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Xiao L, Tang Y, Deng C, Li J, Li R, Zhu H, Guo D, Yang Z, Long H, Feng L, Hu S. Differences in whole-brain metabolism are associated with the expression of genes related to neurovascular unit integrity and synaptic plasticity in temporal lobe epilepsy. Eur J Nucl Med Mol Imaging 2023; 51:168-179. [PMID: 37707571 DOI: 10.1007/s00259-023-06433-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
PURPOSE Temporal lobe epilepsy (TLE) is a common, polygenic epilepsy syndrome that involves glucose hypometabolism in the epileptogenic zone. However, the transcriptional and cellular signatures underlying the metabolism in TLE remain unclear. METHODS In this retrospective study, 2-[18F]-fluoro-2-deoxy-D-glucose ([18F]FDG) positron emission tomography (PET) scans of TLE patients (n = 104) who underwent anterior temporal lobectomy were consecutively collected between 2016 and 2021. The transcriptional profiles of TLE risk genes across the brain were identified by the gene expression analyses from six TLE patients and twelve postmortem donors (six from the Allen Human Brain Atlas). Integrating the neuroimaging and transcriptomic data, we examined the relationship between the expression of TLE-associated genes and metabolic alterations in TLE. Furthermore, we performed functional enrichment analyses of the genes with higher weight in partial least squares regression using Metascape. RESULTS A total of 104 patients with TLE (mean age 29 ± 9 years, 50% male) and 30 healthy controls (HCs) (mean age 31 ± 6 years, 53% male) were enrolled. Compared to that of HCs, patients with TLE showed hypometabolism in the temporal lobes and adjacent structures but hypermetabolism in the thalamus and basal ganglia. The cortical map of inter-group differences in cerebral metabolism was spatially correlated with the expression of a weighted combination of genes enriched in ontology terms and pathways related to neurovascular unit (NVU) integrity and synaptic plasticity. DISCUSSION Our findings, combined with the analysis of neuroimaging and transcriptional data, suggest that genes related to NVU integrity and synaptic plasticity may drive alterations to brain metabolism that mediate the genetic risk of TLE.
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Affiliation(s)
- Ling Xiao
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, 410008, Hunan, China
| | - Yongxiang Tang
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, 410008, Hunan, China
| | - Chijun Deng
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jian Li
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, 410008, Hunan, China
| | - Rong Li
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Haoyue Zhu
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, 410008, Hunan, China
| | - Danni Guo
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, 410008, Hunan, China
| | - Zhiquan Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, 410008, Hunan, China.
| | - Li Feng
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, 410008, Hunan, China.
- Department of Neurology, Xiangya Hospital, Central South University (Jiangxi Branch), Nanchang, Jiangxi, China.
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Shuo Hu
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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2
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Engwerda A, Kerstjens-Frederikse WS, Corsten-Janssen N, Dijkhuizen T, van Ravenswaaij-Arts CMA. The phenotypic spectrum of terminal 6q deletions based on a large cohort derived from social media and literature: a prominent role for DLL1. Orphanet J Rare Dis 2023; 18:59. [PMID: 36935482 PMCID: PMC10024851 DOI: 10.1186/s13023-023-02658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/27/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Terminal 6q deletions are rare, and the number of well-defined published cases is limited. Since parents of children with these aberrations often search the internet and unite via international social media platforms, these dedicated platforms may hold valuable knowledge about additional cases. The Chromosome 6 Project is a collaboration between researchers and clinicians at the University Medical Center Groningen and members of a Chromosome 6 support group on Facebook. The aim of the project is to improve the surveillance of patients with chromosome 6 aberrations and the support for their families by increasing the available information about these rare aberrations. This parent-driven research project makes use of information collected directly from parents via a multilingual online questionnaire. Here, we report our findings on 93 individuals with terminal 6q deletions and 11 individuals with interstitial 6q26q27 deletions, a cohort that includes 38 newly identified individuals. RESULTS Using this cohort, we can identify a common terminal 6q deletion phenotype that includes microcephaly, dysplastic outer ears, hypertelorism, vision problems, abnormal eye movements, dental abnormalities, feeding problems, recurrent infections, respiratory problems, spinal cord abnormalities, abnormal vertebrae, scoliosis, joint hypermobility, brain abnormalities (ventriculomegaly/hydrocephaly, corpus callosum abnormality and cortical dysplasia), seizures, hypotonia, ataxia, torticollis, balance problems, developmental delay, sleeping problems and hyperactivity. Other frequently reported clinical characteristics are congenital heart defects, kidney problems, abnormalities of the female genitalia, spina bifida, anal abnormalities, positional foot deformities, hypertonia and self-harming behaviour. The phenotypes were comparable up to a deletion size of 7.1 Mb, and most features could be attributed to the terminally located gene DLL1. Larger deletions that include QKI (> 7.1 Mb) lead to a more severe phenotype that includes additional clinical characteristics. CONCLUSIONS Terminal 6q deletions cause a common but highly variable phenotype. Most clinical characteristics can be linked to the smallest terminal 6q deletions that include the gene DLL1 (> 500 kb). Based on our findings, we provide recommendations for clinical follow-up and surveillance of individuals with terminal 6q deletions.
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Affiliation(s)
- Aafke Engwerda
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Nicole Corsten-Janssen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Trijnie Dijkhuizen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Conny M A van Ravenswaaij-Arts
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- ATN/Jonx, Groningen, The Netherlands.
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3
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Ferreira Vieira M, Carvalho D, Valentim F, Branco DM, Marinho HM. Terminal 6q27 Microdeletion Syndrome: A Case Report. Cureus 2022; 14:e31037. [DOI: 10.7759/cureus.31037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2022] [Indexed: 11/05/2022] Open
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4
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Pânzaru MC, Popa S, Lupu A, Gavrilovici C, Lupu VV, Gorduza EV. Genetic heterogeneity in corpus callosum agenesis. Front Genet 2022; 13:958570. [PMID: 36246626 PMCID: PMC9562966 DOI: 10.3389/fgene.2022.958570] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
The corpus callosum is the largest white matter structure connecting the two cerebral hemispheres. Agenesis of the corpus callosum (ACC), complete or partial, is one of the most common cerebral malformations in humans with a reported incidence ranging between 1.8 per 10,000 livebirths to 230–600 per 10,000 in children and its presence is associated with neurodevelopmental disability. ACC may occur as an isolated anomaly or as a component of a complex disorder, caused by genetic changes, teratogenic exposures or vascular factors. Genetic causes are complex and include complete or partial chromosomal anomalies, autosomal dominant, autosomal recessive or X-linked monogenic disorders, which can be either de novo or inherited. The extreme genetic heterogeneity, illustrated by the large number of syndromes associated with ACC, highlight the underlying complexity of corpus callosum development. ACC is associated with a wide spectrum of clinical manifestations ranging from asymptomatic to neonatal death. The most common features are epilepsy, motor impairment and intellectual disability. The understanding of the genetic heterogeneity of ACC may be essential for the diagnosis, developing early intervention strategies, and informed family planning. This review summarizes our current understanding of the genetic heterogeneity in ACC and discusses latest discoveries.
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Affiliation(s)
- Monica-Cristina Pânzaru
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Setalia Popa
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
- *Correspondence: Setalia Popa, ; Vasile Valeriu Lupu,
| | - Ancuta Lupu
- Department of Pediatrics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Cristina Gavrilovici
- Department of Pediatrics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Vasile Valeriu Lupu
- Department of Pediatrics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
- *Correspondence: Setalia Popa, ; Vasile Valeriu Lupu,
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
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5
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ÖZDAĞ V, TANIR Y. The Effects of 6q26-q27 Terminal Deletion on Intellectual Disability & Brain Malformations and the Genotype/Phenotype Relationship: A Case Report. Noro Psikiyatr Ars 2022; 59:242-245. [PMID: 36160077 PMCID: PMC9466636 DOI: 10.29399/npa.27797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/09/2021] [Indexed: 06/16/2023] Open
Abstract
Terminal microdeletion of chromosome 6q is a rare syndrome that can result in a spectrum of phenotypes varying from normal intelligence-minimal clinical symptoms to severe neurological defects and developmental delays. The most frequent clinical characteristics include developmental delays prior to and following birth as well as intellectual disability, brain malformations, and facial dysmorphism. These clinical characteristics may not be correlated with the size of the deletion; as many cases have been identified with either minor or major deletions, the genotype-phenotype correlation should be better investigated. To our knowledge, this is the first report of 6q26-q27 chromosome microdeletion in Turkey. In this article, we determine the clinical and genomic characteristics of a 2-year-old female case of 6q26-q27 chromosome microdeletion by investigating the level of development of the patient, brain malformations and dysmorphic characteristics, and ultimately comparing them to other cases reported in literature. Our patient was diagnosed with severe Global Developmental Delays (GDD). Although our case had similar clinical characteristics to corresponding cases in literature, there is a difference in the variety and group of symptoms exhibited.
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Affiliation(s)
- Veysel ÖZDAĞ
- İstanbul University, İstanbul Medical Faculty, Child and Adolescent Psychiatry Department, İstanbul, Turkey
| | - Yaşar TANIR
- İstanbul University, İstanbul Medical Faculty, Child and Adolescent Psychiatry Department, İstanbul, Turkey
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6
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Aksoy Yasar FB, Shingu T, Zamler DB, Zaman MF, Chien DL, Zhang Q, Ren J, Hu J. Quaking but not parkin is the major tumor suppressor in 6q deleted region in glioblastoma. Front Cell Dev Biol 2022; 10:931387. [PMID: 36051438 PMCID: PMC9424994 DOI: 10.3389/fcell.2022.931387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma (GBM) is a high-grade, aggressive brain tumor with dismal median survival time of 15 months. Chromosome 6q (Ch6q) is a hotspot of genomic alterations, which is commonly deleted or hyper-methylated in GBM. Two neighboring genes in this region, QKI and PRKN have been appointed as tumor suppressors in GBM. While a genetically modified mouse model (GEMM) of GBM has been successfully generated with Qk deletion in the central nervous system (CNS), in vivo genetic evidence supporting the tumor suppressor function of Prkn has not been established. In the present study, we generated a mouse model with Prkn-null allele and conditional Trp53 and Pten deletions in the neural stem cells (NSCs) and compared the tumorigenicity of this model to our previous GBM model with Qk deletion within the same system. We find that Qk but not Prkn is the potent tumor suppressor in the frequently altered Ch6q region in GBM.
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Affiliation(s)
- Fatma Betul Aksoy Yasar
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Takashi Shingu
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Daniel B. Zamler
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mohammad Fayyad Zaman
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Derek Lin Chien
- School of Arts and Sciences, University of Rochester, Rochester, NY, United States
| | - Qiang Zhang
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Jiangong Ren
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jian Hu
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- *Correspondence: Jian Hu,
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7
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Genotype–Phenotype Correlations for Putative Haploinsufficient Genes in Deletions of 6q26-q27: Report of Eight Patients and Review of Literature. Glob Med Genet 2022; 9:166-174. [PMID: 35707784 PMCID: PMC9192176 DOI: 10.1055/s-0042-1743568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/11/2022] [Indexed: 11/06/2022] Open
Abstract
Background
Cytogenomic analyses have been used to detect pathogenic copy number variants. Patients with deletions at 6q26-q27 present variable clinical features. We reported clinical and cytogenomic findings of eight unrelated patients with a deletion of 6q26-q27. A systematic review of the literature found 28 patients with a deletion of 6q26-q27 from 2010 to 2020.
Results
For these 36 patients, the sex ratio showed equal occurrence between males and females; 29 patients (81%) had a terminal deletion and seven patients (19%) had a proximal or distal interstitial deletion. Of the 22 patients with parental studies, deletions of de novo, maternal, paternal, and bi-parental inheritance accounted for 64, 18, 14, and 4% of patients, respectively. The most common clinical findings were brain abnormalities (100%) in fetuses observed by ultrasonography followed by developmental delay and intellectual disability (81%), brain abnormalities (72%), facial dysmorphism (66%), hypotonia (63%), learning difficulty or language delay (50%), and seizures (47%) in pediatric and adult patients. Anti-epilepsy treatment showed the effect on controlling seizures in these patients. Cytogenomic mapping defined one proximal critical region at 6q26 containing the putative haploinsufficient gene
PRKN
and one distal critical region at 6q27 containing two haploinsufficient genes
DLL1
and
TBP
. Deletions involving the
PRKN
gene could associate with early-onset Parkinson disease and autism spectrum disorder; deletions involving the
DLL1
gene correlate with the 6q terminal deletion syndrome.
Conclusion
The genotype–phenotype correlations for putative haploinsufficient genes in deletions of 6q26-q27 provided evidence for precise diagnostic interpretation, genetic counseling, and clinical management of patients with a deletion of 6q26-q27.
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8
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Lesieur-Sebellin M, Till M, Khau Van Kien P, Herve B, Bourgon N, Dupont C, Tabet AC, Barrois M, Coussement A, Loeuillet L, Mousty E, Ea V, El Assal A, Mary L, Jaillard S, Beneteau C, Le Vaillant C, Coutton C, Devillard F, Goumy C, Delabaere A, Redon S, Laurent Y, Lamouroux A, Massardier J, Turleau C, Sanlaville D, Cantagrel V, Sonigo P, Vialard F, Salomon LJ, Malan V. Terminal 6q deletions cause brain malformations, a phenotype mimicking heterozygous DLL1 pathogenic variants: A multicenter retrospective case series. Prenat Diagn 2021; 42:118-135. [PMID: 34894355 DOI: 10.1002/pd.6074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Terminal 6q deletion is a rare genetic condition associated with a neurodevelopmental disorder characterized by intellectual disability and structural brain anomalies. Interestingly, a similar phenotype is observed in patients harboring pathogenic variants in the DLL1 gene. Our study aimed to further characterize the prenatal phenotype of this syndrome as well as to attempt to establish phenotype-genotype correlations. METHOD We collected ultrasound findings from 22 fetuses diagnosed with a pure 6qter deletion. We reviewed the literature and compared our 22 cases with 14 fetuses previously reported as well as with patients with heterozygous DLL1 pathogenic variants. RESULTS Brain structural alterations were observed in all fetuses. The most common findings (>70%) were cerebellar hypoplasia, ventriculomegaly, and corpus callosum abnormalities. Gyration abnormalities were observed in 46% of cases. Occasional findings included cerebral heterotopia, aqueductal stenosis, vertebral malformations, dysmorphic features, and kidney abnormalities. CONCLUSION This is the first series of fetuses diagnosed with pure terminal 6q deletion. Based on our findings, we emphasize the prenatal sonographic anomalies, which may suggest the syndrome. Furthermore, this study highlights the importance of chromosomal microarray analysis to search for submicroscopic deletions of the 6q27 region involving the DLL1 gene in fetuses with these malformations.
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Affiliation(s)
- Marion Lesieur-Sebellin
- Service de Médecine Génomique des Maladies Rares, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
- Faculté de Médecine, Sorbonne Université, Paris, France
| | - Marianne Till
- Laboratoire de Cytogénétique, service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | | | - Bérénice Herve
- Département de Génétique, CHI Poissy Saint-Germain, Saint-Germain, France
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
| | - Nicolas Bourgon
- Service d'Obstétrique et de Médecine Fœtale, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - Céline Dupont
- Département de Génétique, Unité de Cytogénétique, Hôpital Robert Debré, APHP Nord, Paris, France
| | - Anne-Claude Tabet
- Département de Génétique, Unité de Cytogénétique, Hôpital Robert Debré, APHP Nord, Paris, France
- Génétique Humaine et Fonctions Cognitives, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris, France
| | - Mathilde Barrois
- Maternité Port Royal, APHP Centre, Hôpital Cochin, Paris, France
| | - Aurélie Coussement
- Service des Maladies Génétiques de système et d'organes, APHP-Centre, Hôpital Cochin, Paris, France
| | - Laurence Loeuillet
- Service de Médecine Génomique des Maladies Rares, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - Eve Mousty
- Service de Gynécologie Obstétrique, Hôpital Caremeau, Nîmes, France
| | - Vuthy Ea
- UF de Cytogénétique et Génétique Médicale, Hôpital Caremeau, Nîmes, France
| | - Amal El Assal
- Département de Gynécologie Obstétrique, CHI Poissy Saint-Germain, Saint-Germain, France
| | - Laura Mary
- Service d'Anatomie Pathologique, CHU Rennes, Rennes, France
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET, Université Rennes 1, Rennes, France
| | - Claire Beneteau
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- UF de Fœtopathologie et Génétique, CHU de Nantes, Nantes, France
| | | | - Charles Coutton
- Service de Génétique, Génomique et Procréation, Hôpital Couple Enfant, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institut pour l'Avancée des Biosciences, Equipe Génétique, Epigénétique et Thérapies de l'infertilité, Grenoble, France
| | - Françoise Devillard
- Service de Génétique, Génomique et Procréation, Hôpital Couple Enfant, CHU Grenoble Alpes, Grenoble, France
| | - Carole Goumy
- Cytogénétique Médicale, CHU Clermont-Ferrand, CHU Estaing, Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand, France
| | | | - Sylvia Redon
- CHU Brest, Inserm, Université de Brest, Brest, France
| | - Yves Laurent
- Service de Gynécologie et Obstétrique, GHBS Lorient, Lorient, France
| | - Audrey Lamouroux
- Service de Génétique Clinique, CHU Montpellier, Université de Montpellier, Montpellier, France
- Service de Gynécologie Obstétrique, CHU Nîmes, Université de Montpellier, Nîmes, France
| | - Jérôme Massardier
- Service de Gynécologie et Obstétrique, Hôpital Femme-Mère-Enfant, Hospices Civils de Lyon, Bron, France
| | - Catherine Turleau
- Service de Médecine Génomique des Maladies Rares, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - Damien Sanlaville
- Laboratoire de Cytogénétique, service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | - Vincent Cantagrel
- Université de Paris, Institut Imagine, Laboratoire de génétique des troubles du neurodéveloppement, Paris, France
- Université de Paris, Paris, France
| | - Pascale Sonigo
- Service de Radiologie Pédiatrique, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - François Vialard
- Département de Génétique, CHI Poissy Saint-Germain, Saint-Germain, France
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
| | - Laurent J Salomon
- Service d'Obstétrique et de Médecine Fœtale, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Paris, France
| | - Valérie Malan
- Service de Médecine Génomique des Maladies Rares, APHP-Centre, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Institut Imagine, Laboratoire de génétique des troubles du neurodéveloppement, Paris, France
- Université de Paris, Paris, France
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Vriend I, Oegema R. Genetic causes underlying grey matter heterotopia. Eur J Paediatr Neurol 2021; 35:82-92. [PMID: 34666232 DOI: 10.1016/j.ejpn.2021.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/21/2021] [Indexed: 11/15/2022]
Abstract
Grey matter heterotopia (GMH) can cause of seizures and are associated with a wide range of neurodevelopmental disorders and syndromes. They are caused by a failure of neuronal migration during fetal development, leading to clusters of neurons that have not reached their final destination in the cerebral cortex. We have performed an extensive literature search in Pubmed, OMIM, and Google scholar and provide an overview of known genetic associations with periventricular nodular heterotopia (PNVH), subcortical band heterotopia (SBH) and other subcortical heterotopia (SUBH). We classified the heterotopias as PVNH, SBH, SUBH or other and collected the genetic information, frequency, imaging features and salient features in tables for every subtype of heterotopia. This resulted in 105 PVNH, 16 SBH and 25 SUBH gene/locus associations, making a total of 146 genes and chromosomal loci. Our study emphasizes the extreme genetic heterogeneity underlying GMH. It will aid the clinician in establishing an differential diagnosis and eventually a molecular diagnosis in GMH patients. A diagnosis enables proper counseling of prognosis and recurrence risks, and enables individualized patient management.
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Affiliation(s)
- Ilona Vriend
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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10
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Selli A, Ventura RV, Fonseca PAS, Buzanskas ME, Andrietta LT, Balieiro JCC, Brito LF. Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations. Animals (Basel) 2021; 11:2696. [PMID: 34573664 PMCID: PMC8472390 DOI: 10.3390/ani11092696] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/25/2022] Open
Abstract
In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions.
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Affiliation(s)
- Alana Selli
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Ricardo V. Ventura
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Pablo A. S. Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Marcos E. Buzanskas
- Department of Animal Science, Federal University of Paraíba, João Pessoa 58051-900, Paraiba, Brazil;
| | - Lucas T. Andrietta
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Júlio C. C. Balieiro
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA;
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Tan R, Zhang G, Liu R, Hou J, Dong Z, Deng C, Wan S, Lai X, Cui H. Identification of Early Diagnostic and Prognostic Biomarkers via WGCNA in Stomach Adenocarcinoma. Front Oncol 2021; 11:636461. [PMID: 34221961 PMCID: PMC8249817 DOI: 10.3389/fonc.2021.636461] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/27/2021] [Indexed: 01/11/2023] Open
Abstract
Stomach adenocarcinoma (STAD) is a leading cause of cancer deaths, and the outcome of the patients remains dismal for the lack of effective biomarkers of early detection. Recent studies have elucidated the landscape of genomic alterations of gastric cancer and reveal some biomarkers of advanced-stage gastric cancer, however, information about early-stage biomarkers is limited. Here, we adopt Weighted Gene Co-expression Network Analysis (WGCNA) to screen potential biomarkers for early-stage STAD using RNA-Seq and clinical data from TCGA database. We find six gene clusters (or modules) are significantly correlated with the stage-I STADs. Among these, five hub genes, i.e., MS4A1, THBS2, VCAN, PDGFRB, and KCNA3 are identified and significantly de-regulated in the stage-I STADs compared with the normal stomach gland tissues, which suggests they can serve as potential early diagnostic biomarkers. Moreover, we show that high expression of VCAN and PDGFRB is associated with poor prognosis of STAD. VCAN encodes a large chondroitin sulfate proteoglycan that is the main component of the extracellular matrix, and PDGFRB encodes a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor (PDGF) family. Consistently, Gene Ontology (GO) analysis of differentially expressed genes in the STADs indicates terms associated with extracellular matrix and receptor ligand activity are significantly enriched. Protein-protein network interaction analysis (PPI) and Gene Set Enrichment Analysis (GSEA) further support the core role of VCAN and PDGFRB in the tumorigenesis. Collectively, our study identifies the potential biomarkers for early detection and prognosis of STAD.
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Affiliation(s)
- Ruoyue Tan
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Guanghui Zhang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Ruochen Liu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Jianbing Hou
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Chaowei Deng
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Sicheng Wan
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Xiaodong Lai
- Department of Critical Care Medicine, The Thirteenth People’s Hospital of Chongqing, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
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12
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Síndrome de deleção 6q. SCIENTIA MEDICA 2021. [DOI: 10.15448/1980-6108.2021.1.37395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Objetivos: Síndrome da deleção 6q é considerada uma anomalia cromossômica rara. Assim, nosso objetivo foi relatar um caso de um menino com essa síndrome, em Manaus/Amazonas.Descrição do caso: Menino com quatro anos de idade que apresenta atraso do crescimento e do desenvolvimento neuropsicomotor, dificuldades de ganho de peso e anormalidades na retina. A análise citogenética do paciente revelou cariótipo com 46, XY, del(6)(q25-qter).Conclusões: Este relato demonstrou a importância das análises citogenéticas para o diagnóstico preciso das anomalias congênitas, pois auxiliam no encaminhamento de tratamentos adequados aos pacientes e na ampliação de conhecimento científico relacionado a essa deleção.
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13
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Stern S, Hacohen N, Meiner V, Yagel S, Zenvirt S, Shkedi-Rafid S, Macarov M, Valsky DV, Porat S, Yanai N, Frumkin A, Daum H. Universal chromosomal microarray analysis reveals high proportion of copy-number variants in low-risk pregnancies. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:813-820. [PMID: 32202684 DOI: 10.1002/uog.22026] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 06/10/2023]
Abstract
OBJECTIVES To evaluate the yield and utility of the routine use of chromosomal microarray analysis (CMA) for prenatal genetic diagnosis in a large cohort of pregnancies with normal ultrasound (US) at the time of genetic testing, compared with pregnancies with abnormal US findings. METHODS We reviewed all prenatal CMA results in our center between November 2013 and December 2018. The prevalence of different CMA results in pregnancies with normal US at the time of genetic testing ('low-risk pregnancies'), was compared with that in pregnancies with abnormal US findings ('high-risk pregnancies'). Medical records were searched in order to evaluate subsequent US follow-up and the outcome of pregnancies with a clinically relevant copy-number variant (CNV), i.e. a pathogenic or likely pathogenic CNV or a susceptibility locus for disease with > 10% penetrance, related to early-onset disease in the low-risk group. RESULTS In a cohort of 6431 low-risk pregnancies that underwent CMA, the prevalence of a clinically significant CNV related to early-onset disease was 1.1% (72/6431), which was significantly lower than the prevalence in high-risk pregnancies (4.9% (65/1326)). Of the low-risk pregnancies, 0.4% (27/6431) had a pathogenic or likely pathogenic CNV, and another 0.7% (45/6431) had a susceptibility locus with more than 10% penetrance. Follow-up of the low-risk pregnancies with a clinically significant early-onset CNV revealed that 31.9% (23/72) were terminated, while outcome data were missing in 26.4% (19/72). In 16.7% (12/72) of low-risk pregnancies, an US abnormality was discovered later on in gestation, after genetic testing had been performed. CONCLUSION Although the background risk of identifying a clinically significant early-onset abnormal CMA result in pregnancies with a low a-priori risk is lower than that observed in high-risk pregnancies, the risk is substantial and should be conveyed to all pregnant women. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- S Stern
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - N Hacohen
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - V Meiner
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - S Yagel
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - S Zenvirt
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - S Shkedi-Rafid
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - M Macarov
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - D V Valsky
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - S Porat
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - N Yanai
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - A Frumkin
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - H Daum
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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14
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Santirocco M, Plaja A, Rodó C, Valenzuela I, Arévalo S, Castells N, Abuli A, Tizzano E, Maiz N, Carreras E. Chromosomal microarray analysis in fetuses with central nervous system anomalies: An 8-year long observational study from a tertiary care university hospital. Prenat Diagn 2020; 41:123-135. [PMID: 32926442 DOI: 10.1002/pd.5829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/01/2020] [Accepted: 09/08/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVES To evaluate the prevalence of DNA copy number variants (CNVs) detected with array comparative genomic hybridization (CGH) in fetuses with central nervous system (CNS) anomalies. Secondary objectives were to describe the prevalence of CNV in specific CNS abnormalities, in isolated defects or associated with other malformations or fetal growth restriction (FGR). METHODS Observational cohort study in 238 fetuses with CNS anomalies in which an array-CGH had been performed between January 2009 and December 2017. Pathogenic CNV and variants of unknown significance (VUS) were reported. RESULTS Pathogenic CNVs were found in 16/238 cases (6.7%), VUS in 18/238 (7.6%), and normal result in 204/238 (85.7%) cases. Pathogenic CNVs were more frequent in posterior fossa anomalies (cerebellar hypoplasia 33%, megacisterna magna 20%), moderate ventriculomegaly (11%) and spina bifida (3.7%). Pathogenic CNVs and VUS were found in 7/182 (3.8%) and 14/182 (7.7%) cases of isolated anomalies, in 9/49 (18.4%) and 4/49 (8.2%) presenting another malformation, and in 0/7 and 0/7 cases with associated FGR (P = .001, P = .741, respectively). CONCLUSION These results provide strong evidence toward performing array in fetuses with CNS anomalies, particular in cases of posterior fossa anomalies. The prevalence of pathogenic CNVs is higher in association with other malformations.
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Affiliation(s)
- Maddalena Santirocco
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alberto Plaja
- Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Carlota Rodó
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Silvia Arévalo
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Neus Castells
- Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Anna Abuli
- Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Eduardo Tizzano
- Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Nerea Maiz
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elena Carreras
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
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An Adolescent with a Rare De Novo Distal Trisomy 6p and Distal Monosomy 6q Chromosomal Combination. Case Rep Genet 2020; 2020:8857628. [PMID: 32934853 PMCID: PMC7479479 DOI: 10.1155/2020/8857628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/11/2020] [Accepted: 08/23/2020] [Indexed: 11/17/2022] Open
Abstract
We report on a 12-year-old female with both a partial duplication and deletion involving chromosome 6. The duplication involves 6p25.3p24.3 (7.585 Mb) while the deletion includes 6q27q27 (6.244 Mb). This chromosomal abnormality is also described as distal trisomy 6p and distal monosomy 6q. The patient has a Chiari II malformation, hydrocephalus, agenesis of the corpus callosum, microcephaly, bilateral renal duplicated collecting system, scoliosis, and myelomeningocele associated with a neurogenic bladder and bladder reflux. Additional features have included seizures, feeding dysfunction, failure to thrive, sleep apnea, global developmental delay, intellectual disability, and absent speech. To our knowledge, our report is just the sixth case in the literature with concomitant distal 6p duplication and distal 6q deletion. Although a majority of chromosomal duplication-deletion cases have resulted from a parental pericentric inversion, the parents of our case have normal chromosomes. This is the first reported de novo case of distal 6p duplication and distal 6q deletion. Alternate explanations for the origin of the patient's chromosome abnormalities include parental gonadal mosaicism, nonallelic homologous recombination, or potentially intrachromosomal transposition of the telomeres of chromosome 6. Nonpaternity was considered but ruled out by whole exome sequencing analysis.
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16
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International consensus recommendations on the diagnostic work-up for malformations of cortical development. Nat Rev Neurol 2020; 16:618-635. [PMID: 32895508 PMCID: PMC7790753 DOI: 10.1038/s41582-020-0395-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2020] [Indexed: 12/22/2022]
Abstract
Malformations of cortical development (MCDs) are neurodevelopmental disorders that result from abnormal development of the cerebral cortex in utero. MCDs place a substantial burden on affected individuals, their families and societies worldwide, as these individuals can experience lifelong drug-resistant epilepsy, cerebral palsy, feeding difficulties, intellectual disability and other neurological and behavioural anomalies. The diagnostic pathway for MCDs is complex owing to wide variations in presentation and aetiology, thereby hampering timely and adequate management. In this article, the international MCD network Neuro-MIG provides consensus recommendations to aid both expert and non-expert clinicians in the diagnostic work-up of MCDs with the aim of improving patient management worldwide. We reviewed the literature on clinical presentation, aetiology and diagnostic approaches for the main MCD subtypes and collected data on current practices and recommendations from clinicians and diagnostic laboratories within Neuro-MIG. We reached consensus by 42 professionals from 20 countries, using expert discussions and a Delphi consensus process. We present a diagnostic workflow that can be applied to any individual with MCD and a comprehensive list of MCD-related genes with their associated phenotypes. The workflow is designed to maximize the diagnostic yield and increase the number of patients receiving personalized care and counselling on prognosis and recurrence risk.
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17
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Accogli A, Severino M, Riva A, Madia F, Balagura G, Iacomino M, Carlini B, Baldassari S, Giacomini T, Croci C, Pisciotta L, Messana T, Boni A, Russo A, Bilo L, Tonziello R, Coppola A, Filla A, Mecarelli O, Casalone R, Pisani F, Falsaperla R, Marino S, Parisi P, Ferretti A, Elia M, Luchetti A, Milani D, Vanadia F, Silvestri L, Rebessi E, Parente E, Vatti G, Mancardi MM, Nobili L, Capra V, Salpietro V, Striano P, Zara F. Targeted re-sequencing in malformations of cortical development: genotype-phenotype correlations. Seizure 2020; 80:145-152. [DOI: 10.1016/j.seizure.2020.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/15/2020] [Accepted: 05/29/2020] [Indexed: 12/25/2022] Open
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Abstract
Any change in either the short (p) or long (q) arm of chromosome six can result in a variety of disorders. A two-year-old female child came to us with a history of sudden onset generalized tonic-clonic seizure. She had a syndromic face with frontal bossing and palpable thinning of the right lower lip and an apparent facial asymmetry while crying due to the hypoplasia of the right depressor angularis oris. Her joints were hypermobile and hypotonic. Chromosomal karyotyping exhibited a normal female karyotype, but pathogenic microarray genetic evaluation showed a loss of approximately 783 kb of the 6q27 terminus. She was diagnosed with chromosome 6q27 terminal deletion and managed with anti-seizure medications. Chromosome 6q27 terminal deletion can present with an array of structural and developmental anomalies. It is, therefore, necessary to understand the typical phenotypic and distinctive clinical features of congenital chromosome 6q27 terminal deletion syndrome for early diagnosis and intervention.
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Affiliation(s)
| | - Marsha Medows
- Pediatrics, Woodhull Hospital Center, Brooklyn, USA.,Pediatrics, New York University School of Medicine, New York, USA
| | - Yogesh Acharya
- Vascular and Endovascular Surgery, Western Vascular Institute, Galway, IRL
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Domínguez MG, Rivera H, Dávalos-Pulido RM, Dávalos-Rodríguez IP. A paternal t(6;22)(q25.3;p12) leading to a deleted and satellited der(6) in a short-lived infant. J Clin Lab Anal 2020; 34:e23355. [PMID: 32399990 PMCID: PMC7439351 DOI: 10.1002/jcla.23355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 11/25/2022] Open
Abstract
Background Non‐acrocentric satellited chromosomes mostly result from familial balanced insertions or translocations with p12 or p13 of any acrocentric. Although all non‐acrocentrics have been involved, only 12 instances of chromosome 6 involvement are known. Case presentation A female infant exhibited clinical features typical of 6qter deletions and also generalized hypertrichosis and synophrys, traits seldom reported in patients with similar imbalances or haploinsufficiency of ARID1B located in 6q25.3. She had a paternal derivative satellited 6q of a t(6;22)(q25.3;p12)pat entailing a 6q terminal deletion, karyotype 46,XX,der(6)t(6;22)(q25.3;p12)pat [16].ish del 6q subtel–. Conclusion Male and female carriers of reciprocal translocations or insertions between chromosome 6 and the short arm of any acrocentric have few unbalanced offspring mostly by adjacent‐1 segregation. In addition, spontaneous abortions or male infertility was present in 7/13 instances of satellited chromosome 6.
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Affiliation(s)
| | - Horacio Rivera
- División de Genética, CIBO, Instituto Mexicano del Seguro Social, Guadalajara, México.,Doctorado en Genética Humana, CUCS, Universidad de Guadalajara, Guadalajara, México
| | | | - Ingrid Patricia Dávalos-Rodríguez
- División de Genética, CIBO, Instituto Mexicano del Seguro Social, Guadalajara, México.,Doctorado en Genética Humana, CUCS, Universidad de Guadalajara, Guadalajara, México
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Chang Q, Yang Y, Peng Y, Liu S, Li L, Deng X, Yang M, Lan Y. Prenatal detection of chromosomal abnormalities and copy number variants in fetuses with ventriculomegaly. Eur J Paediatr Neurol 2020; 25:106-112. [PMID: 32014392 DOI: 10.1016/j.ejpn.2020.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/03/2020] [Accepted: 01/20/2020] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To systematically investigate chromosomal abnormalities and copy number variants (CNVs) in fetuses with different types of ventriculomegaly (VM) by karyotyping and/or chromosomal microarray analysis (CMA). METHODS This retrospective study included 312 fetuses diagnosed with VM. Amniotic fluid and umbilical blood samples were collected by amniocentesis and cordocentesis, respectively, and subjected to karyotyping and/or CMA. Subgroup analysis by VM type, including mild VM (MVM) and severe VM (SVM), unilateral and bilateral VM, isolated VM (IVM), and non-isolated VM (NIVM), was performed. RESULTS The detection rate of chromosomal abnormalities was 12.1% (34/281) by karyotyping and 20.6% when CMA was additionally performed (P < 0.05). Abnormalities were identified by CMA in 17.4% (38/218) of fetuses and pathogenic CNVs in 5.0% (11/218). Notably, CMA detected CNVs in 10.6% (23/218) of fetuses with normal karyotypes. The incidence of chromosomal abnormalities by karyotyping was higher in bilateral than in unilateral VM (20.5% versus 6.5%), whereas the incidence detected by CMA was higher in NIVM than in IVM (21.4% versus 10.3%; both P < 0.05). In NIVM, CMA provided an additional detection rate of 11.4% (16/140) and a detection rate of 10.0% for pathogenic CNVs and aneuploidies. Central nervous system (CNS) abnormalities were the most common other ultrasonic abnormalities. CONCLUSIONS CMA is highly recommended for prenatal diagnosis of fetal VM together with karyotyping, especially in fetuses with bilateral VM and NIVM with abnormal CNS findings. Further study is necessary to explore the relationships between genotypes and phenotypes to facilitate prenatal diagnosis of fetal VM.
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Affiliation(s)
- Qingxian Chang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Yanping Yang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yixian Peng
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Siping Liu
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Liyan Li
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xujie Deng
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ming Yang
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu Lan
- Department of Obstetrics and Gynecology, Guangzhou Red Cross Hospital Affiliated to Jinan University, Guangzhou, Guangdong, China
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Hanna MD, Moretti PN, P de Oliveira C, A Rosa MT, R Versiani B, de Oliveira SF, Pic-Taylor A, F Mazzeu J. Defining the Critical Region for Intellectual Disability and Brain Malformations in 6q27 Microdeletions. Mol Syndromol 2019; 10:202-208. [PMID: 31602192 DOI: 10.1159/000501008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2019] [Indexed: 11/19/2022] Open
Abstract
Terminal microdeletions of the long arm of chromosome 6 are associated with a phenotype that includes multiple brain malformations, intellectual disability, and epilepsy. A 1.7-Mb region has been proposed to contain a gene responsible for the brain anomalies. Here, we present the case of a 12-year-old girl with multiple brain alterations and moderate intellectual disability with a 18-kb deletion in chromosome 6q27, which is smaller than the microdeletions previously described by microarray analysis. We refined the smallest region of overlap possibly associated with the phenotype of brain malformations and intellectual disability to a segment of 325 kb, comprising the DLL1, PSMB1, TBP, and PDCD2 genes since these genes were structurally and/or functionally lost in the smaller deletions described to date. We hypothesize that DLL1 is responsible for brain malformations and possibly interacts with other adjacent genes. The TBP gene encodes a transcription factor which is potentially related to cognitive development. TBP is linked to PSMB1 and PDCD2 in a conserved manner among mammals, suggesting a potential interaction between these genes. In conclusion, the 6q27 microdeletion is a complex syndrome with variable expressivity of brain malformations and intellectual disability phenotypes which are possibly triggered by the 4 genes described and adjacent genes susceptible to gene regulation changes.
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Affiliation(s)
- Marcela D Hanna
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | | | | | - Maria T A Rosa
- Secretaria de Estado de Saúde do Distrito Federal, Brasília, Brazil
| | - Beatriz R Versiani
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil
| | - Silviene F de Oliveira
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Aline Pic-Taylor
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Juliana F Mazzeu
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
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22
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Depuydt P, Boeva V, Hocking TD, Cannoodt R, Ambros IM, Ambros PF, Asgharzadeh S, Attiyeh EF, Combaret V, Defferrari R, Fischer M, Hero B, Hogarty MD, Irwin MS, Koster J, Kreissman S, Ladenstein R, Lapouble E, Laureys G, London WB, Mazzocco K, Nakagawara A, Noguera R, Ohira M, Park JR, Pötschger U, Theissen J, Tonini GP, Valteau-Couanet D, Varesio L, Versteeg R, Speleman F, Maris JM, Schleiermacher G, De Preter K. Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients. J Natl Cancer Inst 2019. [PMID: 29514301 PMCID: PMC6186524 DOI: 10.1093/jnci/djy022] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Neuroblastoma is characterized by substantial clinical heterogeneity. Despite intensive treatment, the survival rates of high-risk neuroblastoma patients are still disappointingly low. Somatic chromosomal copy number aberrations have been shown to be associated with patient outcome, particularly in low- and intermediate-risk neuroblastoma patients. To improve outcome prediction in high-risk neuroblastoma, we aimed to design a prognostic classification method based on copy number aberrations. Methods In an international collaboration, normalized high-resolution DNA copy number data (arrayCGH and SNP arrays) from 556 high-risk neuroblastomas obtained at diagnosis were collected from nine collaborative groups and segmented using the same method. We applied logistic and Cox proportional hazard regression to identify genomic aberrations associated with poor outcome. Results In this study, we identified two types of copy number aberrations that are associated with extremely poor outcome. Distal 6q losses were detected in 5.9% of patients and were associated with a 10-year survival probability of only 3.4% (95% confidence interval [CI] = 0.5% to 23.3%, two-sided P = .002). Amplifications of regions not encompassing the MYCN locus were detected in 18.1% of patients and were associated with a 10-year survival probability of only 5.8% (95% CI = 1.5% to 22.2%, two-sided P < .001). Conclusions Using a unique large copy number data set of high-risk neuroblastoma cases, we identified a small subset of high-risk neuroblastoma patients with extremely low survival probability that might be eligible for inclusion in clinical trials of new therapeutics. The amplicons may also nominate alternative treatments that target the amplified genes.
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Affiliation(s)
- Pauline Depuydt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Valentina Boeva
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, Paris, France.,Institut Curie, Inserm U900, Mines ParisTech, PSL Research University, Paris, France
| | - Toby D Hocking
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Robrecht Cannoodt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium.,Data Mining and Modelling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium
| | - Inge M Ambros
- Children's Cancer Research Institute, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Peter F Ambros
- Children's Cancer Research Institute, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Shahab Asgharzadeh
- Division of Hematology/Oncology, Children's Hospital Los Angeles, University of Southern California Keck School of Medicine, Los Angeles, CA
| | - Edward F Attiyeh
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Childhood Cancer Research, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, University of Pennsylvania, Philadelphia, PA
| | - Valérie Combaret
- Centre Léon-Bérard, Laboratoire de Recherche Translationnelle, Lyon, France
| | | | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University of Cologne, Cologne, Germany.,University Children's Hospital Cologne, Medical Faculty, and Center for Molecular Medicine Cologne
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Michael D Hogarty
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine (MDH), University of Pennsylvania, Philadelphia, PA
| | - Meredith S Irwin
- Division of Hematology-Oncology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Susan Kreissman
- Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Ruth Ladenstein
- Children's Cancer Research Institute, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Eve Lapouble
- Genetic Somatic Unit.,Institut Curie, Paris, France
| | - Geneviève Laureys
- Department of Pediatric Hematology and Oncology, Ghent University Hospital, De Pintelaan, Ghent, Belgium
| | - Wendy B London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Katia Mazzocco
- Department of Pathology, Istituto Giannina Gaslini, Genova, Italy
| | | | - Rosa Noguera
- Pathology Department, Medical School, University of Valencia, Valencia, Spain.,Medical Research Foundation INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | - Miki Ohira
- Research Institute for Clinical Oncology Saitama Cancer Center, Saitama, Japan
| | - Julie R Park
- Seattle Children's Hospital and University of Washington, Seattle, WA
| | | | - Jessica Theissen
- Department of Experimental Pediatric Oncology, University of Cologne, Cologne, Germany
| | - Gian Paolo Tonini
- Laboratory of Neuroblastoma, Onco/Haematology Laboratory, University of Padua, Pediatric Research Institute (IRP)-Città della Speranza, Padova, Italy
| | | | - Luigi Varesio
- Laboratory of Molecular Biology (LV), Istituto Giannina Gaslini, Genova, Italy
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Childhood Cancer Research, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Abramson Family Cancer Research Institute, Philadelphia, PA
| | - Gudrun Schleiermacher
- U830 INSERM, Recherche Translationelle en Oncologie Pédiatrique (RTOP) and Department of Pediatric Oncology
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
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23
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Haploinsufficiency of the Notch Ligand DLL1 Causes Variable Neurodevelopmental Disorders. Am J Hum Genet 2019; 105:631-639. [PMID: 31353024 DOI: 10.1016/j.ajhg.2019.07.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023] Open
Abstract
Notch signaling is an established developmental pathway for brain morphogenesis. Given that Delta-like 1 (DLL1) is a ligand for the Notch receptor and that a few individuals with developmental delay, intellectual disability, and brain malformations have microdeletions encompassing DLL1, we hypothesized that insufficiency of DLL1 causes a human neurodevelopmental disorder. We performed exome sequencing in individuals with neurodevelopmental disorders. The cohort was identified using known Matchmaker Exchange nodes such as GeneMatcher. This method identified 15 individuals from 12 unrelated families with heterozygous pathogenic DLL1 variants (nonsense, missense, splice site, and one whole gene deletion). The most common features in our cohort were intellectual disability, autism spectrum disorder, seizures, variable brain malformations, muscular hypotonia, and scoliosis. We did not identify an obvious genotype-phenotype correlation. Analysis of one splice site variant showed an in-frame insertion of 12 bp. In conclusion, heterozygous DLL1 pathogenic variants cause a variable neurodevelopmental phenotype and multi-systemic features. The clinical and molecular data support haploinsufficiency as a mechanism for the pathogenesis of this DLL1-related disorder and affirm the importance of DLL1 in human brain development.
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24
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Ramírez-Velazco A, Aguayo-Orozco TA, Figuera L, Rivera H, Jave-Suárez L, Aguilar-Lemarroy A, Torres-Reyes LA, Córdova-Fletes C, Barros-Núñez P, Delgadillo-Pérez S, Dávalos-Rodríguez IP, García-Ortiz JE, Domínguez MG. Williams-Beuren syndrome in Mexican patients confirmed by FISH and assessed by aCGH. J Genet 2019; 98:34. [PMID: 31204697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Williams-Beuren syndrome (WBS) has a prevalence of 1/7500-20000 live births and results principally from a de novo deletion in 7q11.23 with a length of 1.5 Mb or 1.8 Mb. This study aimed to determine the frequency of 7q11.23 deletion, size of the segment lost, and involved genes in 47 patients with a clinical diagnosis of WBS and analysed by fluorescence in situ hybridization (FISH); among them, 31 had the expected deletion. Micro-array comparative genomic hybridization (aCGH) confirmed the loss in all 18 positive-patients tested: 14 patients had a 1.5 Mb deletion with the same breakpoints at 7q11.23 (hg19: 72726578-74139390) and comprising 24 coding genes from TRIM50 to GTF2I. Four patients showed an atypical deletion: two had a 1.6 Mb loss encompassing 27 coding genes, from NSUN5 to GTF2IRD2; another had a 1.7 Mb deletion involving 27 coding genes, from POM121 to GTF2I; the remaining patient presented a deletion of 1.2 Mb that included 21 coding genes from POM121 to LIMK1. aCGH confirmed the lack of deletion in 5/16 negative-patients by FISH. All 47 patients had the characteristic facial phenotype of WBS and 45 of 47 had the typical behavioural and developmental abnormalities. Our observations further confirm that patients with a classical deletion present a typical WBS phenotype, whereas those with a high (criteria of the American Association of Pediatrics, APP) clinical score but lacking the expected deletion may harbour an ELN point mutation. Overall, the concomitant CNVs appeared to be incidental findings.
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25
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Williams–Beuren syndrome in Mexican patients confirmed by FISH and assessed by aCGH. J Genet 2019. [DOI: 10.1007/s12041-019-1080-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Hsieh CS, Huang PS, Chang SN, Wu CK, Hwang JJ, Chuang EY, Tsai CT. Genome-Wide Copy Number Variation Association Study of Atrial Fibrillation Related Thromboembolic Stroke. J Clin Med 2019; 8:jcm8030332. [PMID: 30857284 PMCID: PMC6463198 DOI: 10.3390/jcm8030332] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/02/2019] [Accepted: 03/05/2019] [Indexed: 12/12/2022] Open
Abstract
Atrial fibrillation (AF) is a common cardiac arrhythmia and is one of the major causes of ischemic stroke. In addition to the clinical factors such as CHADS2 or CHADS2-VASC score, the impact of genetic factors on the risk of thromboembolic stroke in patients with AF has been largely unknown. Single-nucleotide polymorphisms in several genomic regions have been found to be associated with AF. However, these loci do not contribute to all the genetic risks of AF or AF related thromboembolic risks, suggesting that there are other genetic factors or variants not yet discovered. In the human genome, copy number variations (CNVs) could also contribute to disease susceptibility. In the present study, we sought to identify CNVs determining the AF-related thromboembolic risk. Using a genome-wide approach in 109 patients with AF and thromboembolic stroke and 14,666 controls from the Taiwanese general population (Taiwan Biobank), we first identified deletions in chromosomal regions 1p36.32-1p36.33, 5p15.33, 8q24.3 and 19p13.3 and amplifications in 14q11.2 that were significantly associated with AF-related stroke in the Taiwanese population. In these regions, 148 genes were involved, including several microRNAs and long non-recoding RNAs. Using a pathway analysis, we found deletions in GNB1, PRKCZ, and GNG7 genes related to the alpha-adrenergic receptor signaling pathway that play a major role in determining the risk of an AF-related stroke. In conclusion, CNVs may be genetic predictors of a risk of a thromboembolic stroke for patients with AF, possibly pointing to an impaired alpha-adrenergic signaling pathway in the mechanism of AF-related thromboembolism.
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Affiliation(s)
- Chia-Shan Hsieh
- Department of Life Science, Genome and Systems Biology Degree Program, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan.
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 100, Taiwan.
| | - Pang-Shuo Huang
- Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin 640, Taiwan.
| | - Sheng-Nan Chang
- Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin 640, Taiwan.
| | - Cho-Kai Wu
- Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan.
| | - Juey-Jen Hwang
- Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan.
| | - Eric Y Chuang
- Department of Life Science, Genome and Systems Biology Degree Program, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan.
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 100, Taiwan.
| | - Chia-Ti Tsai
- Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan.
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan.
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27
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Multiple genomic copy number variants associated with periventricular nodular heterotopia indicate extreme genetic heterogeneity. Eur J Hum Genet 2019; 27:909-918. [PMID: 30683929 DOI: 10.1038/s41431-019-0335-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 12/18/2018] [Indexed: 12/27/2022] Open
Abstract
Periventricular nodular heterotopia (PNH) is a brain malformation in which nodules of neurons are ectopically retained along the lateral ventricles. Genetic causes include FLNA abnormalities (classical X-linked PNH), rare variants in ARFGEF2, DCHS1, ERMARD, FAT4, INTS8, MAP1B, MCPH1, and NEDD4L, as well as several chromosomal abnormalities. We performed array-CGH in 106 patients with different malformations of cortical development (MCD) and looked for common pathways possibly involved in PNH. Forty-two patients, including two parent/proband couples, exhibited PNH associated or not with other brain abnormalities, 44 had polymicrogyria and 20 had rarer MCDs. We found an enrichment of either large rearrangements or cryptic copy number variants (CNVs) in PNH (15/42, 35.7%) vs polymicrogyria (4/44, 9.1%) (i.e., 5.6 times increased risk for PNH of carrying a pathogenic CNV). CNVs in seven genomic regions (2p11.2q12.1, 4p15, 14q11.2q12, 16p13.3, 19q13.33, 20q13.33, 22q11) represented novel, potentially causative, associations with PNH. Through in silico analysis of genes included in imbalances whose breakpoints were clearly detailed, we detected in 9/12 unrelated patients in our series and in 15/24 previously published patients, a significant (P < 0.05) overrepresentation of genes involved in vesicle-mediated transport. Rare genomic imbalances, either small CNVs or large rearrangements, are cumulatively a frequent cause of PNH. Dysregulation of specific cellular mechanisms might play a key pathogenic role in PNH but it remains to be determined whether this is exerted through single genes or the cumulative dosage effect of more genes. Array-CGH should be considered as a first-line diagnostic test in PNH, especially if sporadic and non-classical.
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28
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Iwamoto H, Muroi A, Sekine T, Tsurubuchi T, Ishikawa E, Matsumura A. Unusual Form of Obstructive Hydrocephalus in Association with 6q Terminal Deletion Syndrome: A Case Report and Literature Review. Pediatr Neurosurg 2019; 54:419-423. [PMID: 31597145 DOI: 10.1159/000503108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/03/2019] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Terminal deletion of chromosome 6q is a rare chromosomal abnormality associated with intellectual disabilities and various structural brain abnormalities. We present a case of 6q terminal deletion syndrome with unusual magnetic resonance imaging (MRI) findings in a neonate. CASE PRESENTATION The neonate, who was prenatally diagnosed with dilation of both lateral ventricles, was born at 38 weeks of gestation. MRI demonstrated abnormal membranous structure continuing to the hypertrophic massa intermedia in the third ventricle that had obscured the cerebrospinal fluid pathway, causing hydrocephalus. G-band analysis revealed a terminal deletion of 6q with the karyotype 46, XY, add(6)(q25.3) or del(6)(q26). He underwent ventriculoperitoneal shunt successfully, and his head circumference has been stable. DISCUSSION/CONCLUSION 6q terminal deletion impacts the molecular pathway, which is an essential intracellular signaling cascade inducing neurological proliferation, migration, and differentiation during neuronal development. In patients with hydrocephalus in association with hypertrophy of the massa intermedia, this chromosomal abnormality should be taken into consideration. This case may offer an insight into the pathogenesis of hydrocephalus in this rare chromosomal abnormality.
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Affiliation(s)
- Hirofumi Iwamoto
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ai Muroi
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan,
| | - Tomokazu Sekine
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takao Tsurubuchi
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Eiichi Ishikawa
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Akira Matsumura
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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29
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Thakur M, Bronshtein E, Hankerd M, Adekola H, Puder K, Gonik B, Ebrahim S. Genomic detection of a familial 382 Kb 6q27 deletion in a fetus with isolated severe ventriculomegaly and her affected mother. Am J Med Genet A 2018; 176:1985-1990. [PMID: 30194807 DOI: 10.1002/ajmg.a.40376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 04/26/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022]
Abstract
Terminal deletions of the chromosome 6q27 region are rare genomic abnormalities, linked to specific brain malformations and other neurological phenotypes. Reported cases have variable sized genomic deletions that harbor several genes including the DLL1 and TBP. We report on an inherited 0.38 Mb terminal deletion of chromosome 6q27 in a 22-week fetus with isolated bilateral ventriculomegaly and her affected mother using microarray-based comparative genomic hybridization and fluorescent in situ hybridization (FISH). The deleted region harbors at least seven genes including DLL1 and TBP. The affected mother had a history of hydrocephalus, developmental delay, and seizures commonly associated with DLL1 and TBP 6q27 deletions. This deletion is one of the smallest reported isolated 6q27 terminal deletions. Our data provides additional evidence that haploinsufficiency of the DLL1 and TBP genes may be sufficient to cause the ventriculomegaly, seizures, and developmental delays associated with terminal 6q27 deletions, indicating a plausible role in the abnormal development of the central nervous system.
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Affiliation(s)
- Mili Thakur
- Division of Genetic and Metabolic Disorders, Department of Pediatrics and Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan.,Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Elena Bronshtein
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Michael Hankerd
- Cytogenetics Laboratory, Detroit Medical Center University Laboratories, Detroit, Michigan
| | - Henry Adekola
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Karoline Puder
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Bernard Gonik
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Wayne State University/Detroit Medical Center, Detroit, Michigan
| | - Salah Ebrahim
- Cytogenetics Laboratory, Detroit Medical Center University Laboratories, Detroit, Michigan.,Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan
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30
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Genetics and mechanisms leading to human cortical malformations. Semin Cell Dev Biol 2018; 76:33-75. [DOI: 10.1016/j.semcdb.2017.09.031] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 09/21/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
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31
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Qian YQ, Fu XY, Wang XQ, Luo YQ, Chen M, Yan K, Yang YM, Liu B, Wang LY, Huang YZ, Li HG, Pan HY, Jin F, Dong MY. A feasible diagnostic approach for the translocation carrier from the indication of products of conception. Mol Cytogenet 2018; 11:12. [PMID: 29422950 PMCID: PMC5791184 DOI: 10.1186/s13039-018-0362-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/22/2018] [Indexed: 11/29/2022] Open
Abstract
Background Chromosome translocations are rare but frequently associated with infertility. The objective of this study is to investigate the feasibility of using chromosomal microarray analysis (CMA) on products of conception (POC) samples as an indicator of parental balanced translocation. From January 2011 to December 2016, CMA using Affymetrix Cytoscan™750K array was performed on 1294 POC samples in our hospital. Karyotyping and fluorescence in situ hybridization (FISH) using parental blood samples were performed to validate the origin of subchromosomal copy number variations (CNVs). Results In the 1294 cases of POCs, we detected CNVs of terminal duplication and deletion that imply unbalanced translocation derivatives in 16 cases, and accurate diagnosis with the parental study was made in all the cases by karyotyping and/or FISH. In 10/16 (62.5%) of these cases, CNVs were inherited from one carrier parent of balanced translocation (Cases 1 to 10), while 6/16 (37.5%) cases occurred de novo (Cases 11 to 16). Conclusion This study clearly illustrated the importance of the utilization of CMA on POC, followed by parental karyotyping and FISH to better characterize CNVs. This approach is especially useful for couples in whom one partner carries a cryptic/submicroscopic balanced translocation but has an apparently normal karyotype. Electronic supplementary material The online version of this article (10.1186/s13039-018-0362-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ye-Qing Qian
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Xiao-Ying Fu
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Xiao-Qing Wang
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Yu-Qin Luo
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Min Chen
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Kai Yan
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Yan-Mei Yang
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Bei Liu
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Li-Ya Wang
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Ying-Zhi Huang
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Hong-Ge Li
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Hang-Yi Pan
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Fan Jin
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
| | - Min-Yue Dong
- 1Women's Hospital, School of Medicine, Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,2Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, 1, Xueshi Road, Hangzhou, Zhejiang 310006 People's Republic of China
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De Cinque M, Palumbo O, Mazzucco E, Simone A, Palumbo P, Ciavatta R, Maria G, Ferese R, Gambardella S, Angiolillo A, Carella M, Garofalo S. Developmental Coordination Disorder in a Patient with Mental Disability and a Mild Phenotype Carrying Terminal 6q26-qter Deletion. Front Genet 2017; 8:206. [PMID: 29270193 PMCID: PMC5723635 DOI: 10.3389/fgene.2017.00206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/24/2017] [Indexed: 11/13/2022] Open
Abstract
Terminal deletion of chromosome 6q is a rare chromosomal abnormality associated with variable phenotype spectrum. Although intellectual disability, facial dysmorphism, seizures and brain abnormalities are typical features of this syndrome, genotype-phenotype correlation needs to be better understood. We report the case of a 6-year-old Caucasian boy with a clinical diagnosis of intellectual disability, delayed language development and dyspraxia who carries an approximately 8 Mb de novo heterozygous microdeletion in the 6q26-q27 locus identified by karyotype and defined by high-resolution SNP-array analysis. This patient has no significant structural brain or other organ malformation, and he shows a very mild phenotype compared to similar 6q26-qter deletion. The patient phenotype also suggests that a dyspraxia susceptibility gene is located among the deleted genes.
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Affiliation(s)
- Marianna De Cinque
- Dipartimento di Medicina e Scienze della Salute "V. Tiberio", Università degli Studi del Molise, Campobasso, Italy.,Unità Operativa di Medicina Trasfusionale, Azienda Sanitaria Regionale del Molise, Presidio Ospedaliero San Timoteo, Termoli, Italy
| | - Orazio Palumbo
- Unità Operativa Complessa di Genetica Medica, Poliambulatorio "Giovanni Paolo II", IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Ermelinda Mazzucco
- Dipartimento di Medicina e Scienze della Salute "V. Tiberio", Università degli Studi del Molise, Campobasso, Italy
| | - Antonella Simone
- Dipartimento di Medicina e Scienze della Salute "V. Tiberio", Università degli Studi del Molise, Campobasso, Italy.,Unità Operativa di Medicina Trasfusionale, Azienda Sanitaria Regionale del Molise, Presidio Ospedaliero San Timoteo, Termoli, Italy
| | - Pietro Palumbo
- Unità Operativa Complessa di Genetica Medica, Poliambulatorio "Giovanni Paolo II", IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Renata Ciavatta
- Ufficio per la Tutela della Salute Neurologica e Psichica dell'Età Evolutiva, Azienda Sanitaria Regionale del Molise, Termoli, Italy
| | - Giuliana Maria
- Ufficio per la Tutela della Salute Neurologica e Psichica dell'Età Evolutiva, Azienda Sanitaria Regionale del Molise, Termoli, Italy
| | | | | | - Antonella Angiolillo
- Dipartimento di Medicina e Scienze della Salute "V. Tiberio", Università degli Studi del Molise, Campobasso, Italy
| | - Massimo Carella
- Unità Operativa Complessa di Genetica Medica, Poliambulatorio "Giovanni Paolo II", IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Silvio Garofalo
- Dipartimento di Medicina e Scienze della Salute "V. Tiberio", Università degli Studi del Molise, Campobasso, Italy
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Lowther C, Merico D, Costain G, Waserman J, Boyd K, Noor A, Speevak M, Stavropoulos DJ, Wei J, Lionel AC, Marshall CR, Scherer SW, Bassett AS. Impact of IQ on the diagnostic yield of chromosomal microarray in a community sample of adults with schizophrenia. Genome Med 2017; 9:105. [PMID: 29187259 PMCID: PMC5708103 DOI: 10.1186/s13073-017-0488-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background Schizophrenia is a severe psychiatric disorder associated with IQ deficits. Rare copy number variations (CNVs) have been established to play an important role in the etiology of schizophrenia. Several of the large rare CNVs associated with schizophrenia have been shown to negatively affect IQ in population-based controls where no major neuropsychiatric disorder is reported. The aim of this study was to examine the diagnostic yield of microarray testing and the functional impact of genome-wide rare CNVs in a community ascertained cohort of adults with schizophrenia and low (< 85) or average (≥ 85) IQ. Methods We recruited 546 adults of European ancestry with schizophrenia from six community psychiatric clinics in Canada. Each individual was assigned to the low or average IQ group based on standardized tests and/or educational attainment. We used rigorous methods to detect genome-wide rare CNVs from high-resolution microarray data. We compared the burden of rare CNVs classified as pathogenic or as a variant of unknown significance (VUS) between each of the IQ groups and the genome-wide burden and functional impact of rare CNVs after excluding individuals with a pathogenic CNV. Results There were 39/546 (7.1%; 95% confidence interval [CI] = 5.2–9.7%) schizophrenia participants with at least one pathogenic CNV detected, significantly more of whom were from the low IQ group (odds ratio [OR] = 5.01 [2.28–11.03], p = 0.0001). Secondary analyses revealed that individuals with schizophrenia and average IQ had the lowest yield of pathogenic CNVs (n = 9/325; 2.8%), followed by those with borderline intellectual functioning (n = 9/130; 6.9%), non-verbal learning disability (n = 6/29; 20.7%), and co-morbid intellectual disability (n = 15/62; 24.2%). There was no significant difference in the burden of rare CNVs classified as a VUS between any of the IQ subgroups. There was a significantly (p=0.002) increased burden of rare genic duplications in individuals with schizophrenia and low IQ that persisted after excluding individuals with a pathogenic CNV. Conclusions Using high-resolution microarrays we were able to demonstrate for the first time that the burden of pathogenic CNVs in schizophrenia differs significantly between IQ subgroups. The results of this study have implications for clinical practice and may help inform future rare variant studies of schizophrenia using next-generation sequencing technologies. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0488-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chelsea Lowther
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Daniele Merico
- Deep Genomics Inc, Toronto, ON, Canada.,The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gregory Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Kerry Boyd
- Department of Psychiatry & Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Abdul Noor
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Marsha Speevak
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - John Wei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anath C Lionel
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1. .,Institute of Medical Science, University of Toronto, Toronto, ON, Canada. .,Toronto General Research Institute, University Health Network, Toronto, ON, Canada. .,Cambell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada. .,Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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34
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Darouich S, Boutaud L, Bessières B, Bonnière M, Martinovic J, Mechler C, Alby C, Bernard JP, Roth P, Ville Y, Malan V, Vekemans M, Attié-Bitach T, Encha-Razavi F. Fetal Cerebral Ventricular Dilatation: Etiopathogenic Study of 130 Observations. Birth Defects Res 2017; 109:1586-1595. [DOI: 10.1002/bdr2.1093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/18/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Sihem Darouich
- Unité de Foetopathologie, Hôpital Universitaire Habib Bougatfa, Faculté de Médecine de Tunis; Université Tunis El Manar; Tunis Tunisie
| | - Lucile Boutaud
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes; Paris France
| | - Bettina Bessières
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Maryse Bonnière
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Jelena Martinovic
- Unité de Pathologie Fœtale; Hôpital Antoine Béclère, APHP; Paris France
| | - Charlotte Mechler
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Caroline Alby
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Jean-Pierre Bernard
- Service de Gynécologie-Obstétrique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Philippe Roth
- Service de Gynécologie-Obstétrique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Yves Ville
- Service de Gynécologie-Obstétrique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Valerie Malan
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes; Paris France
| | - Michel Vekemans
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes; Paris France
| | - Tania Attié-Bitach
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes; Paris France
| | - Férechté Encha-Razavi
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
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Quintela I, Eirís J, Gómez-Lado C, Pérez-Gay L, Dacruz D, Cruz R, Castro-Gago M, Míguez L, Carracedo Á, Barros F. Copy number variation analysis of patients with intellectual disability from North-West Spain. Gene 2017; 626:189-199. [PMID: 28506748 DOI: 10.1016/j.gene.2017.05.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/07/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
Intellectual disability (ID) is a complex and phenotypically heterogeneous neurodevelopmental disorder characterized by significant deficits in cognitive and adaptive skills, debuting during the developmental period. In the last decade, microarray-based copy number variation (CNV) analysis has been proved as a strategy particularly useful in the discovery of loci and candidate genes associated with these phenotypes and is widely used in the clinics with a diagnostic purpose. In this study, we evaluated the usefulness of two genome-wide high density SNP microarrays -Cytogenetics Whole-Genome 2.7M SNP array (n=126 patients; Group 1) and CytoScan High-Density SNP array (n=447 patients; Group 2)- in the detection of clinically relevant CNVs in a cohort of ID patients from Galicia (NW Spain). In 159 (27.7%) patients, we detected 186 rare exonic chromosomal imbalances, that were grouped into the following classes: Clinically relevant (67/186; 36.0%), of unknown clinical significance (93/186; 50.0%) and benign (26/186; 14.0%). The 67 pathogenic CNVs were identified in 64 patients, which means an overall diagnostic yield of 11.2%. Overall, we confirmed that ID is a genetically heterogeneous condition and emphasized the importance of using genome-wide high density SNP microarrays in the detection of its genetic causes. Additionally, we provided clinical and molecular data of patients with pathogenic or likely pathogenic CNVs and discussed the potential implication in neurodevelopmental disorders of genes located within these variants.
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Affiliation(s)
- Inés Quintela
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformáticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain
| | - Jesús Eirís
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Carmen Gómez-Lado
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Laura Pérez-Gay
- Hospital Universitario Lucus Augusti, Unidad de Neurología Pediátrica, Departamento de Pediatría, Lugo, Spain
| | - David Dacruz
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Raquel Cruz
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBER de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Santiago de Compostela, Spain
| | - Manuel Castro-Gago
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Luz Míguez
- Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformáticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain; King Abdulaziz University, Center of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia
| | - Francisco Barros
- Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain.
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36
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Ayana R, Singh S, Pati S. Decoding Crucial LncRNAs Implicated in Neurogenesis and Neurological Disorders. Stem Cells Dev 2017; 26:541-553. [PMID: 28095733 DOI: 10.1089/scd.2016.0290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Unraveling transcriptional heterogeneity and the labyrinthine nature of neurodevelopment can probe insights into neuropsychiatric disorders. It is noteworthy that adult neurogenesis is restricted to the subventricular and subgranular zones of the brain. Recent studies suggest long non-coding RNAs (lncRNAs) as an avant-garde class of regulators implicated in neurodevelopment. But, paucity exists in the knowledge regarding lncRNAs in neurogenesis and their associations with neurodevelopmental defects. To address this, we extensively reviewed the existing literature databases as well as performed relevant in-silico analysis. We utilized Allen Brain Atlas (ABA) differential search module and generated a catalogue of ∼30,000 transcripts specific to the neurogenic zones, including coding and non-coding transcripts. To explore the existing lncRNAs reported in neurogenesis, we performed extensive literature mining and identified 392 lncRNAs. These degenerate lncRNAs were mapped onto the ABA transcript list leading to detection of 20 lncRNAs specific to neurogenic zones (Dentate gyrus/Lateral ventricle), among which 10 showed associations to several neurodevelopmental disorders following in-silico mapping onto brain disease databases like Simons Foundation Autism Research Initiative, AutDB, and lncRNADisease. Notably, using ABA correlation module, we could establish lncRNA-to-mRNA coexpression networks for the above 10 candidate lncRNAs. Finally, pathway prediction revealed physical, biochemical, or regulatory interactions for nine lncRNAs. In addition, ABA differential search also revealed 54 novel significant lncRNAs from the null set (∼30,000). Conclusively, this review represents an updated catalogue of lncRNAs in neurogenesis and neurological diseases, and overviews the field of OMICs-based data analysis for understanding lncRNome-based regulation in neurodevelopment.
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Affiliation(s)
- R Ayana
- 1 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University , Greater Noida, Uttar Pradesh, India
| | - Shailja Singh
- 1 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University , Greater Noida, Uttar Pradesh, India .,2 Special Center for Molecular Medicine, Jawaharlal Nehru University , Delhi, India
| | - Soumya Pati
- 1 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University , Greater Noida, Uttar Pradesh, India
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Schumann M, Hofmann A, Krutzke SK, Hilger AC, Marsch F, Stienen D, Gembruch U, Ludwig M, Merz WM, Reutter H. Array-based molecular karyotyping in fetuses with isolated brain malformations identifies disease-causing CNVs. J Neurodev Disord 2016; 8:11. [PMID: 27087860 PMCID: PMC4832534 DOI: 10.1186/s11689-016-9144-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/15/2016] [Indexed: 11/21/2022] Open
Abstract
Background The overall birth prevalence for congenital malformations of the central nervous system (CNS) among Europeans may be as high as 1 in 100 live births. The etiological factors remain largely unknown. The aim of this study was to detect causative copy number variations (CNVs) in fetuses of terminated pregnancies with prenatally detected isolated brain malformations. Methods Array-based molecular karyotyping was performed in a cohort of 35 terminated fetuses with isolated CNS malformations. Identified putative disease-causing CNVs were confirmed using quantitative polymerase chain reaction or multiplex ligation-dependent probe amplification. Results Based on their de novo occurrence and/or their established association with congenital brain malformations, we detected five disease-causing CNVs in four fetuses involving chromosomal regions 6p25.1-6p25.3 (FOXC1), 6q27, 16p12.3, Xp22.2-Xp22.32 (MID1), and Xp22.32-Xp22.33. Furthermore, we detected a probably disease-causing CNV involving chromosomal region 3p26.3 in one fetus, and in addition, we detected 12 CNVs in nine fetuses of unknown clinical significance. All CNVs except for two were absent in 1307 healthy in-house controls (frequency <0.0008). Each of the two CNVs present in in-house controls was present only once (frequency = 0.0008). Furthermore, our data suggests the involvement of CNTN6 and KLHL15 in the etiology of agenesis of the corpus callosum, the involvement of RASD1 and PTPRD in Dandy-Walker malformation, and the involvement of ERMARD in ventriculomegaly. Conclusions Our study suggests that CNVs play an important role in the etiology of isolated brain malformations.
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Affiliation(s)
- Madita Schumann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany ; Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | | | - Alina C Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Florian Marsch
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Ulrich Gembruch
- Department of Obstetrics and Prenatal Medicine, University of Bonn Medical School, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Waltraut M Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn Medical School, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany ; Department of Neonatology and Pediatric Intensive Care & Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany
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38
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Li Y, Choy KW, Xie HN, Chen M, He WY, Gong YF, Liu HY, Song YQ, Xian YX, Sun XF, Chen XJ. Congenital hydrocephalus and hemivertebrae associated with de novo partial monosomy 6q (6q25.3→qter). Balkan J Med Genet 2015; 18:77-84. [PMID: 26929909 PMCID: PMC4768829 DOI: 10.1515/bjmg-2015-0009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
This study was conducted to describe a prenatal case of congenital hydrocephalus and hemivertebrae with a 6q terminal deletion and to investigate the possible correlation between the genotype and phenotype of the proband. We performed an array-based comparative genomic hybridization (aCGH) analysis on a fetus diagnosed with congenital hydrocephalus and hemivertebrae. The deletion, spanning 10.06 Mb from 6q25.3 to 6qter, was detected in this fetus. The results of aCGH, karyotype and fluorescent in situ hybridization (FISH) analyses in the healthy parents were normal, which confirmed that the proband’s copy-number variant (CNV) was de novo. This deleted region encompassed 97 genes, including 28 OMIM genes. We discussed four genes (TBP, PSMB1, QKI and Pacrg) that may be responsible for hydrocephalus while the T gene may have a role in hemivertebra. We speculate that five genes in the 6q terminal deletion region were potentially associated with hemivertebrae and hydrocephalus in the proband.
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Affiliation(s)
- Y Li
- Key Laboratory of Reproductive Medicine of Guangdong Province, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - K-W Choy
- Department of Obstetrics & Gynaecology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - H-N Xie
- Department of Ultrasonic Medicine, Fetal Medical Center, First Affiliated hospital of Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - M Chen
- Key Laboratory of Reproductive Medicine of Guangdong Province, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - W-Y He
- Key Laboratory of Reproductive Medicine of Guangdong Province, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Y-F Gong
- Key Laboratory of Reproductive Medicine of Guangdong Province, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - H-Y Liu
- Key Laboratory of Reproductive Medicine of Guangdong Province, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Y-Q Song
- Key Laboratory of Reproductive Medicine of Guangdong Province, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Y-X Xian
- Key Laboratory of Reproductive Medicine of Guangdong Province, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - X-F Sun
- Key Laboratory of Reproductive Medicine of Guangdong Province, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - X-J Chen
- Key Laboratory of Reproductive Medicine of Guangdong Province, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
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Alby C, Malan V, Boutaud L, Marangoni MA, Bessières B, Bonniere M, Ichkou A, Elkhartoufi N, Bahi-Buisson N, Sonigo P, Millischer AE, Thomas S, Ville Y, Vekemans M, Encha-Razavi F, Attié-Bitach T. Clinical, genetic and neuropathological findings in a series of 138 fetuses with a corpus callosum malformation. ACTA ACUST UNITED AC 2015; 106:36-46. [DOI: 10.1002/bdra.23472] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Caroline Alby
- INSERM U1163, Institut Imagine, Hôpital Necker-Enfants Malades
- Service de Gynécologie-Obstétrique, Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Valérie Malan
- INSERM U1163, Institut Imagine, Hôpital Necker-Enfants Malades
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes, Paris Sorbonne Cité
| | - Lucile Boutaud
- INSERM U1163, Institut Imagine, Hôpital Necker-Enfants Malades
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes, Paris Sorbonne Cité
| | | | - Bettina Bessières
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Maryse Bonniere
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Amale Ichkou
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Nadia Elkhartoufi
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Nadia Bahi-Buisson
- INSERM U1163, Institut Imagine, Hôpital Necker-Enfants Malades
- Université Paris Descartes, Paris Sorbonne Cité
- Service de Neuropédiatrie, Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Pascale Sonigo
- Service de Radiologie Pédiatrique, Hôpital Necker-Enfants Malades, APHP; Paris France
| | | | - Sophie Thomas
- INSERM U1163, Institut Imagine, Hôpital Necker-Enfants Malades
- Université Paris Descartes, Paris Sorbonne Cité
| | - Yves Ville
- Service de Gynécologie-Obstétrique, Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes, Paris Sorbonne Cité
| | - Michel Vekemans
- INSERM U1163, Institut Imagine, Hôpital Necker-Enfants Malades
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes, Paris Sorbonne Cité
| | - Férechté Encha-Razavi
- INSERM U1163, Institut Imagine, Hôpital Necker-Enfants Malades
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes, Paris Sorbonne Cité
| | - Tania Attié-Bitach
- INSERM U1163, Institut Imagine, Hôpital Necker-Enfants Malades
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes, Paris Sorbonne Cité
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40
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Grozeva D, Carss K, Spasic-Boskovic O, Tejada MI, Gecz J, Shaw M, Corbett M, Haan E, Thompson E, Friend K, Hussain Z, Hackett A, Field M, Renieri A, Stevenson R, Schwartz C, Floyd JAB, Bentham J, Cosgrove C, Keavney B, Bhattacharya S, Hurles M, Raymond FL. Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability. Hum Mutat 2015; 36:1197-204. [PMID: 26350204 PMCID: PMC4833192 DOI: 10.1002/humu.22901] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/21/2015] [Indexed: 12/20/2022]
Abstract
To identify genetic causes of intellectual disability (ID), we screened a cohort of 986 individuals with moderate to severe ID for variants in 565 known or candidate ID‐associated genes using targeted next‐generation sequencing. Likely pathogenic rare variants were found in ∼11% of the cases (113 variants in 107/986 individuals: ∼8% of the individuals had a likely pathogenic loss‐of‐function [LoF] variant, whereas ∼3% had a known pathogenic missense variant). Variants in SETD5, ATRX, CUL4B, MECP2, and ARID1B were the most common causes of ID. This study assessed the value of sequencing a cohort of probands to provide a molecular diagnosis of ID, without the availability of DNA from both parents for de novo sequence analysis. This modeling is clinically relevant as 28% of all UK families with dependent children are single parent households. In conclusion, to diagnose patients with ID in the absence of parental DNA, we recommend investigation of all LoF variants in known genes that cause ID and assessment of a limited list of proven pathogenic missense variants in these genes. This will provide 11% additional diagnostic yield beyond the 10%–15% yield from array CGH alone.
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Affiliation(s)
- Detelina Grozeva
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Keren Carss
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge, CB2 0PT, United Kingdom
| | - Olivera Spasic-Boskovic
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom.,East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom
| | - Maria-Isabel Tejada
- Molecular Genetics Laboratory, Genetics Service, Cruces University Hospital, BioCruces Health Research Institute, Barakaldo-Bizkaia, 48903, Spain.,Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, 28029, Spain
| | - Jozef Gecz
- Department of Paediatrics and Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, 5006, Australia
| | - Marie Shaw
- Department of Paediatrics and Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, 5006, Australia
| | - Mark Corbett
- Department of Paediatrics and Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, 5006, Australia
| | - Eric Haan
- Department of Paediatrics and Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, 5006, Australia
| | - Elizabeth Thompson
- Department of Paediatrics and Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, 5006, Australia
| | - Kathryn Friend
- SA Pathology, Women's and Children's Hospital, Adelaide, South Australia, 5006, Australia
| | - Zaamin Hussain
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Anna Hackett
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, 2298, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, 2298, Australia
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, 53100, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, 53100, Italy
| | | | | | - James A B Floyd
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.,The Genome Centre, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, United Kingdom
| | - Jamie Bentham
- Department of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, United Kingdom
| | - Catherine Cosgrove
- Department of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, United Kingdom
| | - Bernard Keavney
- Cardiovascular Research Group, Institute of Cardiovascular Sciences, University of Manchester, Manchester, M13 9NT, United Kingdom
| | - Shoumo Bhattacharya
- Department of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, United Kingdom
| | | | | | | | - Matthew Hurles
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - F Lucy Raymond
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
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41
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Zhou L, Chen C, Li H, Chen Y, Xu X, Lin X, Tang S. Delineation variable genotype/phenotype correlations of 6q27 terminal deletion derived from dic(6;18)(q27;p10). Mol Cytogenet 2014; 7:78. [PMID: 25426168 PMCID: PMC4243269 DOI: 10.1186/s13039-014-0078-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/23/2014] [Indexed: 02/06/2023] Open
Abstract
Background Terminal deletion of 6q27 produces a rare syndrome associated with unexplained mental retardation, hypotonia, epilepsy, and multiple malformations. Structural brain malformations are consistently observed, including agenesis of the corpus callosum, hydrocephalus, periventricular nodular heterotopia, polymicrogyria, and cerebellar malformations. Here we report a fetal risk assessment of a 27-year-old woman with mental retardation, hypotonia and dysmorphic features at 17 weeks of pregnancy. Results Cytogenetic analyses revealed an addition at chromosome 6qter in the mother. Haploinsufficiency of 6q27 to 6qter (1.3 Mb) and trisomy of the entire short arm of chromosome 18 (15.2 Mb) were found using a single nucleotide polymorphism based array. Results were confirmed by molecular cytogenetics and multiplex ligation-dependent probe amplification. The karyotype of the mother was 46,XX dic(6;18)(6pter → 6q27::18p10 → 18pter).arr [hg19]6q27(169,591,548-170,898,549) × 1,18p11.3p10(12,842-15,375,878) × 3.ish dic(6;18)(q27;p10)(RP11-614P3-,RP11-1035E2+,D18Z1+). Deletion of 6q27 was associated with the structural brain malformations, whereas trisomy of 18p had minor clinical effects. The unbalanced rearrangement of chromosome 6 and chromosome 18 was de novo and was not inherited by the developing fetus. Conclusions A rare rearrangement between 6q27 and 18p was identified, which led to a de novo 1.3 Mb deletion of 6q27 and a 15.2 Mb duplication of 18p in an adult with mental retardation, hypotonia, epilepsy, and multiple malformations.
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Affiliation(s)
- Lili Zhou
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang China
| | - Chong Chen
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang China
| | - Huanzheng Li
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang China
| | - Yunying Chen
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, China
| | - Xueqin Xu
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang China
| | - Xiaoling Lin
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang China
| | - Shaohua Tang
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang China ; Key Laboratory of Medical Genetics, Zhejiang, China
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