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Scheidecker S, Hull S, Perdomo Y, Studer F, Pelletier V, Muller J, Stoetzel C, Schaefer E, Defoort-Dhellemmes S, Drumare I, Holder GE, Hamel CP, Webster AR, Moore AT, Puech B, Dollfus HJ. Predominantly Cone-System Dysfunction as Rare Form of Retinal Degeneration in Patients With Molecularly Confirmed Bardet-Biedl Syndrome. Am J Ophthalmol 2015; 160:364-372.e1. [PMID: 25982971 DOI: 10.1016/j.ajo.2015.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 02/05/2023]
Abstract
PURPOSE To describe a series of patients with Bardet-Biedl syndrome (BBS) and predominantly retinal cone dysfunction, a previously only rarely reported association. DESIGN Retrospective observational case series. METHODS Seven patients with clinically proven Bardet-Biedl syndrome had undergone detailed ocular phenotyping, which included fundus examination, Goldmann visual fields, fundus autofluorescence imaging (FAF), optical coherence tomography (OCT), and electroretinography (ERG). Mutational screening in the BBS genes was performed either by direct Sanger sequencing or targeted next-generation sequencing. RESULTS All 7 patients had proven BBS mutations; 1 had a cone dystrophy phenotype on ERG and 6 had a cone-rod pattern of dysfunction. Macular atrophy was present in all patients, usually with central hypofluorescence surrounded by a continuous hyperfluorescent ring on fundus autofluorescence imaging. OCT confirmed loss of outer retinal structure within the atrophic areas. No clear genotype-phenotype relationship was evident. CONCLUSIONS Patients with Bardet-Biedl syndrome usually develop early-onset retinitis pigmentosa. In contrast, the patients described herein, with molecularly confirmed Bardet-Biedl syndrome, developed early cone dysfunction, including the first reported case of a cone dystrophy phenotype associated with the disorder. The findings significantly expand the phenotype associated with Bardet-Biedl syndrome.
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153
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Novas R, Cardenas-Rodriguez M, Irigoín F, Badano JL. Bardet-Biedl syndrome: Is it only cilia dysfunction? FEBS Lett 2015; 589:3479-91. [PMID: 26231314 DOI: 10.1016/j.febslet.2015.07.031] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 01/12/2023]
Abstract
Bardet-Biedl syndrome (BBS) is a genetically heterogeneous, pleiotropic disorder, characterized by both congenital and late onset defects. From the analysis of the mutational burden in patients to the functional characterization of the BBS proteins, this syndrome has become a model for both understanding oligogenic patterns of inheritance and the biology of a particular cellular organelle: the primary cilium. Here we briefly review the genetics of BBS to then focus on the function of the BBS proteins, not only in the context of the cilium but also highlighting potential extra-ciliary roles that could be relevant to the etiology of the disorder. Finally, we provide an overview of how the study of this rare syndrome has contributed to the understanding of cilia biology and how this knowledge has informed on the cellular basis of different clinical manifestations that characterize BBS and the ciliopathies.
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Affiliation(s)
- Rossina Novas
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | | | - Florencia Irigoín
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay; Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Montevideo, Gral. Flores 2125, Montevideo CP11800, Uruguay
| | - Jose L Badano
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay.
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154
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Cortés CR, Metzis V, Wicking C. Unmasking the ciliopathies: craniofacial defects and the primary cilium. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 4:637-53. [PMID: 26173831 DOI: 10.1002/wdev.199] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 05/19/2015] [Accepted: 05/30/2015] [Indexed: 12/29/2022]
Abstract
Over the past decade, the primary cilium has emerged as a pivotal sensory organelle that acts as a major signaling hub for a number of developmental signaling pathways. In that time, a vast number of proteins involved in trafficking and signaling have been linked to ciliary assembly and/or function, demonstrating the importance of this organelle during embryonic development. Given the central role of the primary cilium in regulating developmental signaling, it is not surprising that its dysfunction results in widespread defects in the embryo, leading to an expanding class of human congenital disorders known as ciliopathies. These disorders are individually rare and phenotypically variable, but together they affect virtually every vertebrate organ system. Features of ciliopathies that are often overlooked, but which are being reported with increasing frequency, are craniofacial abnormalities, ranging from subtle midline defects to full-blown orofacial clefting. The challenge moving forward is to understand the primary mechanism of disease given the link between the primary cilium and a number of developmental signaling pathways (such as hedgehog, platelet-derived growth factor, and WNT signaling) that are essential for craniofacial development. Here, we provide an overview of the diversity of craniofacial abnormalities present in the ciliopathy spectrum, and reveal those defects in common across multiple disorders. Further, we discuss the molecular defects and potential signaling perturbations underlying these anomalies. This provides insight into the mechanisms leading to ciliopathy phenotypes more generally and highlights the prevalence of widespread dysmorphologies resulting from cilia dysfunction.
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Affiliation(s)
- Claudio R Cortés
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Vicki Metzis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Carol Wicking
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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155
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Ferrarini A, Xumerle L, Griggio F, Garonzi M, Cantaloni C, Centomo C, Vargas SM, Descombes P, Marquis J, Collino S, Franceschi C, Garagnani P, Salisbury BA, Harvey JM, Delledonne M. The Use of Non-Variant Sites to Improve the Clinical Assessment of Whole-Genome Sequence Data. PLoS One 2015; 10:e0132180. [PMID: 26147798 PMCID: PMC4492948 DOI: 10.1371/journal.pone.0132180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/10/2015] [Indexed: 12/19/2022] Open
Abstract
Genetic testing, which is now a routine part of clinical practice and disease management protocols, is often based on the assessment of small panels of variants or genes. On the other hand, continuous improvements in the speed and per-base costs of sequencing have now made whole exome sequencing (WES) and whole genome sequencing (WGS) viable strategies for targeted or complete genetic analysis, respectively. Standard WGS/WES data analytical workflows generally rely on calling of sequence variants respect to the reference genome sequence. However, the reference genome sequence contains a large number of sites represented by rare alleles, by known pathogenic alleles and by alleles strongly associated to disease by GWAS. It’s thus critical, for clinical applications of WGS and WES, to interpret whether non-variant sites are homozygous for the reference allele or if the corresponding genotype cannot be reliably called. Here we show that an alternative analytical approach based on the analysis of both variant and non-variant sites from WGS data allows to genotype more than 92% of sites corresponding to known SNPs compared to 6% genotyped by standard variant analysis. These include homozygous reference sites of clinical interest, thus leading to a broad and comprehensive characterization of variation necessary to an accurate evaluation of disease risk. Altogether, our findings indicate that characterization of both variant and non-variant clinically informative sites in the genome is necessary to allow an accurate clinical assessment of a personal genome. Finally, we propose a highly efficient extended VCF (eVCF) file format which allows to store genotype calls for sites of clinical interest while remaining compatible with current variant interpretation software.
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Affiliation(s)
- Alberto Ferrarini
- Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Luciano Xumerle
- Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy
| | - Francesca Griggio
- Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy
- Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy
| | - Marianna Garonzi
- Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Chiara Cantaloni
- Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy
- Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy
| | - Cesare Centomo
- Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Sergio Marin Vargas
- Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Patrick Descombes
- Functional Genomics, Nestlé Institute of Health Sciences SA, EPFL Innovation Park, bâtiment G, 1015, Lausanne, Switzerland
| | - Julien Marquis
- Functional Genomics, Nestlé Institute of Health Sciences SA, EPFL Innovation Park, bâtiment G, 1015, Lausanne, Switzerland
| | - Sebastiano Collino
- Molecular Biomarkers, Nestlé Institute of Health Sciences SA, EPFL Innovation Park, bâtiment H, 1015, Lausanne, Switzerland
| | - Claudio Franceschi
- Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy
- Department of Experimental, Diagnostic and Specialty Medicine Experimental Pathology, University of Bologna, Via S. Giacomo 12, 40126, Bologna, Italy
- Interdepartmental Centre “L. Galvani” (CIG), University of Bologna, Piazza di Porta S. Donato 1, 40126, Bologna, Italy
- IRCCS, Institute of Neurological Sciences of Bologna, Ospedale Bellaria, Via Altura 3, 40139, Bologna, Italy
| | - Paolo Garagnani
- Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy
- Department of Experimental, Diagnostic and Specialty Medicine Experimental Pathology, University of Bologna, Via S. Giacomo 12, 40126, Bologna, Italy
- Interdepartmental Centre “L. Galvani” (CIG), University of Bologna, Piazza di Porta S. Donato 1, 40126, Bologna, Italy
- Center for Applied Biomedical Research, St. Orsola-Malpighi University Hospital, 40138, Bologna, Italy
| | | | - John Max Harvey
- Knome Inc., Waltham, Massachusetts, 02451, United States of America
| | - Massimo Delledonne
- Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy
- Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy
- * E-mail:
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156
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Cramer MT, Guay-Woodford LM. Cystic kidney disease: a primer. Adv Chronic Kidney Dis 2015; 22:297-305. [PMID: 26088074 DOI: 10.1053/j.ackd.2015.04.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/05/2015] [Accepted: 04/06/2015] [Indexed: 02/07/2023]
Abstract
Renal cystic diseases encompass a broad group of disorders with variable phenotypic expression. Cystic disorders can present during infancy, childhood, or adulthood. Often, but not always, they can be distinguished by the clinical features including age at presentation, renal imaging characteristics, including cyst distribution, and the presence/distribution of extrarenal manifestations. It is important to take the clinical context into consideration when assessing renal cystic disease in children and adults. For example, solitary kidney cysts may be completely benign when they develop during adulthood but may represent early polycystic kidney disease when observed during childhood. In this review, we have categorized renal cystic disease according to inherited single-gene disorders, for example, autosomal recessive polycystic kidney disease; syndromic disorders associated with kidney cysts, for example, tuberous sclerosis complex; and nongenetic forms of renal cystic disease, for example, simple kidney cysts. We present an overview of the clinical characteristics, genetics (when appropriate), and molecular pathogenesis and the diagnostic evaluation and management of each renal cystic disease. We also provide an algorithm that distinguishes kidney cysts based on their clinical features and may serve as a helpful diagnostic tool for practitioners. A review of Autosomal Dominant Polycystic Disease was excluded as this disorder was reviewed in this journal in March 2010, volume 17, issue 2.
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157
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Abstract
Despite remarkable progress in the identification of mutations that drive genetic disorders, progress in understanding the effect of genetic background on the penetrance and expressivity of causal alleles has been modest, in part because of the methodological challenges in identifying genetic modifiers. Nonetheless, the progressive discovery of modifier alleles has improved both our interpretative ability and our analytical tools to dissect such phenomena. In this review, we analyze the genetic properties and behaviors of modifiers as derived from studies in patient populations and model organisms and we highlight conceptual and technological tools used to overcome some of the challenges inherent in modifier mapping and cloning. Finally, we discuss how the identification of these modifiers has facilitated the elucidation of biological pathways and holds the potential to improve the clinical predictive value of primary causal mutations and to develop novel drug targets.
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Affiliation(s)
- Maria Kousi
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27710
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27710
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158
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Triallelic and epigenetic-like inheritance in human disorders of telomerase. Blood 2015; 126:176-84. [PMID: 26024875 DOI: 10.1182/blood-2015-03-633388] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/14/2015] [Indexed: 01/17/2023] Open
Abstract
Dyskeratosis congenita (DC) and related diseases are a heterogeneous group of disorders characterized by impaired telomere maintenance, known collectively as the telomeropathies. Disease-causing variants have been identified in 10 telomere-related genes including the reverse transcriptase (TERT) and the RNA component (TERC) of the telomerase complex. Variants in TERC and TERT can impede telomere elongation causing stem cells to enter premature replicative senescence and/or apoptosis as telomeres become critically short. This explains the major impact of the disease on highly proliferative tissues such as the bone marrow and skin. However, telomerase variants are not always fully penetrant and in some families disease-causing variants are seen in asymptomatic family members. As a result, determining the pathogenic status of newly identified variants in TERC or TERT can be quite challenging. Over a 3-year period, we have identified 26 telomerase variants (16 of which are novel) in 23 families. Additional investigations (including family segregation and functional studies) enabled these to be categorized into 3 groups: (1) disease-causing (n = 15), (2) uncertain status (n = 6), and (3) bystanders (n = 5). Remarkably, this process has also enabled us to identify families with novel mechanisms of inheriting human telomeropathies. These include triallelic mutations, involving 2 different telomerase genes, and an epigenetic-like inheritance of short telomeres in the absence of a telomerase mutation. This study therefore highlights that telomerase variants have highly variable functional and clinical manifestations and require thorough investigation to assess their pathogenic contribution.
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159
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Di Gioia SA, Bedoni N, von Scheven-Gête A, Vanoni F, Superti-Furga A, Hofer M, Rivolta C. Analysis of the genetic basis of periodic fever with aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome. Sci Rep 2015; 5:10200. [PMID: 25988833 PMCID: PMC4437314 DOI: 10.1038/srep10200] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/07/2015] [Indexed: 12/30/2022] Open
Abstract
PFAPA syndrome is the most common autoinflammatory syndrome in children from Western countries. In spite of its strong familial clustering, its genetic basis and inheritance pattern are still unknown. We performed a comprehensive genetic study on 68 individuals from 14 families. Linkage analysis suggested a susceptibility locus on chromosome 8, but direct molecular sequencing did not support this initial statistical finding. Exome sequencing revealed the absence of any gene that was mutated in all patients. Exhaustive screening of genes involved in other autoinflammatory syndromes or encoding components of the human inflammasome showed no DNA variants that could be linked to PFAPA molecular pathology. Among these, the previously-reported missense mutation V198M in the NLRP3 gene was clearly shown not to co-segregate with PFAPA. Our results on this relatively large cohort indicate that PFAPA syndrome is unlikely to be a monogenic condition. Moreover, none of the several genes known to be involved in inflammation or in autoinflammatory disorders seem to be relevant, alone, to its etiology, suggesting that PFAPA results from oligogenic or complex inheritance of variants in multiple disease genes and/or non-genetic factors.
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Affiliation(s)
| | - Nicola Bedoni
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Annette von Scheven-Gête
- Pediatric Rheumatology Unit of Western Switzerland, Department of Pediatrics, CHUV, University Hospital of Lausanne, Lausanne, Switzerland
| | - Federica Vanoni
- Pediatric Rheumatology Unit of Western Switzerland, Department of Pediatrics, CHUV, University Hospital of Lausanne, Lausanne, Switzerland
| | - Andrea Superti-Furga
- Department of Pediatrics, CHUV, University Hospital of Lausanne, Lausanne, Switzerland
| | - Michaël Hofer
- 1] Pediatric Rheumatology Unit of Western Switzerland, Department of Pediatrics, CHUV, University Hospital of Lausanne, Lausanne, Switzerland [2] Department of Pediatrics, HUG, Geneva, Switzerland
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
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160
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Buchner DA, Nadeau JH. Contrasting genetic architectures in different mouse reference populations used for studying complex traits. Genome Res 2015; 25:775-91. [PMID: 25953951 PMCID: PMC4448675 DOI: 10.1101/gr.187450.114] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/31/2015] [Indexed: 01/14/2023]
Abstract
Quantitative trait loci (QTLs) are being used to study genetic networks, protein functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges are many, beginning with the seemingly simple tasks of mapping QTLs and identifying their underlying genetic determinants. Various specialized resources have been developed to study complex traits in many model organisms. In the mouse, remarkably different pictures of genetic architectures are emerging. Chromosome Substitution Strains (CSSs) reveal many QTLs, large phenotypic effects, pervasive epistasis, and readily identified genetic variants. In contrast, other resources as well as genome-wide association studies (GWAS) in humans and other species reveal genetic architectures dominated with a relatively modest number of QTLs that have small individual and combined phenotypic effects. These contrasting architectures are the result of intrinsic differences in the study designs underlying different resources. The CSSs examine context-dependent phenotypic effects independently among individual genotypes, whereas with GWAS and other mouse resources, the average effect of each QTL is assessed among many individuals with heterogeneous genetic backgrounds. We argue that variation of genetic architectures among individuals is as important as population averages. Each of these important resources has particular merits and specific applications for these individual and population perspectives. Collectively, these resources together with high-throughput genotyping, sequencing and genetic engineering technologies, and information repositories highlight the power of the mouse for genetic, functional, and systems studies of complex traits and disease models.
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Affiliation(s)
- David A Buchner
- Department of Genetics and Genome Sciences, Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Joseph H Nadeau
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122, USA
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161
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Bayram Y, Aydin H, Gambin T, Akdemir ZC, Atik MM, Karaca E, Karaman A, Pehlivan D, Jhangiani SN, Gibbs RA, Lupski JR. Exome sequencing identifies a homozygous C5orf42 variant in a Turkish kindred with oral-facial-digital syndrome type VI. Am J Med Genet A 2015; 167A:2132-7. [PMID: 25846457 DOI: 10.1002/ajmg.a.37092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 03/16/2015] [Indexed: 11/08/2022]
Abstract
Oral-facial-digital syndrome type VI (OFDVI) is a rare ciliopathy in the spectrum of Joubert syndrome (JS) and distinguished from other oral-facial-digital syndromes by metacarpal abnormalities with central polydactyly and by a molar tooth sign on cranial MRI. Additional characteristic features include short stature, micrognathia, posteriorly rotated low-set ears, hypertelorism, epicanthal folds, broad nasal tip, tongue hamartoma, upper lip notch, intraoral frenula, cleft lip/palate, and renal anomalies. Recently, novel mutations in C5orf42 were identified in 9 out of 11 OFDVI families. In a subsequent study C5orf42 was found to be mutated in only 2 out of 17 OFDVI probands while 28 patients with a pure JS phenotype also had pathogenic mutations of C5orf42. We report on two affected cousins diagnosed with OFDVI who were born from first degree cousin marriages. Whole exome sequencing (WES) identified a homozygous predicted damaging missense mutation (c.4034A > G; p.Gln1345Arg) in the C5orf42 gene. Our data contribute to the evidence that C5orf42 is one of the causative genes for OFDVI.
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Affiliation(s)
- Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hatip Aydin
- Center of Genetics Diagnosis, Zeynep Kamil Women's and Children's Diseases Training and Research Hospital, Istanbul, Turkey
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mehmed M Atik
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ali Karaman
- Center of Genetics Diagnosis, Zeynep Kamil Women's and Children's Diseases Training and Research Hospital, Istanbul, Turkey
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas
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162
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Abstract
PURPOSE OF REVIEW Nephronophthisis (NPHP) is an autosomal recessive cystic kidney disease and is one of the most common genetic disorders causing end-stage renal disease (ESRD) in children and adolescents. NPHP is a genetically heterogenous disorder with 20 identified genes. NPHP occurs as an isolated kidney disease, but approximately 15% of NPHP patients have additional extrarenal symptoms affecting other organs [e.g. eyes, liver, bones and central nervous system (CNS)]. The pleiotropy in NPHP is explained by the finding that almost all NPHP gene products share expression in primary cilia, a sensory organelle present in most mammalian cells. If extrarenal symptoms are present in addition to NPHP, these disorders are classified as NPHP-related ciliopathies (NPHP-RC). This review provides an update about recent advances in the field of NPHP-RC. RECENT FINDINGS The identification of novel disease-causing genes has improved our understanding of the pathomechanisms contributing to NPHP-RC. Multiple interactions between different NPHP-RC gene products have been published and outline the interconnectivity of the affected proteins and shared pathways. SUMMARY The significance of recently identified genes for NPHP-RC is discussed and the complex role and interaction of NPHP proteins in ciliary function and cellular signalling pathways is highlighted.
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MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Adolescent
- Child
- Cilia/pathology
- Cilia/physiology
- Cytoskeletal Proteins
- Genes, Recessive
- Humans
- Kidney/pathology
- Kidney Diseases, Cystic/complications
- Kidney Diseases, Cystic/congenital
- Kidney Diseases, Cystic/pathology
- Kidney Diseases, Cystic/physiopathology
- Kidney Failure, Chronic/etiology
- Kidney Failure, Chronic/genetics
- Kidney Failure, Chronic/pathology
- Kidney Failure, Chronic/physiopathology
- Membrane Proteins/metabolism
- Mutation/genetics
- Phenotype
- Signal Transduction
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Affiliation(s)
- Matthias T F Wolf
- Division of Pediatric Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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163
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Vatta M, Spoonamore KG. Use of genetic testing to identify sudden cardiac death syndromes. Trends Cardiovasc Med 2015; 25:738-48. [PMID: 25864170 DOI: 10.1016/j.tcm.2015.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 03/06/2015] [Accepted: 03/07/2015] [Indexed: 01/25/2023]
Abstract
Sudden cardiac death (SCD) is a leading cause of mortality worldwide. Although coronary artery disease remains the most common substrate for SCD, primary cardiac genetic diseases, presenting with or without structural heart abnormalities, play a significant role. In the last 30 years, the study of large family pedigrees allowed the discovery of causative genes unveiling the genetic basis of diseases such as primary cardiomyopathies and arrhythmia syndromes, which are known to increase the risk of SCD. However, recent technological advancement with the ability to perform massive parallel sequencing and analyze the entire genome has uncovered a higher level of complexity in the genetic predisposition for cardiac diseases, which are usually characterized by Mendelian inheritance patterns. Clinical genetic testing, historically shaped around a monogenic Mendelian disorder paradigm, is now facing the challenge to adopt and adapt to a more complex model in which a significant portion of subjects may present with multi-allelic inheritance involving additional genes that could modulate the severity and type of disease-related phenotypes. Here, we will try to provide a viewpoint that will hopefully foster further debate in the field.
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Affiliation(s)
- Matteo Vatta
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN; Department of Medicine, Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, IN.
| | - Katherine G Spoonamore
- Department of Medicine, Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, IN
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164
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Rao Damerla R, Gabriel GC, Li Y, Klena NT, Liu X, Chen Y, Cui C, Pazour GJ, Lo CW. Role of cilia in structural birth defects: insights from ciliopathy mutant mouse models. ACTA ACUST UNITED AC 2015; 102:115-25. [PMID: 24975753 DOI: 10.1002/bdrc.21067] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 11/06/2022]
Abstract
Structural birth defect (SBD) is a major cause of morbidity and mortality in the newborn period. Although the etiology of SBD is diverse, a wide spectrum of SBD associated with ciliopathies points to the cilium as having a central role in the pathogenesis of SBDs. Ciliopathies are human diseases arising from disruption of cilia structure and/or function. They are associated with developmental anomalies in one or more organ systems and can involve defects in motile cilia, such as those in the airway epithelia or from defects in nonmotile (primary cilia) that have sensory and cell signaling function. Availability of low cost next generation sequencing has allowed for explosion of new knowledge in genetic etiology of ciliopathies. This has led to the appreciation that many genes are shared in common between otherwise clinically distinct ciliopathies. Further insights into the relevance of the cilium in SBD has come from recovery of pathogenic mutations in cilia-related genes from many large-scale mouse forward genetic screens with differing developmental phenotyping focus. Our mouse mutagenesis screen for congenital heart disease (CHD) using noninvasive fetal echocardiography has yielded a marked enrichment for pathogenic mutations in genes required for motile or primary cilia function. These novel mutant mouse models will be invaluable for modeling human ciliopathies and further interrogating the role of the cilium in the pathogenesis of SBD and CHD. Overall, these findings suggest a central role for the cilium in the pathogenesis of a wide spectrum of developmental anomalies associated with CHD and SBDs.
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Affiliation(s)
- Rama Rao Damerla
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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165
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Mencarelli MA, Heidet L, Storey H, van Geel M, Knebelmann B, Fallerini C, Miglietti N, Antonucci MF, Cetta F, Sayer JA, van den Wijngaard A, Yau S, Mari F, Bruttini M, Ariani F, Dahan K, Smeets B, Antignac C, Flinter F, Renieri A. Evidence of digenic inheritance in Alport syndrome. J Med Genet 2015; 52:163-74. [PMID: 25575550 DOI: 10.1136/jmedgenet-2014-102822] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Alport syndrome is a clinically heterogeneous, progressive nephropathy caused by mutations in collagen IV genes, namely COL4A3 and COL4A4 on chromosome 2 and COL4A5 on chromosome X. The wide phenotypic variability and the presence of incomplete penetrance suggest that a simple Mendelian model cannot completely explain the genetic control of this disease. Therefore, we explored the possibility that Alport syndrome is under digenic control. METHODS Using massively parallel sequencing, we identified 11 patients who had pathogenic mutations in two collagen IV genes. For each proband, we ascertained the presence of the same mutations in up to 12 members of the extended family for a total of 56 persons studied. RESULTS Overall, 23 mutations were found. Individuals with two pathogenic mutations in different genes had a mean age of renal function deterioration intermediate with respect to the autosomal-dominant form and the autosomal-recessive one, in line with molecule stoichiometry of the disruption of the type IV collagen triple helix. CONCLUSIONS Segregation analysis indicated three possible digenic segregation models: (i) autosomal inheritance with mutations on different chromosomes, resembling recessive inheritance (five families); (ii) autosomal inheritance with mutations on the same chromosome resembling dominant inheritance (two families) and (iii) unlinked autosomal and X-linked inheritance having a peculiar segregation (four families). This pedigree analysis provides evidence for digenic inheritance of Alport syndrome. Clinical geneticists and nephrologists should be aware of this possibility in order to more accurately assess inheritance probabilities, predict prognosis and identify other family members at risk.
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Affiliation(s)
- Maria Antonietta Mencarelli
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Laurence Heidet
- APHP, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Service de Néphrologie Pédiatrique, Hôpital Necker-Enfants Malades, Paris, France
| | - Helen Storey
- Molecular Genetics Laboratory, Guy's Hospital, London, UK
| | - Michel van Geel
- Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Bertrand Knebelmann
- APHP, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Service de Néphrologie Pédiatrique, Hôpital Necker-Enfants Malades, Paris, France
| | | | - Nunzia Miglietti
- Clinica Pediatrica, Azienda Ospedaliera Spedali Civili, Brescia, Italy
| | | | | | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, UK
| | | | - Shu Yau
- Molecular Genetics Laboratory, Guy's Hospital, London, UK
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Ariani
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Karin Dahan
- Université Catholique de Louvain, Louvain, Belgium
| | - Bert Smeets
- Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Corinne Antignac
- Inserm UMR 1163, Laboratory of Inherited Kidney Diseases, Paris, France Paris Descartes-Sorbonne Paris Cité Université, Imagine Institute, Paris, France APHP, Department of Genetics, Hôpital Necker-Enfants Malades, Paris, France
| | - Frances Flinter
- Department of Clinical Genetics, Guy's & St Thomas' NHS Foundation Trust, Guy's Hospital, London, UK
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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166
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Sayer JA, Simms RJ. The challenges and surprises of a definitive molecular genetic diagnosis. Kidney Int 2014; 85:748-9. [PMID: 24682124 DOI: 10.1038/ki.2013.432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Making precise molecular genetic diagnoses in inherited kidney diseases is important. Gee et al. describe families with end-stage renal disease secondary to a presumed diagnosis of a nephronophthisis-related ciliopathy (NPHP-RC), in whom a combination of approaches allowed genetic diagnoses to be made. New genetic approaches to the diagnosis of childhood renal failure are becoming mainstream and will hopefully improve patient management, avoid clinical misdiagnoses, reduce the need for invasive investigations, and allow screening of at-risk relatives.
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Affiliation(s)
- John A Sayer
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Roslyn J Simms
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
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167
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Goggolidou P, Stevens JL, Agueci F, Keynton J, Wheway G, Grimes DT, Patel SH, Hilton H, Morthorst SK, DiPaolo A, Williams DJ, Sanderson J, Khoronenkova SV, Powles-Glover N, Ermakov A, Esapa CT, Romero R, Dianov GL, Briscoe J, Johnson CA, Pedersen LB, Norris DP. ATMIN is a transcriptional regulator of both lung morphogenesis and ciliogenesis. Development 2014; 141:3966-77. [PMID: 25294941 PMCID: PMC4197704 DOI: 10.1242/dev.107755] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Initially identified in DNA damage repair, ATM-interactor (ATMIN) further functions as a transcriptional regulator of lung morphogenesis. Here we analyse three mouse mutants, Atmingpg6/gpg6, AtminH210Q/H210Q and Dynll1GT/GT, revealing how ATMIN and its transcriptional target dynein light chain LC8-type 1 (DYNLL1) are required for normal lung morphogenesis and ciliogenesis. Expression screening of ciliogenic genes confirmed Dynll1 to be controlled by ATMIN and further revealed moderately altered expression of known intraflagellar transport (IFT) protein-encoding loci in Atmin mutant embryos. Significantly, Dynll1GT/GT embryonic cilia exhibited shortening and bulging, highly similar to the characterised retrograde IFT phenotype of Dync2h1. Depletion of ATMIN or DYNLL1 in cultured cells recapitulated the in vivo ciliogenesis phenotypes and expression of DYNLL1 or the related DYNLL2 rescued the effects of loss of ATMIN, demonstrating that ATMIN primarily promotes ciliogenesis by regulating Dynll1 expression. Furthermore, DYNLL1 as well as DYNLL2 localised to cilia in puncta, consistent with IFT particles, and physically interacted with WDR34, a mammalian homologue of the Chlamydomonas cytoplasmic dynein 2 intermediate chain that also localised to the cilium. This study extends the established Atmin-Dynll1 relationship into a developmental and a ciliary context, uncovering a novel series of interactions between DYNLL1, WDR34 and ATMIN. This identifies potential novel components of cytoplasmic dynein 2 and furthermore provides fresh insights into the molecular pathogenesis of human skeletal ciliopathies.
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Affiliation(s)
- Paraskevi Goggolidou
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Jonathan L Stevens
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Francesco Agueci
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Jennifer Keynton
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Gabrielle Wheway
- Section of Ophthalmology and Neurosciences, Wellcome Trust Brenner Building, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Daniel T Grimes
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Saloni H Patel
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Helen Hilton
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Stine K Morthorst
- Department of Biology, University of Copenhagen, Universitetsparken 13, Copenhagen, OE DK-2100, Denmark
| | - Antonella DiPaolo
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Debbie J Williams
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Jeremy Sanderson
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Svetlana V Khoronenkova
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-11, Moscow 119991, Russia
| | - Nicola Powles-Glover
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Alexander Ermakov
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Chris T Esapa
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Rosario Romero
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Grigory L Dianov
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - James Briscoe
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Colin A Johnson
- Section of Ophthalmology and Neurosciences, Wellcome Trust Brenner Building, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, Copenhagen, OE DK-2100, Denmark
| | - Dominic P Norris
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
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Shin SJ, Kim M, Chae H, Kwon A, Kim Y, Kim SJ, Yoon HE, Jekarl DW, Lee S. Identification of compound heterozygous mutations in the BBS7 gene in a Korean family with Bardet-Biedl syndrome. Ann Lab Med 2014; 35:181-4. [PMID: 25553308 PMCID: PMC4272959 DOI: 10.3343/alm.2015.35.1.181] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 07/22/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022] Open
Affiliation(s)
- Seok Joon Shin
- Division of Nephrology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea. ; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyojin Chae
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea. ; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea. ; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sung Jun Kim
- Division of Nephrology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hye Eun Yoon
- Division of Nephrology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dong Wook Jekarl
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seungok Lee
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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169
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Bujakowska KM, Consugar M, Place E, Harper S, Lena J, Taub DG, White J, Navarro-Gomez D, Weigel DiFranco C, Farkas MH, Gai X, Berson EL, Pierce EA. Targeted exon sequencing in Usher syndrome type I. Invest Ophthalmol Vis Sci 2014; 55:8488-96. [PMID: 25468891 PMCID: PMC4280089 DOI: 10.1167/iovs.14-15169] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 11/16/2014] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Patients with Usher syndrome type I (USH1) have retinitis pigmentosa, profound congenital hearing loss, and vestibular ataxia. This syndrome is currently thought to be associated with at least six genes, which are encoded by over 180 exons. Here, we present the use of state-of-the-art techniques in the molecular diagnosis of a cohort of 47 USH1 probands. METHODS The cohort was studied with selective exon capture and next-generation sequencing of currently known inherited retinal degeneration genes, comparative genomic hybridization, and Sanger sequencing of new USH1 exons identified by human retinal transcriptome analysis. RESULTS With this approach, we were able to genetically solve 14 of the 47 probands by confirming the biallelic inheritance of mutations. We detected two likely pathogenic variants in an additional 19 patients, for whom family members were not available for cosegregation analysis to confirm biallelic inheritance. Ten patients, in addition to primary disease-causing mutations, carried rare likely pathogenic USH1 alleles or variants in other genes associated with deaf-blindness, which may influence disease phenotype. Twenty-one of the identified mutations were novel among the 33 definite or likely solved patients. Here, we also present a clinical description of the studied cohort at their initial visits. CONCLUSIONS We found a remarkable genetic heterogeneity in the studied USH1 cohort with multiplicity of mutations, of which many were novel. No obvious influence of genotype on phenotype was found, possibly due to small sample sizes of the genotypes under study.
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Affiliation(s)
- Kinga M. Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Mark Consugar
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Emily Place
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Shyana Harper
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States
| | - Jaclyn Lena
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Daniel G. Taub
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Joseph White
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Carol Weigel DiFranco
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States
| | - Michael H. Farkas
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Xiaowu Gai
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Eliot L. Berson
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States
| | - Eric A. Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States
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170
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Bullich G, Trujillano D, Santín S, Ossowski S, Mendizábal S, Fraga G, Madrid Á, Ariceta G, Ballarín J, Torra R, Estivill X, Ars E. Targeted next-generation sequencing in steroid-resistant nephrotic syndrome: mutations in multiple glomerular genes may influence disease severity. Eur J Hum Genet 2014; 23:1192-9. [PMID: 25407002 PMCID: PMC4538209 DOI: 10.1038/ejhg.2014.252] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 10/14/2014] [Accepted: 10/16/2014] [Indexed: 01/26/2023] Open
Abstract
Genetic diagnosis of steroid-resistant nephrotic syndrome (SRNS) using Sanger sequencing is complicated by the high genetic heterogeneity and phenotypic variability of this disease. We aimed to improve the genetic diagnosis of SRNS by simultaneously sequencing 26 glomerular genes using massive parallel sequencing and to study whether mutations in multiple genes increase disease severity. High-throughput mutation analysis was performed in 50 SRNS and/or focal segmental glomerulosclerosis (FSGS) patients, a validation cohort of 25 patients with known pathogenic mutations, and a discovery cohort of 25 uncharacterized patients with probable genetic etiology. In the validation cohort, we identified the 42 previously known pathogenic mutations across NPHS1, NPHS2, WT1, TRPC6, and INF2 genes. In the discovery cohort, disease-causing mutations in SRNS/FSGS genes were found in nine patients. We detected three patients with mutations in an SRNS/FSGS gene and COL4A3. Two of them were familial cases and presented a more severe phenotype than family members with mutation in only one gene. In conclusion, our results show that massive parallel sequencing is feasible and robust for genetic diagnosis of SRNS/FSGS. Our results indicate that patients carrying mutations in an SRNS/FSGS gene and also in COL4A3 gene have increased disease severity.
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Affiliation(s)
- Gemma Bullich
- 1] Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain [2] Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
| | - Daniel Trujillano
- 1] Genomics and Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Catalonia, Spain [2] Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain [3] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain [4] CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Catalonia, Spain
| | - Sheila Santín
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
| | - Stephan Ossowski
- 1] Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain [2] Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Catalonia, Spain
| | - Santiago Mendizábal
- Pediatric Nephrology Department, Hospital Universitario La Fe, Valencia, Spain
| | - Gloria Fraga
- Pediatric Nephrology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Catalonia, Spain
| | - Álvaro Madrid
- Pediatric Nephrology Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - Gema Ariceta
- Pediatric Nephrology Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - José Ballarín
- Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
| | - Roser Torra
- Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
| | - Xavier Estivill
- 1] Genomics and Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Catalonia, Spain [2] Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain [3] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain [4] CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Catalonia, Spain
| | - Elisabet Ars
- 1] Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain [2] Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Catalonia, Spain
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171
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Bachmann-Gagescu R. Complexité génétique des ciliopathies et identification de nouveaux gènes. Med Sci (Paris) 2014; 30:1011-23. [DOI: 10.1051/medsci/20143011016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Abstract
Mammalian sex determination is the unique process whereby a single organ, the bipotential gonad, undergoes a developmental switch that promotes its differentiation into either a testis or an ovary. Disruptions of this complex genetic process during human development can manifest as disorders of sex development (DSDs). Sex development can be divided into two distinct processes: sex determination, in which the bipotential gonads form either testes or ovaries, and sex differentiation, in which the fully formed testes or ovaries secrete local and hormonal factors to drive differentiation of internal and external genitals, as well as extragonadal tissues such as the brain. DSDs can arise from a number of genetic lesions, which manifest as a spectrum of gonadal (gonadal dysgenesis to ovotestis) and genital (mild hypospadias or clitoromegaly to ambiguous genitalia) phenotypes. The physical attributes and medical implications associated with DSDs confront families of affected newborns with decisions, such as gender of rearing or genital surgery, and additional concerns, such as uncertainty over the child's psychosexual development and personal wishes later in life. In this Review, we discuss the underlying genetics of human sex determination and focus on emerging data, genetic classification of DSDs and other considerations that surround gender development and identity in individuals with DSDs.
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Affiliation(s)
- Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095-7088, USA
| | - David E Sandberg
- Department of Pediatrics, Division of Child Behavioral Health and Child Health Evaluation &Research (CHEAR) Unit, University of Michigan, 300 North Ingalls Street, Ann Arbor, MI 48109-5456, USA
| | - Eric Vilain
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095-7088, USA
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Rubio-Cabezas O, Hattersley AT, Njølstad PR, Mlynarski W, Ellard S, White N, Chi DV, Craig ME. ISPAD Clinical Practice Consensus Guidelines 2014. The diagnosis and management of monogenic diabetes in children and adolescents. Pediatr Diabetes 2014; 15 Suppl 20:47-64. [PMID: 25182307 DOI: 10.1111/pedi.12192] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 12/18/2022] Open
Affiliation(s)
- Oscar Rubio-Cabezas
- Department of Paediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
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174
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Mutations of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing. Hum Genet 2014; 133:1255-71. [DOI: 10.1007/s00439-014-1460-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/03/2014] [Indexed: 12/01/2022]
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175
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Poulton CJ, Schot R, Seufert K, Lequin MH, Accogli A, Annunzio GD, Villard L, Philip N, de Coo R, Catsman-Berrevoets C, Grasshoff U, Kattentidt-Mouravieva A, Calf H, de Vreugt-Gronloh E, van Unen L, Verheijen FW, Galjart N, Morris-Rosendahl DJ, Mancini GMS. Severe presentation ofWDR62mutation: Is there a role for modifying genetic factors? Am J Med Genet A 2014; 164A:2161-71. [DOI: 10.1002/ajmg.a.36611] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 04/06/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Cathryn J. Poulton
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam Germany
| | - Rachel Schot
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam Germany
| | - Katja Seufert
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | | | - Andrea Accogli
- Department of Pediatrics; Gaslini Institute; Genova Italy
| | | | | | - Nicole Philip
- Inserm U910; Aix Marseille University; Marseille France
| | - René de Coo
- Department of Child Neurology; Erasmus Medical Center; Rotterdam Germany
| | | | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics; University Hospital Tuebingen; Tuebingen Germany
| | | | - Hans Calf
- ASVZ Zuid West; Rotterdam the Netherlands
| | | | - Leontine van Unen
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam Germany
| | - Frans W. Verheijen
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam Germany
| | - Niels Galjart
- Department of Cell Biology; Erasmus Medical Center; Rotterdam the Netherlands
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Lindstrand A, Davis E, Carvalho C, Pehlivan D, Willer J, Tsai IC, Ramanathan S, Zuppan C, Sabo A, Muzny D, Gibbs R, Liu P, Lewis R, Banin E, Lupski J, Clark R, Katsanis N. Recurrent CNVs and SNVs at the NPHP1 locus contribute pathogenic alleles to Bardet-Biedl syndrome. Am J Hum Genet 2014; 94:745-54. [PMID: 24746959 DOI: 10.1016/j.ajhg.2014.03.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic interval has also been detected in individuals with Joubert syndrome (JBTS), and in the mouse, Nphp1 interacts genetically with Ahi1, a known JBTS locus. Given these observations, we investigated the contribution of NPHP1 in Bardet-Biedl syndrome (BBS), a ciliopathy of intermediate severity. By using a combination of array-comparative genomic hybridization, TaqMan copy number assays, and sequencing, we studied 200 families affected by BBS. We report a homozygous NPHP1 deletion CNV in a family with classical BBS that is transmitted with autosomal-recessive inheritance. Further, we identified heterozygous NPHP1 deletions in two more unrelated persons with BBS who bear primary mutations at another BBS locus. In parallel, we identified five families harboring an SNV in NPHP1 resulting in a conserved missense change, c.14G>T (p.Arg5Leu), that is enriched in our Hispanic pedigrees; in each case, affected individuals carried additional bona fide pathogenic alleles in another BBS gene. In vivo functional modeling in zebrafish embryos demonstrated that c.14G>T is a loss-of-function variant, and suppression of nphp1 in concert with each of the primary BBS loci found in our NPHP1-positive pedigrees exacerbated the severity of the phenotype. These results suggest that NPHP1 mutations are probably rare primary causes of BBS that contribute to the mutational burden of the disorder.
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177
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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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178
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Drosophila models of early onset cognitive disorders and their clinical applications. Neurosci Biobehav Rev 2014; 46 Pt 2:326-42. [PMID: 24661984 DOI: 10.1016/j.neubiorev.2014.01.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 12/28/2022]
Abstract
The number of genes known to cause human monogenic diseases is increasing rapidly. For the extremely large, genetically and phenotypically heterogeneous group of intellectual disability (ID) disorders, more than 600 causative genes have been identified to date. However, knowledge about the molecular mechanisms and networks disrupted by these genetic aberrations is lagging behind. The fruit fly Drosophila has emerged as a powerful model organism to close this knowledge gap. This review summarizes recent achievements that have been made in this model and envisions its future contribution to our understanding of ID genetics and neuropathology. The available resources and efficiency of Drosophila place it in a position to tackle the main challenges in the field: mapping functional modules of ID genes to provide conceptually novel insights into the genetic control of cognition, tailored functional studies to improve 'next-generation' diagnostics, and identification of reversible ID phenotypes and medication. Drosophila's behavioral repertoire and powerful genetics also open up perspectives for modeling genetically complex forms of ID and neuropsychiatric disorders, which overlap in their genetic etiologies. In conclusion, Drosophila provides many opportunities to advance future medical genomics of early onset cognitive disorders.
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179
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Comprehensive molecular diagnosis of Bardet-Biedl syndrome by high-throughput targeted exome sequencing. PLoS One 2014; 9:e90599. [PMID: 24608809 PMCID: PMC3946549 DOI: 10.1371/journal.pone.0090599] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 01/31/2014] [Indexed: 01/28/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is an autosomal recessive disorder with significant genetic heterogeneity. BBS is linked to mutations in 17 genes, which contain more than 200 coding exons. Currently, BBS is diagnosed by direct DNA sequencing for mutations in these genes, which because of the large genomic screening region is both time-consuming and expensive. In order to develop a practical method for the clinic diagnosis of BBS, we have developed a high-throughput targeted exome sequencing (TES) for genetic diagnosis. Five typical BBS patients were recruited and screened for mutations in a total of 144 known genes responsible for inherited retinal diseases, a hallmark symptom of BBS. The genomic DNA of these patients and their families were subjected to high-throughput DNA re-sequencing. Deep bioinformatics analysis was carried out to filter the massive sequencing data, which were further confirmed through co-segregation analysis. TES successfully revealed mutations in BBS genes in each patient and family member. Six pathological mutations, including five novel mutations, were revealed in the genes BBS2, MKKS, ARL6, MKS1. This study represents the first report of targeted exome sequencing in BBS patients and demonstrates that high-throughput TES is an accurate and rapid method for the genetic diagnosis of BBS.
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180
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Ramachandran H, Schäfer T, Kim Y, Herfurth K, Hoff S, Lienkamp SS, Kramer-Zucker A, Walz G. Interaction with the Bardet-Biedl gene product TRIM32/BBS11 modifies the half-life and localization of Glis2/NPHP7. J Biol Chem 2014; 289:8390-401. [PMID: 24500717 DOI: 10.1074/jbc.m113.534024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the two ciliopathies Bardet-Biedl syndrome and nephronophthisis share multiple clinical manifestations, the molecular basis for this overlap remains largely unknown. Both BBS11 and NPHP7 are unusual members of their respective gene families. Although BBS11/TRIM32 represents a RING finger E3 ubiquitin ligase also involved in hereditary forms of muscular dystrophy, NPHP7/Glis2 is a Gli-like transcriptional repressor that localizes to the nucleus, deviating from the ciliary localization of most other ciliopathy-associated gene products. We found that BBS11/TRIM32 and NPHP7/Glis2 can physically interact with each other, suggesting that both proteins form a functionally relevant protein complex in vivo. This hypothesis was further supported by the genetic interaction and synergist cyst formation in the zebrafish pronephros model. However, contrary to our expectation, the E3 ubiquitin ligase BBS11/TRIM32 was not responsible for the short half-life of NPHP7/Glis2 but instead promoted the accumulation of mixed Lys(48)/Lys(63)-polyubiquitylated NPHP7/Glis2 species. This modification not only prolonged the half-life of NPHP7/Glis2, but also altered the subnuclear localization and the transcriptional activity of NPHP7/Glis2. Thus, physical and functional interactions between NPHP and Bardet-Biedl syndrome gene products, demonstrated for Glis2 and TRIM32, may help to explain the phenotypic similarities between these two syndromes.
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Affiliation(s)
- Haribaskar Ramachandran
- From the Department of Medicine, Renal Division, University of Freiburg Medical Center, 79106 Freiburg, Germany
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181
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Alqahtani AR, Elahmedi M, Alqahtani YA. Bariatric surgery in monogenic and syndromic forms of obesity. Semin Pediatr Surg 2014; 23:37-42. [PMID: 24491367 DOI: 10.1053/j.sempedsurg.2013.10.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Currently, no topic is more controversial in bariatric surgery than performing these procedures on children with monogenic and syndromic forms of obesity. The medical community and the caregivers of those patients are struggling to find a solution that can alleviate their suffering and save their life. In all forms of obesity, dieting and physical activity do not result in significant weight loss and is associated with a high rate of weight regain. Additionally, effective medical therapy is not available yet. While there is significant debate about the risks and benefits of bariatric surgery in the adolescent population, there is an increasing number of studies that demonstrate the success of this option for the appropriate patients. Similarly, our experience demonstrated the same success not only in normal children and adolescents but also in those with monogenic and syndromic form of obesity.
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Affiliation(s)
- Aayed R Alqahtani
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia.
| | - Mohamed Elahmedi
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Yara A Alqahtani
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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182
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Hall EA, Keighren M, Ford MJ, Davey T, Jarman AP, Smith LB, Jackson IJ, Mill P. Acute versus chronic loss of mammalian Azi1/Cep131 results in distinct ciliary phenotypes. PLoS Genet 2013; 9:e1003928. [PMID: 24415959 PMCID: PMC3887133 DOI: 10.1371/journal.pgen.1003928] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/14/2013] [Indexed: 01/20/2023] Open
Abstract
Defects in cilium and centrosome function result in a spectrum of clinically-related disorders, known as ciliopathies. However, the complex molecular composition of these structures confounds functional dissection of what any individual gene product is doing under normal and disease conditions. As part of an siRNA screen for genes involved in mammalian ciliogenesis, we and others have identified the conserved centrosomal protein Azi1/Cep131 as required for cilia formation, supporting previous Danio rerio and Drosophila melanogaster mutant studies. Acute loss of Azi1 by knock-down in mouse fibroblasts leads to a robust reduction in ciliogenesis, which we rescue by expressing siRNA-resistant Azi1-GFP. Localisation studies show Azi1 localises to centriolar satellites, and traffics along microtubules becoming enriched around the basal body. Azi1 also localises to the transition zone, a structure important for regulating traffic into the ciliary compartment. To study the requirement of Azi1 during development and tissue homeostasis, Azi1 null mice were generated (Azi1Gt/Gt). Surprisingly, Azi1Gt/Gt MEFs have no discernible ciliary phenotype and moreover are resistant to Azi1 siRNA knock-down, demonstrating that a compensation mechanism exists to allow ciliogenesis to proceed despite the lack of Azi1. Cilia throughout Azi1 null mice are functionally normal, as embryonic patterning and adult homeostasis are grossly unaffected. However, in the highly specialised sperm flagella, the loss of Azi1 is not compensated, leading to striking microtubule-based trafficking defects in both the manchette and the flagella, resulting in male infertility. Our analysis of Azi1 knock-down (acute loss) versus gene deletion (chronic loss) suggests that Azi1 plays a conserved, but non-essential trafficking role in ciliogenesis. Importantly, our in vivo analysis reveals Azi1 mediates novel trafficking functions necessary for flagellogenesis. Our study highlights the importance of both acute removal of a protein, in addition to mouse knock-out studies, when functionally characterising candidates for human disease. Cilia are slender projections from the surface of most mammalian cells and have sensory and sometimes motile functions. They are essential for mammalian development and defects in cilia lead to a group of human diseases, termed ciliopathies, with variable symptoms including embryonic lethality, lung and kidney defects, blindness and infertility. Cilia are complex structures composed of hundreds of components, whose individual functions are poorly understood. We screened for mammalian genes important in building cilia, and identified Azi1/Cep131, a gene previously shown to be required for cilia formation and function in fish and flies. We show that if we acutely reduce levels of Azi1 in mouse cells, fewer cells form cilia, but if we generate cells chronically lacking all Azi1, cilia form normally. In addition, mice without any Azi1 are healthy and viable, confirming normal cilia function. However, in these mice, the highly specialised ciliary structure of the sperm tail does not form, resulting in male infertility. We suggest Azi1 has conserved trafficking roles in both primary cilia and the specialised sperm flagella. Abruptly removing Azi1 results in instability causing the existing cilia network to collapse, whereas chronic deletion of Azi1 allows the system to re-equilibrate, and cilia to form normally.
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Affiliation(s)
- Emma A. Hall
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at The University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Margaret Keighren
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at The University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Matthew J. Ford
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at The University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Tracey Davey
- Electron Microscopy Research Services, Medical School, Newcastle University, Newcastle, United Kingdom
| | - Andrew P. Jarman
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Lee B. Smith
- MRC Centre for Reproductive Health, University of Edinburgh, The Queen's Medical Research Institute, Edinburgh, United Kingdom
| | - Ian J. Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at The University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- * E-mail: (IJJ); (PM)
| | - Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at The University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- * E-mail: (IJJ); (PM)
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183
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M'hamdi O, Ouertani I, Chaabouni-Bouhamed H. Update on the genetics of bardet-biedl syndrome. Mol Syndromol 2013; 5:51-6. [PMID: 24715851 DOI: 10.1159/000357054] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2013] [Indexed: 12/18/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is an autosomal recessive disease characterized by retinal dystrophy, obesity, postaxial polydactyly, learning disabilities, renal involvement, and male hypogenitalism. BBS is genetically heterogeneous, and to date 18 genes (BBS1-18) have been described. Mutations in known BBS genes account for approximately 70-80% of cases, and triallelic inheritance has been suggested in about 5%. Many minor features can be helpful in making the clinical diagnosis. Recently, the use of next-generation sequencing technologies has accelerated the identification of novel genes and causative disease mutations in known genes. This report presents a concise overview of the current knowledge on clinical data in BBS and the progress in molecular genetics research. A future objective will be the development of BBS diagnosis kits in order to offer genetic counseling for families at risk.
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Affiliation(s)
- O M'hamdi
- Department of Human Genetics, Faculty of Medicine, Tunis El-Manar University, Tunis, Tunisia
| | - I Ouertani
- Department of Human Genetics, Faculty of Medicine, Tunis El-Manar University, Tunis, Tunisia ; Department of Hereditary and Congenital Disorders, Charles Nicolle Hospital, Tunis, Tunisia
| | - H Chaabouni-Bouhamed
- Department of Human Genetics, Faculty of Medicine, Tunis El-Manar University, Tunis, Tunisia ; Department of Hereditary and Congenital Disorders, Charles Nicolle Hospital, Tunis, Tunisia
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184
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González-Del Pozo M, Méndez-Vidal C, Santoyo-Lopez J, Vela-Boza A, Bravo-Gil N, Rueda A, García-Alonso L, Vázquez-Marouschek C, Dopazo J, Borrego S, Antiñolo G. Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet-Biedl family. Mol Genet Genomic Med 2013; 2:124-33. [PMID: 24689075 PMCID: PMC3960054 DOI: 10.1002/mgg3.50] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 12/15/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a model ciliopathy characterized by a wide range of clinical variability. The heterogeneity of this condition is reflected in the number of underlying gene defects and the epistatic interactions between the proteins encoded. BBS is generally inherited in an autosomal recessive trait. However, in some families, mutations across different loci interact to modulate the expressivity of the phenotype. In order to investigate the magnitude of epistasis in one BBS family with remarkable intrafamilial phenotypic variability, we designed an exome sequencing-based approach using SOLID 5500xl platform. This strategy allowed the reliable detection of the primary causal mutations in our family consisting of two novel compound heterozygous mutations in McKusick-Kaufman syndrome (MKKS) gene (p.D90G and p.V396F). Additionally, exome sequencing enabled the detection of one novel heterozygous NPHP4 variant which is predicted to activate a cryptic acceptor splice site and is only present in the most severely affected patient. Here, we provide an exome sequencing analysis of a BBS family and show the potential utility of this tool, in combination with network analysis, to detect disease-causing mutations and second-site modifiers. Our data demonstrate how next-generation sequencing (NGS) can facilitate the dissection of epistatic phenomena, and shed light on the genetic basis of phenotypic variability.
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Affiliation(s)
- María González-Del Pozo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocio/Consejo Superior de Investigaciones Científicas/University of Seville Seville, Spain ; Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocio/Consejo Superior de Investigaciones Científicas/University of Seville Seville, Spain ; Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville, Spain
| | - Javier Santoyo-Lopez
- Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA) Seville, Spain
| | - Alicia Vela-Boza
- Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA) Seville, Spain
| | - Nereida Bravo-Gil
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocio/Consejo Superior de Investigaciones Científicas/University of Seville Seville, Spain
| | - Antonio Rueda
- Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA) Seville, Spain
| | - Luz García-Alonso
- Department of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF) Valencia, Spain
| | | | - Joaquín Dopazo
- Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA) Seville, Spain ; Department of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF) Valencia, Spain ; Functional Genomics Node (INB), CIPF Valencia, Spain
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocio/Consejo Superior de Investigaciones Científicas/University of Seville Seville, Spain ; Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville, Spain
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocio/Consejo Superior de Investigaciones Científicas/University of Seville Seville, Spain ; Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville, Spain ; Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA) Seville, Spain
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185
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Abstract
Primary cilia are generally solitary organelles that emanate from the surface of almost all vertebrate cell types. Until recently, details regarding the function of these structures were lacking; however, extensive evidence now suggests that primary cilia have critical roles in sensing the extracellular environment, and in coordinating developmental and homeostatic signalling pathways. Furthermore, disruption of these functions seems to underlie a diverse spectrum of disorders, known as primary ciliopathies. These disorders are characterized by wide-ranging clinical and genetic heterogeneity, but with substantial overlap among distinct conditions. Indeed, ciliopathies are associated with a large variety of manifestations that often include distinctive neurological findings. Herein, we review neurological features associated with primary ciliopathies, highlight genotype-phenotype correlations, and discuss potential mechanisms underlying these findings.
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186
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Wang KY, Wang CC, Cheng CY, Chen YC, Chen TH, Sue YM. The case: hexadactyly, blindness, obesity, and end-stage renal disease. Kidney Int 2013; 84:1291-2. [PMID: 24280758 DOI: 10.1038/ki.2013.180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kuan-Ying Wang
- 1] Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan [2] These authors contributed equally to this work
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187
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Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A. A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell 2013; 155:70-80. [PMID: 24074861 DOI: 10.1016/j.cell.2013.08.030] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/30/2013] [Accepted: 08/16/2013] [Indexed: 12/19/2022]
Abstract
Although countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely unresolved. By mining the medical records of over 110 million patients, we examine the extent to which Mendelian variation contributes to complex disease risk. We detect thousands of associations between Mendelian and complex diseases, revealing a nondegenerate, phenotypic code that links each complex disorder to a unique collection of Mendelian loci. Using genome-wide association results, we demonstrate that common variants associated with complex diseases are enriched in the genes indicated by this "Mendelian code." Finally, we detect hundreds of comorbidity associations among Mendelian disorders, and we use probabilistic genetic modeling to demonstrate that Mendelian variants likely contribute nonadditively to the risk for a subset of complex diseases. Overall, this study illustrates a complementary approach for mapping complex disease loci and provides unique predictions concerning the etiologies of specific diseases.
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Affiliation(s)
- David R Blair
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA
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188
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Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132:1077-130. [PMID: 23820649 PMCID: PMC3778950 DOI: 10.1007/s00439-013-1331-2] [Citation(s) in RCA: 417] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023]
Abstract
Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as 'reduced (or incomplete) penetrance'. Reduced penetrance is not uncommon; indeed, there are many known examples of 'disease-causing mutations' that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.
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Affiliation(s)
- David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, 24105 Kiel, Germany
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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189
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Efficient disruption of Zebrafish genes using a Gal4-containing gene trap. BMC Genomics 2013; 14:619. [PMID: 24034702 PMCID: PMC3848861 DOI: 10.1186/1471-2164-14-619] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 09/06/2013] [Indexed: 11/10/2022] Open
Abstract
Background External development and optical transparency of embryos make zebrafish exceptionally suitable for in vivo insertional mutagenesis using fluorescent proteins to visualize expression patterns of mutated genes. Recently developed Gene Breaking Transposon (GBT) vectors greatly improve the fidelity and mutagenicity of transposon-based gene trap vectors. Results We constructed and tested a bipartite GBT vector with Gal4-VP16 as the primary gene trap reporter. Our vector also contains a UAS:eGFP cassette for direct detection of gene trap events by fluorescence. To confirm gene trap events, we generated a UAS:mRFP tester line. We screened 270 potential founders and established 41 gene trap lines. Three of our gene trap alleles display homozygous lethal phenotypes ranging from embryonic to late larval: nsf tpl6, atp1a3atpl10 and flrtpl19. Our gene trap cassette is flanked by direct loxP sites, which enabled us to successfully revert nsf tpl6, atp1a3atpl10 and flrtpl19 gene trap alleles by injection of Cre mRNA. The UAS:eGFP cassette is flanked by direct FRT sites. It can be readily removed by injection of Flp mRNA for use of our gene trap alleles with other tissue-specific GFP-marked lines. The Gal4-VP16 component of our vector provides two important advantages over other GBT vectors. The first is increased sensitivity, which enabled us to detect previously unnoticed expression of nsf in the pancreas. The second advantage is that all our gene trap lines, including integrations into non-essential genes, can be used as highly specific Gal4 drivers for expression of other transgenes under the control of Gal4 UAS. Conclusions The Gal4-containing bipartite Gene Breaking Transposon vector presented here retains high specificity for integrations into genes, high mutagenicity and revertibility by Cre. These features, together with utility as highly specific Gal4 drivers, make gene trap mutants presented here especially useful to the research community.
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190
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Fedick A, Jalas C, Abeliovich D, Krakinovsky Y, Ekstein J, Ekstein A, Treff N. Carrier frequency of twoBBS2mutations in the Ashkenazi population. Clin Genet 2013; 85:578-82. [DOI: 10.1111/cge.12231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/03/2013] [Accepted: 07/03/2013] [Indexed: 01/17/2023]
Affiliation(s)
- A. Fedick
- Department of Microbiology and Molecular Genetics; UMDNJ-Robert Wood Johnson Medical School; Piscataway NJ USA
- Reproductive Medicine Associates of New Jersey; Basking Ridge NJ USA
| | - C. Jalas
- Center for Rare Jewish Genetic Disorders; Brooklyn NY USA
| | - D. Abeliovich
- Committee for Prevention of Jewish Genetic Diseases; Jerusalem Israel
- Mogen Body Laboratory LTD; Jerusalem Israel
| | | | - J. Ekstein
- Committee for Prevention of Jewish Genetic Diseases; Jerusalem Israel
- Committee for Prevention of Jewish Genetic Diseases; Brooklyn NY USA
| | - A. Ekstein
- Committee for Prevention of Jewish Genetic Diseases; Jerusalem Israel
| | - N.R. Treff
- Department of Microbiology and Molecular Genetics; UMDNJ-Robert Wood Johnson Medical School; Piscataway NJ USA
- Reproductive Medicine Associates of New Jersey; Basking Ridge NJ USA
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191
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Poot M. Late breaking chromosomes. Mol Syndromol 2013; 4:211-2. [PMID: 23885227 DOI: 10.1159/000350003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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192
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Abstract
Joubert syndrome is a congenital cerebellar ataxia with autosomal recessive or X-linked inheritance, the diagnostic hallmark of which is a unique cerebellar and brainstem malformation recognisable on brain imaging-the so-called molar tooth sign. Neurological signs are present from the neonatal period and include hypotonia progressing to ataxia, global developmental delay, ocular motor apraxia, and breathing dysregulation. These signs are variably associated with multiorgan involvement, mainly of the retina, kidneys, skeleton, and liver. 21 causative genes have been identified so far, all of which encode for proteins of the primary cilium or its apparatus. The primary cilium is a subcellular organelle that has key roles in development and in many cellular functions, making Joubert syndrome part of the expanding family of ciliopathies. Notable clinical and genetic overlap exists between distinct ciliopathies, which can co-occur even within families. Such variability is probably explained by an oligogenic model of inheritance, in which the interplay of mutations, rare variants, and polymorphisms at distinct loci modulate the expressivity of the ciliary phenotype.
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193
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Posterior microphthalmia and nanophthalmia in Tunisia caused by a founder c.1059_1066insC mutation of the PRSS56 gene. Gene 2013; 528:288-94. [PMID: 23820083 DOI: 10.1016/j.gene.2013.06.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 06/10/2013] [Indexed: 01/08/2023]
Abstract
Congenital microphthalmia (CMIC) is a common developmental ocular disorder characterized by a small, and sometimes malformed, eye. Posterior microphthalmia (PM) and nanophthalmia are two rare subtypes of isolated CMIC characterized by extreme hyperopia due to short axial length and elevated lens/eye volume ratio. While nanophthalmia is associated with a reduced size in both anterior and posterior segments, PM involves a normal-size anterior chamber but a small posterior segment. Several genes encoding transcription and non-transcription regulators have been identified in different forms of CMIC. MFRP gene mutations have, for instance, been associated with nanophthalmia, and mutations in the recently identified PRSS56 gene have been linked to PM. So far, these two forms of CMIC have been associated with 9 mutations in PRSS56. Of particular interest, a c.1059_1066insC mutation has recently been reported in four Tunisian families with isolated PM and one Tunisian family with nanophthalmia. Here, we performed a genome-wide scan using a high density single nucleotide polymorphism (SNP) array 50 K in a large consanguineous Tunisian family (PM7) affected with PM and identified the same causative disease mutation. A total of 24 polymorphic markers spanning the PRSS56 gene in 6 families originating from different regions of Tunisia were analyzed to investigate the origin of the c.1059_1066insC mutation and to determine whether it arose in a common ancestor. A highly significant disease-associated haplotype, spanning across the 146 kb of the 2q37.1 chromosome, was conserved in those families, suggesting that c.1059_1066insC arose from a common founder. The age of the mutation in this haplotype was estimated to be around 1,850 years. The identification of such 'founder effects' may greatly simplify diagnostic genetic screening and lead to better prognostic counseling.
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194
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Daiger SP, Sullivan LS, Bowne SJ. Genes and mutations causing retinitis pigmentosa. Clin Genet 2013; 84:132-41. [PMID: 23701314 PMCID: PMC3856531 DOI: 10.1111/cge.12203] [Citation(s) in RCA: 409] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/20/2013] [Accepted: 05/20/2013] [Indexed: 12/19/2022]
Abstract
Retinitis pigmentosa (RP) is a heterogeneous set of inherited retinopathies with many disease-causing genes, many known mutations, and highly varied clinical consequences. Progress in finding treatments is dependent on determining the genes and mutations causing these diseases, which includes both gene discovery and mutation screening in affected individuals and families. Despite the complexity, substantial progress has been made in finding RP genes and mutations. Depending on the type of RP, and the technology used, it is possible to detect mutations in 30-80% of cases. One of the most powerful approaches to genetic testing is high-throughput 'deep sequencing', that is, next-generation sequencing (NGS). NGS has identified several novel RP genes but a substantial fraction of previously unsolved cases have mutations in genes that are known causes of retinal disease but not necessarily RP. Apparent discrepancy between the molecular defect and clinical findings may warrant reevaluation of patients and families. In this review, we summarize the current approaches to gene discovery and mutation detection for RP, and indicate pitfalls and unsolved problems. Similar considerations apply to other forms of inherited retinal disease.
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Affiliation(s)
- S P Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA.
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195
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Abstract
Digenic inheritance (DI) is the simplest form of inheritance for genetically complex diseases. By contrast with the thousands of reports that mutations in single genes cause human diseases, there are only dozens of human disease phenotypes with evidence for DI in some pedigrees. The advent of high-throughput sequencing (HTS) has made it simpler to identify monogenic disease causes and could similarly simplify proving DI because one can simultaneously find mutations in two genes in the same sample. However, through 2012, I could find only one example of human DI in which HTS was used; in that example, HTS found only the second of the two genes. To explore the gap between expectation and reality, I tried to collect all examples of human DI with a narrow definition and characterise them according to the types of evidence collected, and whether there has been replication. Two strong trends are that knowledge of candidate genes and knowledge of protein–protein interactions (PPIs) have been helpful in most published examples of human DI. By contrast, the positional method of genetic linkage analysis, has been mostly unsuccessful in identifying genes underlying human DI. Based on the empirical data, I suggest that combining HTS with growing networks of established PPIs may expedite future discoveries of human DI and strengthen the evidence for them.
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196
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Västinsalo H, Jalkanen R, Bergmann C, Neuhaus C, Kleemola L, Jauhola L, Bolz HJ, Sankila EM. Extended mutation spectrum of Usher syndrome in Finland. Acta Ophthalmol 2013; 91:325-34. [PMID: 22681893 DOI: 10.1111/j.1755-3768.2012.02397.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
PURPOSE The Finnish distribution of clinical Usher syndrome (USH) types is 40% USH3, 34% USH1 and 12% USH2. All patients with USH3 carry the founder mutation in clarin 1 (CLRN1), whereas we recently reported three novel myosin VIIA (MYO7A) mutations in two unrelated patients with USH1. This study was carried out to further investigate the USH mutation spectrum in Finnish patients. METHODS We analysed samples from nine unrelated USH patients/families without known mutations and two USH3 families with atypically severe phenotype. The Asper Ophthalmics USH mutation chip was used to screen for known mutations and to evaluate the chip in molecular diagnostics of Finnish patients. RESULTS The chip revealed a heterozygous usherin (USH2A) mutation, p.N346H, in one patient. Sequencing of MYO7A and/or USH2A in three index patients revealed two novel heterozygous mutations, p.R873W in MYO7A and c.14343+2T>C in USH2A. We did not identify definite pathogenic second mutations in the patients, but identified several probably nonpathogenic variations that may modify the disease phenotype. Possible digenism could not be excluded in two families segregating genomic variations in both MYO7A and USH2A, and two families with CLRN1 and USH2A. CONCLUSION We conclude that there is considerable genetic heterogeneity of USH1 and USH2 in Finland, making molecular diagnostics and genetic counselling of patients and families challenging.
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Affiliation(s)
- Hanna Västinsalo
- The Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland.
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197
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Margolin DH, Kousi M, Chan YM, Lim ET, Schmahmann JD, Hadjivassiliou M, Hall JE, Adam I, Dwyer A, Plummer L, Aldrin SV, O'Rourke J, Kirby A, Lage K, Milunsky A, Milunsky JM, Chan J, Hedley-Whyte ET, Daly MJ, Katsanis N, Seminara SB. Ataxia, dementia, and hypogonadotropism caused by disordered ubiquitination. N Engl J Med 2013; 368:1992-2003. [PMID: 23656588 PMCID: PMC3738065 DOI: 10.1056/nejmoa1215993] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND The combination of ataxia and hypogonadism was first described more than a century ago, but its genetic basis has remained elusive. METHODS We performed whole-exome sequencing in a patient with ataxia and hypogonadotropic hypogonadism, followed by targeted sequencing of candidate genes in similarly affected patients. Neurologic and reproductive endocrine phenotypes were characterized in detail. The effects of sequence variants and the presence of an epistatic interaction were tested in a zebrafish model. RESULTS Digenic homozygous mutations in RNF216 and OTUD4, which encode a ubiquitin E3 ligase and a deubiquitinase, respectively, were found in three affected siblings in a consanguineous family. Additional screening identified compound heterozygous truncating mutations in RNF216 in an unrelated patient and single heterozygous deleterious mutations in four other patients. Knockdown of rnf216 or otud4 in zebrafish embryos induced defects in the eye, optic tectum, and cerebellum; combinatorial suppression of both genes exacerbated these phenotypes, which were rescued by nonmutant, but not mutant, human RNF216 or OTUD4 messenger RNA. All patients had progressive ataxia and dementia. Neuronal loss was observed in cerebellar pathways and the hippocampus; surviving hippocampal neurons contained ubiquitin-immunoreactive intranuclear inclusions. Defects were detected at the hypothalamic and pituitary levels of the reproductive endocrine axis. CONCLUSIONS The syndrome of hypogonadotropic hypogonadism, ataxia, and dementia can be caused by inactivating mutations in RNF216 or by the combination of mutations in RNF216 and OTUD4. These findings link disordered ubiquitination to neurodegeneration and reproductive dysfunction and highlight the power of whole-exome sequencing in combination with functional studies to unveil genetic interactions that cause disease. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- David H Margolin
- Department of Neurology, Massachusetts General Hospital, Boston 02115, USA
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Caliskan Y, Gharavi AG. Working out nephronophthisis genetics one family at a time. J Am Soc Nephrol 2013; 24:865-8. [PMID: 23687355 DOI: 10.1681/asn.2013040427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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199
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Hoefele J, Wilhelm C, Schiesser M, Mack R, Heinrich U, Weber LT, Biskup S, Daumer-Haas C, Klein HG, Rost I. Expanding the mutation spectrum for Fraser syndrome: Identification of a novel heterozygous deletion in FRAS1. Gene 2013; 520:194-7. [DOI: 10.1016/j.gene.2013.02.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 02/12/2013] [Accepted: 02/13/2013] [Indexed: 11/28/2022]
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200
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M'hamdi O, Redin C, Stoetzel C, Ouertani I, Chaabouni M, Maazoul F, M'rad R, Mandel JL, Dollfus H, Muller J, Chaabouni H. Clinical and genetic characterization of Bardet-Biedl syndrome in Tunisia: defining a strategy for molecular diagnosis. Clin Genet 2013; 85:172-7. [PMID: 23432027 DOI: 10.1111/cge.12129] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 02/18/2013] [Accepted: 02/18/2013] [Indexed: 01/11/2023]
Abstract
Bardet-Biedl syndrome (BBS, OMIM 209900) is a rare genetic disorder characterized by obesity, retinitis pigmentosa, post axial polydactyly, cognitive impairment, renal anomalies and hypogonadism. The aim of this study is to provide a comprehensive clinical and molecular analysis of a cohort of 11 Tunisian BBS consanguineous families in order to give insight into clinical and genetic spectrum and the genotype-phenotype correlations. Molecular analysis using combined sequence capture and high-throughput sequencing of 30 ciliopathies genes revealed 11 mutations in 11 studied families. Five mutations were novel and six were previously described. Novel mutations included c.1110G>A and c.39delA (p.G13fs*41) in BBS1, c.115+5G>A in BBS2, c.1272+1G>A in BBS6, c.1181_1182insGCATTTATACC in BBS10 (p.S396Lfs*6). Described mutations included c.436C>T (p.R146*) and c.1473+4A>G in BBS1, c.565C> (p.R189*) in BBS2, deletion of exons 4-6 in BBS4, c.149T>G (p.L50R) in BBS5, and c.459+1G>A in BBS8; most frequent mutations were described in BBS1 (4/11, 37%) and BBS2 (2/11, 18%) genes. No phenotype-genotype correlation was evidenced. This data expands the mutations profile of BBS genes in Tunisia and suggests a divergence of the genetic spectrum comparing Tunisian and other populations.
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Affiliation(s)
- O M'hamdi
- Faculté de médecine de Tunis, Université de Tunis El-Manar, Tunis, Tunisie
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