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Bachmann-Gagescu R, Dempsey JC, Phelps IG, O'Roak BJ, Knutzen DM, Rue TC, Ishak GE, Isabella CR, Gorden N, Adkins J, Boyle EA, de Lacy N, O'Day D, Alswaid A, Ramadevi A R, Lingappa L, Lourenço C, Martorell L, Garcia-Cazorla À, Ozyürek H, Haliloğlu G, Tuysuz B, Topçu M, Chance P, Parisi MA, Glass IA, Shendure J, Doherty D. Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity. J Med Genet 2015; 52:514-22. [PMID: 26092869 PMCID: PMC5082428 DOI: 10.1136/jmedgenet-2015-103087] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/01/2015] [Indexed: 12/23/2022]
Abstract
BACKGROUND Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterised by hypotonia, ataxia, cognitive impairment, abnormal eye movements, respiratory control disturbances and a distinctive mid-hindbrain malformation. JS demonstrates substantial phenotypic variability and genetic heterogeneity. This study provides a comprehensive view of the current genetic basis, phenotypic range and gene-phenotype associations in JS. METHODS We sequenced 27 JS-associated genes in 440 affected individuals (375 families) from a cohort of 532 individuals (440 families) with JS, using molecular inversion probe-based targeted capture and next-generation sequencing. Variant pathogenicity was defined using the Combined Annotation Dependent Depletion algorithm with an optimised score cut-off. RESULTS We identified presumed causal variants in 62% of pedigrees, including the first B9D2 mutations associated with JS. 253 different mutations in 23 genes highlight the extreme genetic heterogeneity of JS. Phenotypic analysis revealed that only 34% of individuals have a 'pure JS' phenotype. Retinal disease is present in 30% of individuals, renal disease in 25%, coloboma in 17%, polydactyly in 15%, liver fibrosis in 14% and encephalocele in 8%. Loss of CEP290 function is associated with retinal dystrophy, while loss of TMEM67 function is associated with liver fibrosis and coloboma, but we observe no clear-cut distinction between JS subtypes. CONCLUSIONS This work illustrates how combining advanced sequencing techniques with phenotypic data addresses extreme genetic heterogeneity to provide diagnostic and carrier testing, guide medical monitoring for progressive complications, facilitate interpretation of genome-wide sequencing results in individuals with a variety of phenotypes and enable gene-specific treatments in the future.
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Affiliation(s)
- R Bachmann-Gagescu
- Institute for Molecular Life Sciences and Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - J C Dempsey
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - I G Phelps
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - B J O'Roak
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - D M Knutzen
- Department of Oncology, Franciscan Health System, Tacoma, Washington, USA
| | - T C Rue
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - G E Ishak
- Department of Radiology, University of Washington, Seattle Children's Hospital, Seattle, Washington, USA
| | - C R Isabella
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - N Gorden
- Department of Internal Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - J Adkins
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - E A Boyle
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - N de Lacy
- Department of Psychiatry, University of Washington, Seattle, Washington, USA
| | - D O'Day
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - A Alswaid
- Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | | | - L Lingappa
- Department of Child Neurology, Rainbow Children Hospital, Hyderabad, India
| | - C Lourenço
- Department of Neurosciences and Behavior Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - L Martorell
- Department of Genetica Molecular, Hospital Sant Joan de Deu, Barcelona, Spain
| | - À Garcia-Cazorla
- Department of Neurology, Neurometabolic Unit, Hospital Sant Joan de Déu and CIBERER, ISCIII, Barcelona, Spain
| | - H Ozyürek
- Department of Pediatric Neurology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - G Haliloğlu
- Department of Pediatric Neurology, Hacettepe University Children's Hospital, Ankara, Turkey
| | - B Tuysuz
- Department of Pediatric Genetics, Cerrahpasa Medical School, Istanbul University, Istanbul, Turkey
| | - M Topçu
- Department of Pediatric Neurology, Hacettepe University Children's Hospital, Ankara, Turkey
| | - P Chance
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - M A Parisi
- National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - I A Glass
- Department of Pediatrics, University of Washington, Seattle, Washington, USA Seattle Children's Research Institute, Seattle, Washington, USA
| | - J Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - D Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA Seattle Children's Research Institute, Seattle, Washington, USA
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Utine GE, Akpınar B, Arslan U, Kiper PÖŞ, Volkan-Salancı B, Alanay Y, Aktaş D, Haliloğlu G, Oğuz KK, Boduroğlu K, Alikaşifoğlu M. Neurochemical evaluation of brain function with 1H magnetic resonance spectroscopy in patients with fragile X syndrome. Am J Med Genet A 2013; 164A:99-105. [PMID: 24259304 DOI: 10.1002/ajmg.a.36207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 08/12/2013] [Indexed: 11/06/2022]
Abstract
Fragile X syndrome (FXS) is the most common hereditary disorder of intellectual disability. Cognitive deficits involve executive function, attention, learning and memory. Advanced neuroimaging techniques are available, and (1)H magnetic resonance spectroscopy (MRS) can be used as a complementary method to MR imaging to understand disease processes in brain, by in vivo demonstration of brain metabolites. MRS was performed in 13 male patients with FXS full mutation, and 13 age- and sex-matched healthy controls. FXS diagnosis was based on clinical evaluation, followed by detection of FMR1 full mutation. Axial T2 TSE, sagittal T1 SE and coronal 3D MPRAGE images were obtained for both morphological imaging and voxel localization. Following evaluation of conventional images, multivoxel MRS (CSI) through supraventricular white matter and single voxel MRS (svs) with an intermediate echo time (TE:135 ms) from the cerebellar vermis were performed. Choline/Creatine (Cho/Cr), N-acetyl aspartate/Creatine (NAA/Cr), and Choline/N-acetyl aspartate (Cho/NAA) ratios were examined at right frontal (RF), left frontal (LF), right parietal (RP), left parietal (LP), and cerebellar vermian (C) white matter. Statistical analyses were done using t-test and Mann-Whitney U tests. A statistically significant difference was observed in RP Cho/NAA ratio (cell membrane marker/neuroaxonal marker), FXS patients having lower levels than controls (P = 0.016). The results should be evaluated cautiously in parallel to consequences in brain metabolism leading to alterations in neurotransmitter levels, osmoregulation, energy metabolism and oxidative stress response described in animal models. MRS may serve to define a metabolic signature and biomarkers associated with FXS.
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Affiliation(s)
- G E Utine
- Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara, Turkey; Department of Pediatric Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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Utine GE, Kiper PÖ, Alanay Y, Haliloğlu G, Aktaş D, Boduroğlu K, Tunçbilek E, Alikaşifoğlu M. Searching for Copy Number Changes in Nonsyndromic X-Linked Intellectual Disability. Mol Syndromol 2011; 2:64-71. [PMID: 22511893 DOI: 10.1159/000334289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2011] [Indexed: 11/19/2022] Open
Abstract
Intellectual disability (ID) has a prevalence of 2-3% with 0.3% of the population being severely retarded. Etiology is heterogeneous, owing to numerous genetic and environmental factors. Underlying etiology remains undetermined in 75-80% of mildly disabled patients and 20-50% of those severely disabled. Twelve percent of all ID is thought to be X-linked (XLID). This study covers copy number analysis of some of the known XLID genes, using multiplex ligation-dependent probe amplification (MLPA) in 100 nonsyndromic patients. One of the patients was found to have duplication in all exons of MECP2 gene, and another had duplication in the fifth exon of TM4SF2/TSPAN7 gene. Affymetrix® 6.0 whole-genome SNP microarray confirmed the duplication in MECP2 and showed duplication of exons 2-7 in TM4SF2/TSPAN7, respectively. MECP2 duplication has recently been recognized as a syndromic cause of XLID in males, whereas duplications in TM4SF2/TSPAN7 are yet to be determined as a cause of XLID. Being an efficient, rapid, easy-to-perform, easy-to-interpret, and cost-effective method of copy number analysis of specific DNA sequences, MLPA presents wide clinical utility and may be included in diagnostic workup of ID, particularly when microarrays are unavailable as a first-line approach.
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Affiliation(s)
- G E Utine
- Clinical Genetics Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
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Balci B, Wilichowski E, Haliloğlu G, Talim B, Aurino S, Kremer E, Ebinger F, Senbil N, Anlar B, Kale G, Nigro V, Topaloğlu H, Bonnemann C, Dinçer P. Beta-sarcoglycan gene mutations in Turkey. Acta Myol 2004; 23:154-8. [PMID: 15938573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The term limb-girdle muscular dystrophy (LGMD) refers to a group of muscular dystrophies that, at the outset, affect primarily the muscles of the hip and shoulder girdle. Limb-girdle muscular dystrophy is genetically heterogeneous comprising autosomal dominant (types LGMD 1A-1E) as well as autosomal recessive forms (types LGMD 2A-2J known). A subgroup among the autosomal recessive forms comprises the sarcoglycanopathies (LGMD2C-2F), caused by mutations in the gamma (gamma-SG), alpha (alpha-SG), beta (beta-SG) and delta (delta-SG) sarcoglycan genes, respectively. The sarcoglycans form the sarcoglycan complex, part of the dystrophin-associated glycoproteins. Mutations in the beta-SG gene causes LGMD2E. Disease severity, in this form, varies from mild to severe phenotypes depending on the individual mutation. Homozygous missense mutations in critical locations may result in the total absence of alpha-, beta- and gamma-sarcoglycan from the muscle membrane and a phenotype as severe as null mutations. In the present study, through screening 80 unrelated LGMD2 families, we identified 13 families with LGMD2E. Mutations in the beta-SG gene were identified in 12 patients from nine families. One of these patients carried a previously reported truncating mutation (Q11X), while the other 11 carried novel missense/rameshift mutations (M1L, V89M, I92T, I92S, 739insA), some of which were seen in more than one patient and may, therefore, be more common in the Turkish population.
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Affiliation(s)
- B Balci
- Hacettepe University, Faculty of Medicine, Department of Medical Biology, Turkey
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