame and thus eliminating the protein specifically in photoreceptor cells. Cell types other than photoreceptors skip exon 2A from the mature BBS8 transcript, which renders them immune to the mutation. We also show that the splicing of Bbs8 exon 2A in photoreceptors is directed exclusively by redundant splicing enhancers located in the adjacent introns. These intronic sequences are sufficient for photoreceptor-cell-specific splicing of heterologous exons, including an exon with a randomized sequence.
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Downs LM, Wallin-Håkansson B, Bergström T, Mellersh CS. A novel mutation in TTC8 is associated with progressive retinal atrophy in the golden retriever. Canine Genet Epidemiol 2014; 1:4. [PMID: 26401321 PMCID: PMC4574394 DOI: 10.1186/2052-6687-1-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/14/2014] [Indexed: 01/19/2023] Open
Abstract
Background Generalized progressive retinal atrophy (PRA) is a group of inherited eye diseases characterised by progressive retinal degeneration that ultimately leads to blindness in dogs. To date, more than 20 different mutations causing canine-PRA have been described and several breeds including the Golden Retriever are affected by more than one form of PRA. Genetically distinct forms of PRA may have different clinical characteristics such as rate of progression and age of onset. However, in many instances the phenotype of different forms of PRA cannot be distinguished at the basic clinical level achieved during routine ophthalmoscopic examination. Mutations in two distinct genes have been reported to cause PRA in Golden Retrievers (prcd-PRA and GR_PRA1), but for approximately 39% of cases in this breed the causal mutation remains unknown. Results A genome-wide association study of 10 PRA cases and 16 controls identified an association on chromosome 8 not previously associated with PRA (praw = 1.30×10-6 and corrected with 100,000 permutations, pgenome = 0.148). Using haplotype analysis we defined a 737 kb critical region containing 6 genes. Two of the genes (TTC8 and SPATA7) have been associated with Retinitis Pigmentosa (RP) in humans. Using targeted next generation sequencing a single nucleotide deletion was identified in exon 8 of the TTC8 gene of affected Golden Retrievers. The frame shift mutation was predicted to cause a premature termination codon. In a larger cohort, this mutation, TTC8c.669delA, segregates correctly in 22 out of 29 cases tested (75.9%). Of the PRA controls none are homozygous for the mutation, only 3.5% carry the mutation and 96.5% are homozygous wildtype. Conclusions Our results show that PRA is genetically heterogeneous in one of the world’s numerically largest breeds, the Golden Retriever, and is caused by multiple, distinct mutations. Here we discuss the mutation that causes a form of PRA, that we have termed PRA2, that accounts for approximately 30% of PRA cases in the breed. The genetic explanation for approximately 9% of cases remains to be identified. PRA2 is a naturally occurring animal model for Retinitis Pigmentosa, and potentially Bardet-Biedl Syndrome. Electronic supplementary material The online version of this article (doi:10.1186/2052-6687-1-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Louise M Downs
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, UK
| | - Berit Wallin-Håkansson
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, UK ; The Swedish Kennel Club (SKK), Stockholm, Sweden
| | - Tomas Bergström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Cathryn S Mellersh
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, UK
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Diagnosis of bardet-biedl syndrome in consecutive pregnancies affected with echogenic kidneys and polydactyly in a consanguineous couple. Case Rep Genet 2013; 2013:159143. [PMID: 23533844 PMCID: PMC3603615 DOI: 10.1155/2013/159143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 02/03/2013] [Indexed: 11/18/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is an autosomal recessive ciliopathic human genetic disorder with variable expression that is difficult to diagnose in pregnancy without known risk factors. Homozygosity testing has been shown to be a useful tool in identifying BBS mutations and candidate genes in affected individuals. We present the first case of prenatal diagnosis of BBS in consecutive pregnancies aided by homozygosity testing via SNP microarray analysis. This case demonstrates a novel approach to the evaluation of recurrent echogenic kidneys in consanguineous couple with no significant family history.
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Casey J, Kawaguchi R, Morrissey M, Sun H, McGettigan P, Nielsen JE, Conroy J, Regan R, Kenny E, Cormican P, Morris DW, Tormey P, Chróinín MN, Kennedy BN, Lynch S, Green A, Ennis S. First implication of STRA6 mutations in isolated anophthalmia, microphthalmia, and coloboma: a new dimension to the STRA6 phenotype. Hum Mutat 2011; 32:1417-26. [PMID: 21901792 DOI: 10.1002/humu.21590] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 07/25/2011] [Indexed: 11/11/2022]
Abstract
Microphthalmia, anophthalmia, and coloboma (MAC) are structural congenital eye malformations that cause a significant proportion of childhood visual impairments. Several disease genes have been identified but do not account for all MAC cases, suggesting that additional risk loci exist. We used single nucleotide polymorphism (SNP) homozygosity mapping (HM) and targeted next-generation sequencing to identify the causative mutation for autosomal recessive isolated colobomatous microanophthalmia (MCOPCB) in a consanguineous Irish Traveller family. We identified a double-nucleotide polymorphism (g.1157G>A and g.1156G>A; p.G304K) in STRA6 that was homozygous in all of the MCOPCB patients. The STRA6 p.G304K mutation was subsequently detected in additional MCOPCB patients, including one individual with Matthew-Wood syndrome (MWS; MCOPS9). STRA6 encodes a transmembrane receptor involved in vitamin A uptake, a process essential to eye development and growth. We have shown that the G304K mutant STRA6 protein is mislocalized and has severely reduced vitamin A uptake activity. Furthermore, we reproduced the MCOPCB phenotype in a zebrafish disease model by inhibiting retinoic acid (RA) synthesis, suggesting that diminished RA levels account for the eye malformations in STRA6 p.G304K patients. The current study demonstrates that STRA6 mutations can cause isolated eye malformations in addition to the congenital anomalies observed in MWS.
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Affiliation(s)
- Jillian Casey
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
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Molecular diagnosis reveals genetic heterogeneity for the overlapping MKKS and BBS phenotypes. Eur J Med Genet 2011; 54:157-60. [DOI: 10.1016/j.ejmg.2010.10.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 10/13/2010] [Indexed: 11/18/2022]
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Muller J, Stoetzel C, Vincent MC, Leitch CC, Laurier V, Danse JM, Hellé S, Marion V, Bennouna-Greene V, Vicaire S, Megarbane A, Kaplan J, Drouin-Garraud V, Hamdani M, Sigaudy S, Francannet C, Roume J, Bitoun P, Goldenberg A, Philip N, Odent S, Green J, Cossée M, Davis EE, Katsanis N, Bonneau D, Verloes A, Poch O, Mandel JL, Dollfus H. Identification of 28 novel mutations in the Bardet-Biedl syndrome genes: the burden of private mutations in an extensively heterogeneous disease. Hum Genet 2010; 127:583-93. [PMID: 20177705 DOI: 10.1007/s00439-010-0804-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 02/10/2010] [Indexed: 12/01/2022]
Abstract
Bardet-Biedl syndrome (BBS), an emblematic disease in the rapidly evolving field of ciliopathies, is characterized by pleiotropic clinical features and extensive genetic heterogeneity. To date, 14 BBS genes have been identified, 3 of which have been found mutated only in a single BBS family each (BBS11/TRIM32, BBS13/MKS1 and BBS14/MKS4/NPHP6). Previous reports of systematic mutation detection in large cohorts of BBS families (n > 90) have dealt only with a single gene, or at most small subsets of the known BBS genes. Here we report extensive analysis of a cohort of 174 BBS families for 12/14 genes, leading to the identification of 28 novel mutations. Two pathogenic mutations in a single gene have been found in 117 families, and a single heterozygous mutation in 17 families (of which 8 involve the BBS1 recurrent mutation, M390R). We confirm that BBS1 and BBS10 are the most frequently mutated genes, followed by BBS12. No mutations have been found in BBS11/TRIM32, the identification of which as a BBS gene only relies on a single missense mutation in a single consanguineous family. While a third variant allele has been observed in a few families, they are in most cases missenses of uncertain pathogenicity, contrasting with the type of mutations observed as two alleles in a single gene. We discuss the various strategies for diagnostic mutation detection, including homozygosity mapping and targeted arrays for the detection of previously reported mutations.
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Affiliation(s)
- Jean Muller
- Laboratoire de Diagnostic Génétique, CHU Strasbourg Nouvel Hôpital Civil, 1 place de l'Hôpital, 67000 Strasbourg, France.
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Hjortshøj TD, Grønskov K, Philp AR, Nishimura DY, Riise R, Sheffield VC, Rosenberg T, Brøndum-Nielsen K. Bardet-Biedl syndrome in Denmark-report of 13 novel sequence variations in six genes. Hum Mutat 2010; 31:429-36. [DOI: 10.1002/humu.21204] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Moulton HM, Moulton JD. Antisense Morpholino Oligomers and Their Peptide Conjugates. THERAPEUTIC OLIGONUCLEOTIDES 2008. [DOI: 10.1039/9781847558275-00043] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Hong M. Moulton
- AVI BioPharma Inc. 4575 SW Research Way Corvallis OR 97333 USA
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Hjortshøj TD, Grønskov K, Philp AR, Nishimura DY, Adeyemo A, Rotimi CN, Sheffield VC, Rosenberg T, Brøndum-Nielsen K. Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients. Am J Med Genet A 2008; 146A:517-20. [PMID: 18203199 PMCID: PMC2578871 DOI: 10.1002/ajmg.a.32136] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Abstract
The incomplete prediction of clinical phenotype from genotype in monogenic disorders assumes other complex mechanisms are responsible. Recent examples derived from well-known human diseases will be discussed in this review in the context of the roles of modifier genes, digenic and triallelic inheritance, and the consequence of imprinting and opposite transcripts in known human genetic disorders. Specifically, this review will focus on cystic fibrosis, Huntington's disease, sensory neural deafness due to Connexin gene mutations, Bardet-Biedl syndrome, and the Beckwith-Wiedemann syndrome as there is evidence that complex inheritance is responsible for at least part of the phenotypic variability that is not explainable by the genotype alone. This review is meant to extend and complement the other topics in this issue as the concept of atypical inheritance is explored in more detail.
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Affiliation(s)
- Andrea L Gropman
- Department of Neurology, Center for Neuroscience and Behavioral Medicine, Children's National Medical Center, The George Washington University, Washington, DC 20010, USA.
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Abstract
Hereditary degenerations of the human retina are genetically heterogeneous, with well over 100 genes implicated so far. This Seminar focuses on the subset of diseases called retinitis pigmentosa, in which patients typically lose night vision in adolescence, side vision in young adulthood, and central vision in later life because of progressive loss of rod and cone photoreceptor cells. Measures of retinal function, such as the electroretinogram, show that photoreceptor function is diminished generally many years before symptomic night blindness, visual-field scotomas, or decreased visual acuity arise. More than 45 genes for retinitis pigmentosa have been identified. These genes account for only about 60% of all patients; the remainder have defects in as yet unidentified genes. Findings of controlled trials indicate that nutritional interventions, including vitamin A palmitate and omega-3-rich fish, slow progression of disease in many patients. Imminent treatments for retinitis pigmentosa are greatly anticipated, especially for genetically defined subsets of patients, because of newly identified genes, growing knowledge of affected biochemical pathways, and development of animal models.
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Affiliation(s)
- Dyonne T Hartong
- Ocular Molecular Genetics Institute, Harvard Medical School, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114, USA
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