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Hitchen R, Woolhouse M, Holch P. Breaking the silence: A qualitative exploration of parental perspectives of children with Goldenhar Syndrome. Heliyon 2024; 10:e24328. [PMID: 38318028 PMCID: PMC10839885 DOI: 10.1016/j.heliyon.2024.e24328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/15/2023] [Accepted: 01/07/2024] [Indexed: 02/07/2024] Open
Abstract
Background Goldenhar Syndrome is a rare congenital condition, typically characterized by craniofacial abnormalities and vertebral malformations. Due to its rare and complex nature, the etiology is unconfirmed, resulting in parental uncertainty and subsequent emotional sequelae. Clinical manifestations have been researched but few studies have explored parental wellbeing and Quality of Life (QoL). In this qualitative study, we explore parental views of the challenges and lived experience of raising a child with Goldenhar Syndrome. Methods Ten biological parents (five mothers and five fathers), recruited at the Goldenhar UK Conference, took part in audio-recorded, semi-structured interviews. Interviews explored emotional wellbeing, views surrounding causation, support accessed, challenges faced, experience of stigma and future outlooks. Reflexive thematic analysis was employed, and transcripts were subject to deductive and inductive coding. Results Seven themes were identified: support networks (Goldenhar UK), rollercoaster of emotion; gendered coping; uncertainty; societal reactions; coping with challenge and acceptance. Conclusions This is the first-time the life perspectives of parents, raising a child with Goldenhar Syndrome, have been explored via interviews. We have unearthed prominent issues that impact parental QoL including isolation and distress at the point of diagnosis, and throughout the multidisciplinary health journey. We have also established significant indicators of the ongoing QoL challenges faced by young people with Goldenhar Syndrome. Future work is underway exploring these issues further with teenagers, young people and adults with Goldenhar to develop a conceptual framework of their QoL. This will be used to develop a bespoke patient reported outcome (PRO) to give voice to the challenges children and young adults face during their medical journey.
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Affiliation(s)
- Rebecca Hitchen
- Leeds Beckett University, Psychology, School of Humanities and Social Sciences, Portland Building, City Campus, Leeds, LS1 3HE, West Yorkshire, UK
| | - Maxine Woolhouse
- Leeds Beckett University, Psychology, School of Humanities and Social Sciences, Portland Building, City Campus, Leeds, LS1 3HE, West Yorkshire, UK
| | - Patricia Holch
- Leeds Beckett University, Psychology, School of Humanities and Social Sciences, Portland Building, City Campus, Leeds, LS1 3HE, West Yorkshire, UK
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2
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Chawla A, Nagy C, Turecki G. Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits. Int J Mol Sci 2021; 22:7612. [PMID: 34299232 PMCID: PMC8305586 DOI: 10.3390/ijms22147612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023] Open
Abstract
The genetic architecture of complex traits is multifactorial. Genome-wide association studies (GWASs) have identified risk loci for complex traits and diseases that are disproportionately located at the non-coding regions of the genome. On the other hand, we have just begun to understand the regulatory roles of the non-coding genome, making it challenging to precisely interpret the functions of non-coding variants associated with complex diseases. Additionally, the epigenome plays an active role in mediating cellular responses to fluctuations of sensory or environmental stimuli. However, it remains unclear how exactly non-coding elements associate with epigenetic modifications to regulate gene expression changes and mediate phenotypic outcomes. Therefore, finer interrogations of the human epigenomic landscape in associating with non-coding variants are warranted. Recently, chromatin-profiling techniques have vastly improved our understanding of the numerous functions mediated by the epigenome and DNA structure. Here, we review various chromatin-profiling techniques, such as assays of chromatin accessibility, nucleosome distribution, histone modifications, and chromatin topology, and discuss their applications in unraveling the brain epigenome and etiology of complex traits at tissue homogenate and single-cell resolution. These techniques have elucidated compositional and structural organizing principles of the chromatin environment. Taken together, we believe that high-resolution epigenomic and DNA structure profiling will be one of the best ways to elucidate how non-coding genetic variations impact complex diseases, ultimately allowing us to pinpoint cell-type targets with therapeutic potential.
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Affiliation(s)
- Anjali Chawla
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
| | - Corina Nagy
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
| | - Gustavo Turecki
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
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3
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4
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Zhang Y, Liu X, Gao H, He R, Zhao Y. Identifying of 22q11.2 variations in Chinese patients with development delay. BMC Med Genomics 2021; 14:26. [PMID: 33482818 PMCID: PMC7821542 DOI: 10.1186/s12920-020-00849-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022] Open
Abstract
Background 22q11.2 variation is a significant genetic factor relating to development delay and/or intellectual disability. However, the prevalence, genetic characteristics and clinical phenotype in Chinese patients are unknown. Methods In total 6034 patients with development delay and/or intellectual disability were screened by multiplex ligation-dependent probe amplification (MLPA) P245 and G-band karyotyping. The positive patients with 22q11.2 imbalance were confirmed by MLPA P250 assay. Results 52 (0.86%) patients were found to carry different levels of 22q11.2 variations, in which 37 cases (71.2%) had heterozygous deletions, whereas 15 (28.8%) had heterogeneous duplications. 34 cases (65.4%) carried typical imbalance from low copy repeat (LCR) 22 A to D. The other cases had atypical variations, relating to LCR22 A-B, LCR22 C-D, LCR22 B-D, LCR22 D-E, LCR22 E-F and LCR22 B-F region. The phenotypes of these 52 patients were variable, including development delay, language delay, facial anomalies, heart defects, psychiatric/behavior problems, epilepsy, periventricular leukomalacia, hearing impairment, growth delay etc. Conclusion These data revealed the prevalence and variability of 22q11.2 genomic imbalance in Chinese patients with development delay and/or intellectual disability. It suggested that genetic detection of 22q11.2 is necessary, especially for the patients with mental retardation and development disorders, which deserves the attention of all pediatricians in their daily work.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoliang Liu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Haiming Gao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Rong He
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yanyan Zhao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China.
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5
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Duan J, Sanders AR, Gejman PV. From Schizophrenia Genetics to Disease Biology: Harnessing New Concepts and Technologies. JOURNAL OF PSYCHIATRY AND BRAIN SCIENCE 2019; 4:e190014. [PMID: 31555746 PMCID: PMC6760308 DOI: 10.20900/jpbs.20190014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Schizophrenia (SZ) is a severe mental disorder afflicting around 1% of the population. It is highly heritable but with complex genetics. Recent research has unraveled a plethora of risk loci for SZ. Accordingly, our conceptual understanding of SZ genetics has been rapidly evolving, from oligogenic models towards polygenic or even omnigenic models. A pressing challenge to the field, however, is the translation of the many genetic findings of SZ into disease biology insights leading to more effective treatments. Bridging this gap requires the integration of genetic findings and functional genomics using appropriate cellular models. Harnessing new technologies, such as the development of human induced pluripotent stem cells (hiPSC) and the CRISPR/Cas-based genome/epigenome editing approach are expected to change our understanding of SZ disease biology to a fundamentally higher level. Here, we discuss some new developments.
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Affiliation(s)
- Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neurosciences, The University of Chicago, Chicago, IL 60637, USA
| | - Alan R. Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neurosciences, The University of Chicago, Chicago, IL 60637, USA
| | - Pablo V. Gejman
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neurosciences, The University of Chicago, Chicago, IL 60637, USA
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6
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Huynh L, Hormozdiari F. TAD fusion score: discovery and ranking the contribution of deletions to genome structure. Genome Biol 2019; 20:60. [PMID: 30898144 PMCID: PMC6427865 DOI: 10.1186/s13059-019-1666-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/01/2019] [Indexed: 11/17/2022] Open
Abstract
Deletions that fuse two adjacent topologically associating domains (TADs) can cause severe developmental disorders. We provide a formal method to quantify deletions based on their potential disruption of the three-dimensional genome structure, denoted as the TAD fusion score. Furthermore, we show that deletions that cause TAD fusion are rare and under negative selection in the general population. Finally, we show that our method correctly gives higher scores to deletions reported to cause various disorders, including developmental disorders and cancer, in comparison to the deletions reported in the 1000 Genomes Project. The TAD fusion score tool is publicly available at https://github.com/HormozdiariLab/TAD-fusion-score .
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Affiliation(s)
| | - Fereydoun Hormozdiari
- Genome Center, UC Davis, Davis, USA.
- UC Davis MIND Institute, Sacramento, USA.
- Department of Biochemistry and Molecular Medicine, UC Davis, Sacramento, USA.
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Oliveira LDFS, Júlio-Costa A, Dos Santos FC, Carvalho MRS, Haase VG. Numerical Processing Impairment in 22q11.2 (LCR22-4 to LCR22-5) Microdeletion: A Cognitive-Neuropsychological Case Study. Front Psychol 2018; 9:2193. [PMID: 30524331 PMCID: PMC6258774 DOI: 10.3389/fpsyg.2018.02193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/23/2018] [Indexed: 11/23/2022] Open
Abstract
Although progress has been made, the cognitive, biological and, particularly, the genetic underpinnings of math learning difficulties (MD) remain largely unknown. This difficulty stems from the heterogeneity of MD and from the large contribution of environmental factors to its etiology. Understanding endophenotypes, e.g., the role of the Approximate Number System (ANS), may help understanding the nature of MD. MD associated with ANS impairments has been described in some genetic conditions, e.g., 22q11.2 deletion syndrome (22q11.2DS or Velocardiofacial syndrome, VCFS). Recently, a girl with MD was identified in a school population screening. She has a new syndrome resulting from a microdeletion in 22q11.2 (LCR22-4 to LCR22-5), a region adjacent to but not overlapping with region 22q11.2 (LCR22-2 to LCR22-4), typically deleted in VCFS. Here, we describe her cognitive-neuropsychological and numerical-cognitive profiles. The girl was assessed twice, at 8 and 11 years. Her numerical-cognitive performance at both times was compared to demographically similar girls with normal intelligence in a single-case, quasi-experimental study. Neuropsychological assessment was normal, except for relatively minor impairments in executive functions. She presented severe and persistent difficulties in the simplest single-digit calculations. Difficulties in commutative operations improved from the first to the second assessment. Difficulties in subtraction persisted and were severe. No difficulties were observed in Arabic number writing. Difficulties in single-digit calculation co-occurred with basic numerical processing impairments in symbolic and non-symbolic (single-digit comparison, dot sets size comparison and estimation) tasks. Her difficulties suggest ANS impairment. No difficulties were detected in visuospatial/visuoconstructional and in phonological processing tasks. The main contributions of the present study are: (a) this is the first characterization of the neuropsychological phenotype in 22q11.2DS (LCR22-4 to LCR22.5) with normal intelligence; (b) mild forms of specific genetic conditions contribute to persistent MD in otherwise typical persons; (c) heterogeneity of neurogenetic underpinnings of MD is suggested by poor performance in non-symbolic numerical processing, dissociated from visuospatial/visuoconstructional and phonological impairments; (d) similar to what happens in 22q11.2DS (LCR22-2 to LCR22-4), ANS impairments may also characterize 22q11.2DS (LCR22-4 to LCR22-5).
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Affiliation(s)
- Lívia de Fátima Silva Oliveira
- Laboratório de Neuropsicologia do Desenvolvimento, Departamento de Psicologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Programa de Pós-Graduação em Neurociências, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Annelise Júlio-Costa
- Laboratório de Neuropsicologia do Desenvolvimento, Departamento de Psicologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Vitor Geraldi Haase
- Laboratório de Neuropsicologia do Desenvolvimento, Departamento de Psicologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Programa de Pós-Graduação em Neurociências, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Programa de Pós-graduação em Psicologia, Cognição e Comportamento, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Programa de Pós-graduação em Saúde da Criança e do Adolescente, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Instituto Nacional de Ciência e Tecnologia sobre Comportamento, Cognição e Ensino, São Carlos, Brazil
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8
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Li Z, Zheng M, Abdalla BA, Zhang Z, Xu Z, Ye Q, Xu H, Luo W, Nie Q, Zhang X. Genome-wide association study of aggressive behaviour in chicken. Sci Rep 2016; 6:30981. [PMID: 27485826 PMCID: PMC4971532 DOI: 10.1038/srep30981] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/12/2016] [Indexed: 11/09/2022] Open
Abstract
In the poultry industry, aggressive behaviour is a large animal welfare issue all over the world. To date, little is known about the underlying genetics of the aggressive behaviour. Here, we performed a genome-wide association study (GWAS) to explore the genetic mechanism associated with aggressive behaviour in chickens. The GWAS results showed that a total of 33 SNPs were associated with aggressive behaviour traits (P < 4.6E-6). rs312463697 on chromosome 4 was significantly associated with aggression (P = 2.10905E-07), and it was in the intron region of the sortilin-related VPS10 domain containing receptor 2 (SORCS2) gene. In addition, biological function analysis of the nearest 26 genes around the significant SNPs was performed with Ingenuity Pathway Analysis. An interaction network contained 17 genes was obtained and SORCS2 was involved in this network, interacted with nerve growth factor (NGF), nerve growth factor receptor (NGFR), dopa decarboxylase (L-dopa) and dopamine. After knockdown of SORCS2, the mRNA levels of NGF, L-dopa and dopamine receptor genes DRD1, DRD2, DRD3 and DRD4 were significantly decreased (P < 0.05). In summary, our data indicated that SORCS2 might play an important role in chicken aggressive behaviour through the regulation of dopaminergic pathways and NGF.
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Affiliation(s)
- Zhenhui Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Ming Zheng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Bahareldin Ali Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Zhe Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Zhenqiang Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China.,Wens NanFang Poultry Breeding Co., Ltd., YunFu 527400, Guangdong, China
| | - Qiao Ye
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Haiping Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Wei Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
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The Identification of Microdeletion and Reciprocal Microduplication in 22q11.2 Using High-Resolution CMA Technology. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7415438. [PMID: 27123452 PMCID: PMC4830712 DOI: 10.1155/2016/7415438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/13/2016] [Indexed: 01/05/2023]
Abstract
The chromosome 22q11.2 region has long been implicated in genomic diseases. Some genomic regions exhibit numerous low copy repeats with high identity in which they provide increased genomic instability and mediate deletions and duplications in many disorders. DiGeorge Syndrome is the most common deletion syndrome and reciprocal duplications could be occurring in half of the frequency of microdeletions. We described five patients with phenotypic variability that carries deletions or reciprocal duplications at 22q11.2 detected by Chromosomal Microarray Analysis. The CytoScan HD technology was used to detect changes in the genome copy number variation of patients who had clinical indication to global developmental delay and a normal karyotype. We observed in our study three microdeletions and two microduplications in 22q11.2 region with variable intervals containing known genes and unstudied transcripts as well as the LCRs that are often flanking and within this genomic rearrangement. The identification of these variants is of particular interest because it may provide insight into genes or genomic regions that are crucial for specific phenotypic manifestations and are useful to assist in the quest for understanding the mechanisms subjacent to genomic deletions and duplications.
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10
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Poirsier C, Besseau-Ayasse J, Schluth-Bolard C, Toutain J, Missirian C, Le Caignec C, Bazin A, de Blois MC, Kuentz P, Catty M, Choiset A, Plessis G, Basinko A, Letard P, Flori E, Jimenez M, Valduga M, Landais E, Lallaoui H, Cartault F, Lespinasse J, Martin-Coignard D, Callier P, Pebrel-Richard C, Portnoi MF, Busa T, Receveur A, Amblard F, Yardin C, Harbuz R, Prieur F, Le Meur N, Pipiras E, Kleinfinger P, Vialard F, Doco-Fenzy M. A French multicenter study of over 700 patients with 22q11 deletions diagnosed using FISH or aCGH. Eur J Hum Genet 2015; 24:844-51. [PMID: 26508576 DOI: 10.1038/ejhg.2015.219] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/02/2015] [Accepted: 09/08/2015] [Indexed: 12/31/2022] Open
Abstract
Although 22q11.2 deletion syndrome (22q11.2DS) is the most recurrent human microdeletion syndrome associated with a highly variable phenotype, little is known about the condition's true incidence and the phenotype at diagnosis. We performed a multicenter, retrospective analysis of postnatally diagnosed patients recruited by members of the Association des Cytogénéticiens de Langue Française (the French-Speaking Cytogeneticists Association). Clinical and cytogenetic data on 749 cases diagnosed between 1995 and 2013 were collected by 31 French cytogenetics laboratories. The most frequent reasons for referral of postnatally diagnosed cases were a congenital heart defect (CHD, 48.6%), facial dysmorphism (49.7%) and developmental delay (40.7%). Since 2007 (the year in which array comparative genomic hybridization (aCGH) was introduced for the routine screening of patients with intellectual disability), almost all cases have been diagnosed using FISH (96.1%). Only 15 cases (all with an atypical phenotype) were diagnosed with aCGH; the deletion size ranged from 745 to 2904 kb. The deletion was inherited in 15.0% of cases and was of maternal origin in 85.5% of the latter. This is the largest yet documented cohort of patients with 22q11.2DS (the most commonly diagnosed microdeletion) from the same population. French cytogenetics laboratories diagnosed at least 108 affected patients (including fetuses) per year from among a national population of ∼66 million. As observed for prenatal diagnoses, CHDs were the most frequently detected malformation in postnatal diagnoses. The most common CHD in postnatal diagnoses was an isolated septal defect.
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Affiliation(s)
| | | | | | | | | | - Cédric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Inserm UMR957, Faculté de Médecine, Nantes, France
| | - Anne Bazin
- Laboratoire de Cytogénétique Pasteur-Cerba, Saint-Ouen l'Aumône, France
| | - Marie Christine de Blois
- Service de Cytogénétique, CHU de Necker, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Paul Kuentz
- Service de Cytogénétique, CHU de Besançon, Besançon, France
| | - Marie Catty
- Service de Cytogénétique, Biolille, Lille, France
| | - Agnès Choiset
- Service de Cytogénétique, Hôpital Saint Vincent de Paul, Paris, France
| | - Ghislaine Plessis
- Laboratoire de Cytogénétique Postnatal, CHU Clemenceau, Caen, France
| | - Audrey Basinko
- Service de Cytogénétique et Biologie de la Reproduction, CHRU de Brest, Brest, France
| | | | - Elisabeth Flori
- Service de Cytogénétique, CHU de Strasbourg, Strasbourg, France
| | | | | | | | | | - François Cartault
- Service de Cytogénétique, Hôpital de Saint-Denis, Saint-Denis de la Réunion, France
| | | | | | | | - Céline Pebrel-Richard
- Univ Clermont 1, UFR Médecine, Histologie Embryologie Cytogénétique, Clermont-Ferrand, France.,CHU-Estaing Clermont-Ferrand, Cytogénétique Médicale, Clermont-Ferrand, France.,EA 4677 ERTICA, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, France
| | | | - Tiffany Busa
- Departement de Genétique Medicale, Hopital de la Timone, CHU de Marseille, Marseille, France
| | | | | | | | - Radu Harbuz
- Service de Génétique, CHU de Poitiers, Poitiers, France
| | - Fabienne Prieur
- Service de Cytogénétique, CHU de Saint-Etienne, Saint-Etienne, France
| | - Nathalie Le Meur
- Service de Cytogénétique, Etablissement Français du Sang de Normandie, Rouen, France
| | - Eva Pipiras
- Hôpital Jean Verdier, UF de Cytogénétique, CHU Paris, Paris, France.,Université Paris 13, Sorbonne Paris Cité, INSERM 1141, Paris, France
| | - Pascale Kleinfinger
- Laboratoire de Cytogénétique Pasteur-Cerba, Saint-Ouen l'Aumône, France.,Association des Cytogénéticiens de Langue Française (French-Speaking Cytogeneticists Association), Paris, France
| | - François Vialard
- Service de Cytogénétique, Hôpital Poissy/Saint-Germain-en-Laye, Poissy, France.,Association des Cytogénéticiens de Langue Française (French-Speaking Cytogeneticists Association), Paris, France.,GIG, UVSQ, Versailles, Paris, France
| | - Martine Doco-Fenzy
- Département de Génétique, CHU de Reims, Reims, France.,Association des Cytogénéticiens de Langue Française (French-Speaking Cytogeneticists Association), Paris, France.,EA3801, SFR-CAP Santé, Reims, France
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11
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Burnside RD. 22q11.21 Deletion Syndromes: A Review of Proximal, Central, and Distal Deletions and Their Associated Features. Cytogenet Genome Res 2015; 146:89-99. [PMID: 26278718 DOI: 10.1159/000438708] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 04/13/2024] Open
Abstract
Chromosome 22q11.21 contains a cluster of low-copy repeats (LCRs), referred to as LCR22A-H, that mediate meiotic non-allelic homologous recombination, resulting in either deletion or duplication of various intervals in the region. The deletion of the DiGeorge/velocardiofacial syndrome interval LCR22A-D is the most common recurrent microdeletion in humans, with an estimated incidence of ∼1:4,000 births. Deletion of other intervals in 22q11.21 have also been described, but the literature is often confusing, as the terms 'proximal', 'nested', 'distal', and 'atypical' have all been used to describe various of the other intervals. Individuals with deletions tend to have features with widely variable expressivity, even among families. This review concisely delineates each interval and classifies the reported literature accordingly.
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Affiliation(s)
- Rachel D Burnside
- Department of Cytogenetics, Laboratory Corporation of America Holdings, Center for Molecular Biology and Pathology, Research Triangle Park, N.C., USA
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Beleza-Meireles A, Hart R, Clayton-Smith J, Oliveira R, Reis CF, Venâncio M, Ramos F, Sá J, Ramos L, Cunha E, Pires LM, Carreira IM, Scholey R, Wright R, Urquhart JE, Briggs TA, Kerr B, Kingston H, Metcalfe K, Donnai D, Newman WG, Saraiva JM, Tassabehji M. Oculo-auriculo-vertebral spectrum: clinical and molecular analysis of 51 patients. Eur J Med Genet 2015. [PMID: 26206081 DOI: 10.1016/j.ejmg.2015.07.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Oculo-auriculo-vertebral spectrum (OAVS OMIM 164210) is a craniofacial developmental disorder affecting the development of the structures derived from the 1st and the 2nd branchial arches during embryogenesis, with consequential maxillary, mandibular, and ear abnormalities. The phenotype in OAVS is variable and associated clinical features can involve the cardiac, renal, skeletal, and central nervous systems. Its aetiology is still poorly understood. METHODS We have evaluated the clinical phenotypes of 51 previously unpublished patients with OAVS and their parents, and performed comparative genomic hybridization microarray studies to identify potential causative loci. RESULTS Of all 51 patients, 16 (31%) had a family history of OAVS. Most had no relevant pre-natal history and only 5 (10%) cases had a history of environmental exposures that have previously been described as risk factors for OAVS. In 28 (55%) cases, the malformations were unilateral. When the involvement was bilateral, it was asymmetric. Ear abnormalities were present in 47 (92%) patients (unilateral in 24; and bilateral in 23). Hearing loss was common (85%), mostly conductive, but also sensorineural, or a combination of both. Hemifacial microsomia was present in 46 (90%) patients (17 also presented facial nerve palsy). Ocular anomalies were present in 15 (29%) patients. Vertebral anomalies were confirmed in 10 (20%) cases; 50% of those had additional heart, brain and/or other organ abnormalities. Brain abnormalities were present in 5 (10%) patients; developmental delay was more common among these patients. Limb abnormalities were found in 6 (12%) patients, and urogenital anomalies in 5 (10%). Array-CGH analysis identified 22q11 dosage anomalies in 10 out of 22 index cases screened. DISCUSSION In this study we carried out in-depth phenotyping of OAVS in a large, multicentre cohort. Clinical characteristics are in line with those reported previously, however, we observed a higher incidence of hemifacial microsomia and lower incidence of ocular anomalies. Furthermore our data suggests that OAVS patients with vertebral anomalies or congenital heart defects have a higher frequency of additional brain, limb or other malformations. We had a higher rate of familial cases in our cohort in comparison with previous reports, possibly because these cases were referred preferentially to our genetic clinic where family members underwent examination. We propose that familial OAVS cases show phenotypic variability, hence, affected relatives might have been misclassified in previous reports. Moreover, in view of its phenotypic variability, OAVS is potentially a spectrum of conditions, which overlap with other conditions, such as mandibulofacial dysostosis. Array CGH in our cohort identified recurrent dosage anomalies on 22q11, which may contribute to, or increase the risk of OAVS. We hypothesize that although the 22q11 locus may harbour gene(s) or regulatory elements that play a role in the regulation of craniofacial symmetry and 1st and 2nd branchial arch development, OAVS is a heterogeneous condition and many cases have a multifactorial aetiology or are caused by mutations in as yet unidentified gene(s).
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Affiliation(s)
- Ana Beleza-Meireles
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal; Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK.
| | - Rachel Hart
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK; Mersey Regional Genetic Service, Alder Hey Hospital, Liverpool, UK
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK; Central Manchester University Hospitals NHS Foundation Trust as part of Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Renata Oliveira
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Cláudia Falcão Reis
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Margarida Venâncio
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Fabiana Ramos
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joaquim Sá
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Lina Ramos
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Elizabete Cunha
- Unidade Hematologia Molecular, Serviço de Hematologia, CHUC, Portugal
| | - Luís Miguel Pires
- Faculdade de Medicina da Universidade de Coimbra, Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Isabel Marques Carreira
- Faculdade de Medicina da Universidade de Coimbra, Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Rachel Scholey
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Ronnie Wright
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, USA
| | - Jill E Urquhart
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, USA
| | - Tracy A Briggs
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Helen Kingston
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Dian Donnai
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - William G Newman
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK; Central Manchester University Hospitals NHS Foundation Trust as part of Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Jorge Manuel Saraiva
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal; Faculdade de Medicina da Universidade de Coimbra, Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - May Tassabehji
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK; Central Manchester University Hospitals NHS Foundation Trust as part of Manchester Academic Health Science Centre (MAHSC), Manchester, UK.
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Harewood L, Fraser P. The impact of chromosomal rearrangements on regulation of gene expression. Hum Mol Genet 2014; 23:R76-82. [PMID: 24907073 DOI: 10.1093/hmg/ddu278] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The effects that coding region single-nucleotide polymorphisms or mutations have on gene expression have been well documented, predominantly owing to their association with disease. The effects of structural chromosomal rearrangements are also receiving increasing attention with the development of new techniques that allow accurate, high-resolution data, whether genomic interaction or transcriptome data, to be generated right down to the single-cell level. Over the past 18 months, these advances in experimental techniques have been used to further confirm and delineate the substantial effects that chromosome rearrangements can have on the regulation of gene expression and provide evidence of direct links between the two.
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Affiliation(s)
- Louise Harewood
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
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Blumenthal I, Ragavendran A, Erdin S, Klei L, Sugathan A, Guide J, Manavalan P, Zhou J, Wheeler V, Levin J, Ernst C, Roeder K, Devlin B, Gusella J, Talkowski M. Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families. Am J Hum Genet 2014; 94:870-83. [PMID: 24906019 DOI: 10.1016/j.ajhg.2014.05.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/12/2014] [Indexed: 12/18/2022] Open
Abstract
Reciprocal copy-number variation (CNV) of a 593 kb region of 16p11.2 is a common genetic cause of autism spectrum disorder (ASD), yet it is not completely penetrant and can manifest in a wide array of phenotypes. To explore its molecular consequences, we performed RNA sequencing of cerebral cortex from mouse models with CNV of the syntenic 7qF3 region and lymphoblast lines from 34 members of 7 multiplex ASD-affected families harboring the 16p11.2 CNV. Expression of all genes in the CNV region correlated well with their DNA copy number, with no evidence of dosage compensation. We observed effects on gene expression outside the CNV region, including apparent positional effects in cis and in trans at genomic segments with evidence of physical interaction in Hi-C chromosome conformation data. One of the most significant positional effects was telomeric to the 16p11.2 CNV and includes the previously described "distal" 16p11.2 microdeletion. Overall, 16p11.2 CNV was associated with altered expression of genes and networks that converge on multiple hypotheses of ASD pathogenesis, including synaptic function (e.g., NRXN1, NRXN3), chromatin modification (e.g., CHD8, EHMT1, MECP2), transcriptional regulation (e.g., TCF4, SATB2), and intellectual disability (e.g., FMR1, CEP290). However, there were differences between tissues and species, with the strongest effects being consistently within the CNV region itself. Our analyses suggest that through a combination of indirect regulatory effects and direct effects on nuclear architecture, alteration of 16p11.2 genes disrupts expression networks that involve other genes and pathways known to contribute to ASD, suggesting an overlap in mechanisms of pathogenesis.
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