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Toren Y, Ziv Y, Sragovich S, McKinney RA, Barak S, Shazman S, Gozes I. Sex-Specific ADNP/NAP (Davunetide) Regulation of Cocaine-Induced Plasticity. J Mol Neurosci 2024; 74:76. [PMID: 39251453 PMCID: PMC11384652 DOI: 10.1007/s12031-024-02234-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 09/11/2024]
Abstract
Cocaine use disorder (CUD) is a chronic neuropsychiatric disorder estimated to effect 1-3% of the population. Activity-dependent neuroprotective protein (ADNP) is essential for brain development and functioning, shown to be protective in fetal alcohol syndrome and to regulate alcohol consumption in adult mice. The goal of this study was to characterize the role of ADNP, and its active peptide NAP (NAPVSIPQ), which is also known as davunetide (investigational drug) in mediating cocaine-induced neuroadaptations. Real time PCR was used to test levels of Adnp and Adnp2 in the nucleus accumbens (NAc), ventral tegmental area (VTA), and dorsal hippocampus (DH) of cocaine-treated mice (15 mg/kg). Adnp heterozygous (Adnp +/-)and wild-type (Adnp +/-) mice were further tagged with excitatory neuronal membrane-expressing green fluorescent protein (GFP) that allowed for in vivo synaptic quantification. The mice were treated with cocaine (5 injections; 15 mg/kg once every other day) with or without NAP daily injections (0.4 µg/0.1 ml) and sacrificed following the last treatment. We analyzed hippocampal CA1 pyramidal cells from 3D confocal images using the Imaris x64.8.1.2 (Oxford Instruments) software to measure changes in dendritic spine density and morphology. In silico ADNP/NAP/cocaine structural modeling was performed as before. Cocaine decreased Adnp and Adnp2 expression 2 h after injection in the NAc and VTA of male mice, with mRNA levels returning to baseline levels after 24 h. Cocaine further reduced hippocampal spine density, particularly synaptically weaker immature thin and stubby spines, in male Adnp+/+) mice while increasing synaptically stronger mature (mushroom) spines in Adnp+/-) male mice and thin and stubby spines in females. Lastly, we showed that cocaine interacts with ADNP on a zinc finger domain identical to ketamine and adjacent to a NAP-zinc finger interaction site. Our results implicate ADNP in cocaine abuse, further placing the ADNP gene as a key regulator in neuropsychiatric disorders. Ketamine/cocaine and NAP treatment may be interchangeable to some degree, implicating an interaction with adjacent zinc finger motifs on ADNP and suggestive of a potential sex-dependent, non-addictive NAP treatment for CUD.
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Affiliation(s)
- Yael Toren
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Yarden Ziv
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 6997801, Israel
- School of Psychological Sciences, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shlomo Sragovich
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - R Anne McKinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Segev Barak
- School of Psychological Sciences, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shula Shazman
- Department of Mathematics and Computer Science, The Open University of Israel, Ra'anana, Israel
| | - Illana Gozes
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 6997801, Israel.
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Zhou B, Purmann C, Guo H, Shin G, Huang Y, Pattni R, Meng Q, Greer SU, Roychowdhury T, Wood RN, Ho M, zu Dohna H, Abyzov A, Hallmayer JF, Wong WH, Ji HP, Urban AE. Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints. Proc Natl Acad Sci U S A 2024; 121:e2322834121. [PMID: 39042694 PMCID: PMC11295037 DOI: 10.1073/pnas.2322834121] [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: 12/28/2023] [Accepted: 06/15/2024] [Indexed: 07/25/2024] Open
Abstract
We developed a generally applicable method, CRISPR/Cas9-targeted long-read sequencing (CTLR-Seq), to resolve, haplotype-specifically, the large and complex regions in the human genome that had been previously impenetrable to sequencing analysis, such as large segmental duplications (SegDups) and their associated genome rearrangements. CTLR-Seq combines in vitro Cas9-mediated cutting of the genome and pulse-field gel electrophoresis to isolate intact large (i.e., up to 2,000 kb) genomic regions that encompass previously unresolvable genomic sequences. These targets are then sequenced (amplification-free) at high on-target coverage using long-read sequencing, allowing for their complete sequence assembly. We applied CTLR-Seq to the SegDup-mediated rearrangements that constitute the boundaries of, and give rise to, the 22q11.2 Deletion Syndrome (22q11DS), the most common human microdeletion disorder. We then performed de novo assembly to resolve, at base-pair resolution, the full sequence rearrangements and exact chromosomal breakpoints of 22q11.2DS (including all common subtypes). Across multiple patients, we found a high degree of variability for both the rearranged SegDup sequences and the exact chromosomal breakpoint locations, which coincide with various transposons within the 22q11.2 SegDups, suggesting that 22q11DS can be driven by transposon-mediated genome recombination. Guided by CTLR-Seq results from two 22q11DS patients, we performed three-dimensional chromosomal folding analysis for the 22q11.2 SegDups from patient-derived neurons and astrocytes and found chromosome interactions anchored within the SegDups to be both cell type-specific and patient-specific. Lastly, we demonstrated that CTLR-Seq enables cell-type specific analysis of DNA methylation patterns within the deletion haplotype of 22q11DS.
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Affiliation(s)
- Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Hanmin Guo
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
- Department of Statistics, Stanford University, Stanford, CA94305
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
| | - GiWon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Yiling Huang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Qingxi Meng
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Stephanie U. Greer
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Tanmoy Roychowdhury
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN55905
| | - Raegan N. Wood
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Marcus Ho
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Heinrich zu Dohna
- Department of Biology, American University of Beirut, Beirut1107 2020, Lebanon
| | - Alexej Abyzov
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN55905
| | - Joachim F. Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
| | - Wing H. Wong
- Department of Statistics, Stanford University, Stanford, CA94305
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
- Program on Genetics of Brain Function, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA94305
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3
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Zhao Y, Deng W, Wang Z, Wang Y, Zheng H, Zhou K, Xu Q, Bai L, Liu H, Ren Z, Jiang Z. Genetics of congenital heart disease. Clin Chim Acta 2024; 552:117683. [PMID: 38030030 DOI: 10.1016/j.cca.2023.117683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023]
Abstract
During embryonic development, the cardiovascular system and the central nervous system exhibit a coordinated developmental process through intricate interactions. Congenital heart disease (CHD) refers to structural or functional abnormalities that occur during embryonic or prenatal heart development and is the most common congenital disorder. One of the most common complications in CHD patients is neurodevelopmental disorders (NDD). However, the specific mechanisms, connections, and precise ways in which CHD co-occurs with NDD remain unclear. According to relevant research, both genetic and non-genetic factors are significant contributors to the co-occurrence of sporadic CHD and NDD. Genetic variations, such as chromosomal abnormalities and gene mutations, play a role in the susceptibility to both CHD and NDD. Further research should aim to identify common molecular mechanisms that underlie the co-occurrence of CHD and NDD, possibly originating from shared genetic mutations or shared gene regulation. Therefore, this review article summarizes the current advances in the genetics of CHD co-occurring with NDD, elucidating the application of relevant gene detection techniques. This is done with the aim of exploring the genetic regulatory mechanisms of CHD co-occurring with NDD at the gene level and promoting research and treatment of developmental disorders related to the cardiovascular and central nervous systems.
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Affiliation(s)
- Yuanqin Zhao
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Wei Deng
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Zhaoyue Wang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Yanxia Wang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Hongyu Zheng
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Kun Zhou
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Qian Xu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Le Bai
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Huiting Liu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Zhong Ren
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Zhisheng Jiang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
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Pan Z, Tian H, Fang T, Liu Z, Liu X, Dou G, Huang G, Zhang Z, Chen G, Wang W, Zhuo C. OGDHL Variant rs2293239: A Potential Genetic Driver of Chinese Familial Depressive Disorder. Front Psychiatry 2022; 13:771950. [PMID: 35370858 PMCID: PMC8971628 DOI: 10.3389/fpsyt.2022.771950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/21/2022] [Indexed: 12/16/2022] Open
Abstract
Depressive disorders are a severe psychiatric and social problem that affect more than 4% of the global population. Depressive disorders have explicit hereditary characteristics; however, the precise driving genetic force behind these disorders has not yet been clearly illustrated. In the present study, we recruited a three-generation Chinese pedigree in which 5 of 17 members had long-term depression. We conducted whole-exome sequencing to identify the genetic mutation profiles of the family, and a list of susceptible genetic variations that were highly associated with depression onset was revealed via multiple omics analysis. In particular, a non-synonymous single nucleotide variation in the oxoglutarate dehydrogenase-like (OGDHL) gene, rs2293239 (p.Asn725Ser), was identified as one of the major driving genetic forces for depression onset in the family. This variant causes an important conformational change in the transketolase domain of OGDHL, thus reducing its binding affinity with the cofactor thiamine pyrophosphate and eventually resulting in the abnormal accumulation of glutamate in the brain. Brain imaging analysis further linked the rs2293239 variant with an enlarged amygdala and cerebellum in depressive family members. In summary, the present study enhances the current genetic understanding of depressive disorders. It also provides new options for prioritizing better clinical therapeutic regimens, as well as identifying a new protein target for the design of highly specific drugs to treat depressive disorders.
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Affiliation(s)
- Zhi Pan
- Key Laboratory of Genetic Psychiatry, Wenzhou Seventh People Hospital, Wenzhou, China
| | - Hongjun Tian
- Key Laboratory of Real Time Tracing of Brain Circuits of Neurology and Psychiatry, Nankai University Affiliated Tianjin Fourth Center Hospital, Tianjin Medical University Affiliated Tianjin Fourth Center Hospital, Tianjin Fourth Center Hospital, Tianjin, China
| | - Tao Fang
- Key Laboratory of Real Time Tracing of Brain Circuits of Neurology and Psychiatry, Nankai University Affiliated Tianjin Fourth Center Hospital, Tianjin Medical University Affiliated Tianjin Fourth Center Hospital, Tianjin Fourth Center Hospital, Tianjin, China
| | - Zhidong Liu
- Key Laboratory of Real Time Tracing of Brain Circuits of Neurology and Psychiatry, Nankai University Affiliated Tianjin Fourth Center Hospital, Tianjin Medical University Affiliated Tianjin Fourth Center Hospital, Tianjin Fourth Center Hospital, Tianjin, China
| | - Xiangdong Liu
- Key Laboratory of Real Time Tracing of Brain Circuits of Neurology and Psychiatry, Nankai University Affiliated Tianjin Fourth Center Hospital, Tianjin Medical University Affiliated Tianjin Fourth Center Hospital, Tianjin Fourth Center Hospital, Tianjin, China
| | - Guangqian Dou
- Key Laboratory of Real Time Tracing of Brain Circuits of Neurology and Psychiatry, Nankai University Affiliated Tianjin Fourth Center Hospital, Tianjin Medical University Affiliated Tianjin Fourth Center Hospital, Tianjin Fourth Center Hospital, Tianjin, China
| | - Guoyong Huang
- Key Laboratory of Genetic Psychiatry, Wenzhou Seventh People Hospital, Wenzhou, China
| | - Zhenqing Zhang
- Department of Psychiatry, Xiamen Xianyue Hospital, Xiamen, China
| | - Guangdong Chen
- Key Laboratory of Genetic Psychiatry, Wenzhou Seventh People Hospital, Wenzhou, China
| | - Wenqiang Wang
- Department of Psychiatry, Xiamen Xianyue Hospital, Xiamen, China
| | - Chuanjun Zhuo
- Key Laboratory of Real Time Tracing of Brain Circuits of Neurology and Psychiatry, Nankai University Affiliated Tianjin Fourth Center Hospital, Tianjin Medical University Affiliated Tianjin Fourth Center Hospital, Tianjin Fourth Center Hospital, Tianjin, China.,Department of Psychiatry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Biological Psychiatry International Joint Laboratory of Henan, Zhengzhou University, Zhengzhou, China
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5
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Wang Y, Jiang T, Tang P, Wu Y, Jiang Z, Dai J, Gu Y, Xu J, Da M, Ma H, Jin G, Mo X, Li Q, Wang X, Hu Z. Family-based whole-genome sequencing identifies compound heterozygous protein-coding and noncoding mutations in tetralogy of Fallot. Gene 2020; 741:144555. [PMID: 32165302 DOI: 10.1016/j.gene.2020.144555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/08/2020] [Indexed: 12/28/2022]
Abstract
Tetralogy of Fallot (TOF) is one of most serious cyanotic congenital heart disease (CHD) and the prevalence is estimated to be 1 in 3000 live births worldwide. Though multiple studies have found genetic variants as risk factors for TOF, they could only explain a small fraction of the pathogenesis. Here, we performed whole genome sequencing (WGS) for 6 individuals derived from 2 families to evaluate pathogenic mutations located in both coding and noncoding regions. We characterized the annotated deleterious coding mutations and impaired noncoding mutations in regulatory elements by various data analysis. Additionally, functional assays were conducted to validate function regulatory elements and noncoding mutations. Interestingly, a compound heterozygous pattern with pathogenic coding and noncoding mutations was identified in probands. In proband 1, biallelic mutations (g.139409115A > T, encoding p.Asn685Ile; g.139444949C > A) in NOTCH1 exon and its regulatory element were detected. In vitro experiments revealed that the regulatory element acted as a silencer and the noncoding mutation decreased the expression of NOTCH1. In proband 2, we also found compound heterozygous mutations (g. 216235029C > T, encoding p.Val2281Met; g. 216525154A > C) which potentially regulated the function of FN1 gene. In summary, our study firstly reported an instance of newly identified noncoding mutation in regulatory element within the compound heterozygous pattern in TOF. The results provided a deeper understanding of TOF genetic architectures.
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Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Pushi Tang
- Department of Cardiovascular Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China
| | - Yifei Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhu Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Yayun Gu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Jing Xu
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Min Da
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xuming Mo
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Qingguo Li
- Department of Cardiovascular Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China.
| | - Xiaowei Wang
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China.
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Favre E, Leleu A, Peyroux E, Baudouin JY, Franck N, Demily C. Exploratory case study of monozygotic twins with 22q11.2DS provides further clues to circumscribe neurocognitive markers of psychotic symptoms. Neuroimage Clin 2019; 24:101987. [PMID: 31446315 PMCID: PMC6713843 DOI: 10.1016/j.nicl.2019.101987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 07/16/2019] [Accepted: 08/16/2019] [Indexed: 01/09/2023]
Abstract
Variation in facial emotion processing abilities may contribute to variability in penetrance for psychotic symptoms in 22q11.2DS. However, the precise nature of the social cognitive dysfunction (i.e., facial expression perception vs. emotion recognition), the potential additional roles of genetic and environmental variabilities, and consequently the possibility of using this neurocognitive marker in clinical monitoring remain unclear. The present case study aimed at testing the hypothesis that when confounding factors are controlled, the presence of psychotic symptoms in 22q11.2DS is associated, at the individual level, with a neural marker of facial expression perception rather than explicit emotional face recognition. Two monozygotic twins with 22q11.2DS discordant for psychiatric manifestations performed (1) a classical facial emotion labelling task and (2) an implicit neural measurement of facial expression perception using a frequency-tagging approach in electroencephalography (EEG). Analysis of the periodic brain response elicited by a change of facial expression from neutrality indicated that the twin with psychotic symptoms did not detect emotion among neutral faces while the twin without the symptoms did. In contrast, both encountered difficulties labelling facial emotion. The results from this exploratory twin study support the idea that impaired facial expression perception rather than explicit recognition of the emotion expressed might be a neurocognitive endophenotype of psychotic symptoms that could be reliable at a clinical level. Although confirmatory studies should be required, it facilitates further discussion on the etiology of the clinical phenotype in 22q11.2DS.
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Affiliation(s)
- Emilie Favre
- GénoPsy, Centre de Référence Maladies Rares à Expression Psychiatrique, Centre Hospitalier Le Vinatier, 95 bd Pinel BP300.91, F-69 678 BRON Cedex, France; Equipe EDR-Psy, Institut de Sciences Cognitives Marc Jeannerod, CNRS-UMR5229 & Université Lyon 1 Claude Bernard, 67 bd Pinel, F-69 500 BRON, France.
| | - Arnaud Leleu
- Équipe Éthologie Développementale et Psychologie Cognitive, Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, UMR 6265 CNRS, UMR 1324 INRA, Université Bourgogne Franche-Comté, 9 bd Jeanne d'Arc, F-21 000 Dijon, France.
| | - Elodie Peyroux
- GénoPsy, Centre de Référence Maladies Rares à Expression Psychiatrique, Centre Hospitalier Le Vinatier, 95 bd Pinel BP300.91, F-69 678 BRON Cedex, France; Equipe EDR-Psy, Institut de Sciences Cognitives Marc Jeannerod, CNRS-UMR5229 & Université Lyon 1 Claude Bernard, 67 bd Pinel, F-69 500 BRON, France; Centre ressource pour la réhabilitation psychosociale et la remédiation cognitive, Centre Hospitalier Le Vinatier, 5 rue Jean Sarrazin, F-69 008 Lyon, France.
| | - Jean-Yves Baudouin
- Équipe Éthologie Développementale et Psychologie Cognitive, Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, UMR 6265 CNRS, UMR 1324 INRA, Université Bourgogne Franche-Comté, 9 bd Jeanne d'Arc, F-21 000 Dijon, France; Laboratoire Développement, Individu, Processus, Handicap, Education (DIPHE), Departement Psychologie du Développement, de l'Education et des Vulnérabilités (PsyDEV), Institut de psychologie, Université Lumière Lyon 2, 5 av Pierre Mendès-France, F-69676 Bron, France.
| | - Nicolas Franck
- Equipe EDR-Psy, Institut de Sciences Cognitives Marc Jeannerod, CNRS-UMR5229 & Université Lyon 1 Claude Bernard, 67 bd Pinel, F-69 500 BRON, France; Centre ressource pour la réhabilitation psychosociale et la remédiation cognitive, Centre Hospitalier Le Vinatier, 5 rue Jean Sarrazin, F-69 008 Lyon, France.
| | - Caroline Demily
- GénoPsy, Centre de Référence Maladies Rares à Expression Psychiatrique, Centre Hospitalier Le Vinatier, 95 bd Pinel BP300.91, F-69 678 BRON Cedex, France; Equipe EDR-Psy, Institut de Sciences Cognitives Marc Jeannerod, CNRS-UMR5229 & Université Lyon 1 Claude Bernard, 67 bd Pinel, F-69 500 BRON, France.
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Rhoades R, Jackson F, Teng S. Discovery of rare variants implicated in schizophrenia using next-generation sequencing. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2019; 3:1-20. [PMID: 33981965 PMCID: PMC8112455 DOI: 10.20517/jtgg.2018.26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Schizophrenia is a highly heritable psychiatric disorder that affects 1% of the population. Genome-wide association studies have identified common variants in candidate genes associated with schizophrenia, but the genetics mechanisms of this disorder have not yet been elucidated. The discovery of rare genetic variants that contribute to schizophrenia symptoms promises to help explain the missing heritability of the disease. Next generation sequencing techniques are revolutionizing the field of psychiatric genetics. Various statistical approaches have been developed for rare variant association testing in case-control and family studies. Targeted resequencing, whole exome sequencing and whole genome sequencing combined with these computational tools are used for the discovery of rare genetic variations in schizophrenia. The findings provide useful information for characterizing the rare mutations and elucidating the genetic mechanisms by which the variants cause schizophrenia.
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Affiliation(s)
- Raina Rhoades
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Fatimah Jackson
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC 20059, USA
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8
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Yang Y, Xia C, Zhou Z, Wei D, Xu K, Jia J, Xu W, Zhang H. A multiplex ligation‑dependent probe amplification‑based next‑generation sequencing approach for the detection of copy number variations in the human genome. Mol Med Rep 2018; 18:5823-5833. [PMID: 30365071 DOI: 10.3892/mmr.2018.9581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 09/28/2018] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to describe a multiplex ligation‑dependent probe amplification (MLPA)‑based next‑generation sequencing (NGS) assay that exhibited a significantly higher efficiency in detecting copy number variations (CNVs) and known single‑nucleotide variants, compared with traditional MLPA. MLPA polymerase chain reaction products were used to construct a library with indexed adapters, which was subsequently tested on an NGS platform, and the resulting data were analyzed by a series of analytical software. The reads from each probe reflected genetic variations in the target regions, and fragment differentiation was based on the specific base composition of the sequences, rather than fragment length, which was determined by capillary electrophoresis. The results of this approach were not only consistent with the MLPA results following capillary electrophoresis, but also coincided with the CNV results from the single‑nucleotide polymorphism array chip. This method allowed high‑throughput screening for the number of fragments and samples by integrating additional indices for detection. Furthermore, this technology precisely and accurately performed large‑scale detection and quantification of DNA variations, thereby serving as an effective and sensitive method for diagnosing genetic disorders caused by CNVs and known single‑nucleotide variations. Notably, MLPA‑NGS circumvents the problems associated with the inaccuracies of NGS in CNV detection due to the use of target sequence capture.
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Affiliation(s)
- Yongchen Yang
- Department of Laboratory Medicine, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai 200040, P.R. China
| | - Chaoran Xia
- Shanghai Institute of Medical Genetics, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai 200040, P.R. China
| | - Zaiwei Zhou
- Product Department, WuXi Health Net Co., Ltd., Shanghai 200131, P.R. China
| | - Dongkai Wei
- BasePair Biotechnology Co., Ltd., Suzhou, Jiangsu 215028, P.R. China
| | - Kangping Xu
- BasePair Biotechnology Co., Ltd., Suzhou, Jiangsu 215028, P.R. China
| | - Jia Jia
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai 201203, P.R. China
| | - Wuhen Xu
- Department of Laboratory Medicine, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai 200040, P.R. China
| | - Hong Zhang
- Department of Laboratory Medicine, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai 200040, P.R. China
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9
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Impact of genetic studies on comprehension and treatment of congenital heart disease. PROGRESS IN PEDIATRIC CARDIOLOGY 2018. [DOI: 10.1016/j.ppedcard.2018.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Schwartz TS, Wojcik MH, Pelletier RC, Edward HL, Picker JD, Holm IA, Towne MC, Beggs AH, Agrawal PB. Expanding the phenotypic spectrum associated with OPHN1 variants. Eur J Med Genet 2018; 62:137-143. [PMID: 29960046 DOI: 10.1016/j.ejmg.2018.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
Abstract
Genomic sequencing has allowed for the characterization of new gene-to-disease relationships, as well as the identification of variants in established disease genes in patients who do not fit the classically-described phenotype. This is especially true in rare syndromes where the clinical spectrum is not fully known. After a lengthy and costly diagnostic odyssey, patients with atypical presentations may be left with many questions even after a genetic diagnosis is identified. We present a 22-year old male with hypotonia, developmental delay, seizure disorder, and dysmorphic facial features who enrolled in our rare disease research center at 18 years of age, where exome sequencing revealed a novel, likely pathogenic variant in the OPHN1 gene. Through efforts by the study team and collaborations with the larger genetics community, contacts with other families with OPHN1 variants were eventually made, and outreach by these families expanded the patient network. This partnership between families and researchers facilitated the gathering of phenotypic information, allowing for comparison of clinical presentations among three new patients and those previously reported in the literature. These comparisons found previously unreported commonalities between the newly identified patients, such as the presence of otitis media and the lack of genitourinary abnormalities (i.e. hypoplastic scrotum, microphallus, cryptorchidism), which had been noted to be classic features of patients with OPHN1 variants. As genomic sequencing becomes more common, connecting patients with novel variants in the same gene will facilitate phenotypic analysis and continue to refine the clinical spectrum associated with that gene.
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Affiliation(s)
- Talia S Schwartz
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Monica H Wojcik
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Renee C Pelletier
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Center for Cancer Risk Assessment, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Heather L Edward
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Jonathan D Picker
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Ingrid A Holm
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Meghan C Towne
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Ambry Genetics, Aliso Viejo, CA, USA
| | - Alan H Beggs
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Pankaj B Agrawal
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA.
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Calcagni G, Unolt M, Digilio MC, Baban A, Versacci P, Tartaglia M, Baldini A, Marino B. Congenital heart disease and genetic syndromes: new insights into molecular mechanisms. Expert Rev Mol Diagn 2017; 17:861-870. [PMID: 28745539 DOI: 10.1080/14737159.2017.1360766] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Advances in genetics allowed a better definition of the role of specific genetic background in the etiology of syndromic congenital heart defects (CHDs). The identification of a number of disease genes responsible for different syndromes have led to the identification of several transcriptional regulators and signaling transducers and modulators that are critical for heart morphogenesis. Understanding the genetic background of syndromic CHDs allowed a better characterization of the genetic basis of non-syndromic CHDs. In this sense, the well-known association of typical CHDs in Down syndrome, 22q11.2 microdeletion and Noonan syndrome represent paradigms as chromosomal aneuploidy, chromosomal microdeletion and intragenic mutation, respectively. Area covered: For each syndrome the anatomical features, distinctive cardiac phenotype and molecular mechanisms are discussed. Moreover, the authors include recent genetic findings that may shed light on some aspects of still unclear molecular mechanisms of these syndromes. Expert commentary: Further investigations are needed to enhance the translational approach in the field of genetics of CHDs. When there is a well-established definition of genotype-phenotype (reverse medicine) and genotype-prognosis (predictive and personalized medicine) correlations, hopefully preventive medicine will make its way in this field. Subsequently a reduction will be achieved in the morbidity and mortality of children with CHDs.
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Affiliation(s)
- Giulio Calcagni
- a Department of Pediatric Cardiology and Cardiac Surgery , Bambino Gesù Children's Hospital and Research Institute , Rome , Italy
| | - Marta Unolt
- b Department of Pediatrics , Sapienza University , Rome , Italy
| | - Maria Cristina Digilio
- c Genetics and Rare Diseases Research Division , Bambino Gesù Children's Hospital and Research Institute , Rome , Italy
| | - Anwar Baban
- a Department of Pediatric Cardiology and Cardiac Surgery , Bambino Gesù Children's Hospital and Research Institute , Rome , Italy
| | - Paolo Versacci
- b Department of Pediatrics , Sapienza University , Rome , Italy
| | - Marco Tartaglia
- c Genetics and Rare Diseases Research Division , Bambino Gesù Children's Hospital and Research Institute , Rome , Italy
| | - Antonio Baldini
- d CNR Institute of Genetics and Biophysics Adriano Buzzati Traverso; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II , Naples , Italy
| | - Bruno Marino
- b Department of Pediatrics , Sapienza University , Rome , Italy
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Differences between germline and somatic mutation rates in humans and mice. Nat Commun 2017; 8:15183. [PMID: 28485371 PMCID: PMC5436103 DOI: 10.1038/ncomms15183] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 03/08/2017] [Indexed: 12/22/2022] Open
Abstract
The germline mutation rate has been extensively studied and has been found to vary greatly between species, but much less is known about the somatic mutation rate in multicellular organisms, which remains very difficult to determine. Here, we present data on somatic mutation rates in mice and humans, obtained by sequencing single cells and clones derived from primary fibroblasts, which allows us to make the first direct comparison with germline mutation rates in these two species. The results indicate that the somatic mutation rate is almost two orders of magnitude higher than the germline mutation rate and that both mutation rates are significantly higher in mice than in humans. Our findings demonstrate both the privileged status of germline genome integrity and species-specific differences in genome maintenance. Germline mutation rates are known to vary between species but somatic mutation rates are less well understood. Here the authors compare mice and humans, observing that somatic mutation rates were nearly two orders of magnitude higher in both species, with both mutation rates significantly higher in mice.
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13
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Guo X, Delio M, Haque N, Castellanos R, Hestand MS, Vermeesch JR, Morrow BE, Zheng D. Variant discovery and breakpoint region prediction for studying the human 22q11.2 deletion using BAC clone and whole genome sequencing analysis. Hum Mol Genet 2016; 25:3754-3767. [PMID: 27436579 DOI: 10.1093/hmg/ddw221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 11/13/2022] Open
Abstract
Velo-cardio-facial syndrome/DiGeorge syndrome/22q11.2 deletion syndrome (22q11.2DS) is caused by meiotic non-allelic homologous recombination events between flanking low copy repeats termed LCR22A and LCR22D, resulting in a 3 million base pair (Mb) deletion. Due to their complex structure, large size and high sequence identity, genetic variation within LCR22s among different individuals has not been well characterized. In this study, we sequenced 13 BAC clones derived from LCR22A/D and aligned them with 15 previously available BAC sequences to create a new genetic variation map. The thousands of variants identified by this analysis were not uniformly distributed in the two LCR22s. Moreover, shared single nucleotide variants between LCR22A and LCR22D were enriched in the Breakpoint Cluster Region pseudogene (BCRP) block, suggesting the existence of a possible recombination hotspot there. Interestingly, breakpoints for atypical 22q11.2 rearrangements have previously been located to BCRPs To further explore this finding, we carried out in-depth analyses of whole genome sequence (WGS) data from two unrelated probands harbouring a de novo 3Mb 22q11.2 deletion and their normal parents. By focusing primarily on WGS reads uniquely mapped to LCR22A, using the variation map from our BAC analysis to help resolve allele ambiguity, and by performing PCR analysis, we infer that the deletion breakpoints were most likely located near or within the BCRP module. In summary, we found a high degree of sequence variation in LCR22A and LCR22D and a potential recombination breakpoint near or within the BCRP block, providing a starting point for future breakpoint mapping using additional trios.
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Affiliation(s)
| | | | | | | | | | | | | | - Deyou Zheng
- Department of Neurology .,Department of Genetics.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
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Abstract
22q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal microdeletion disorder, estimated to result mainly from de novo non-homologous meiotic recombination events occurring in approximately 1 in every 1,000 fetuses. The first description in the English language of the constellation of findings now known to be due to this chromosomal difference was made in the 1960s in children with DiGeorge syndrome, who presented with the clinical triad of immunodeficiency, hypoparathyroidism and congenital heart disease. The syndrome is now known to have a heterogeneous presentation that includes multiple additional congenital anomalies and later-onset conditions, such as palatal, gastrointestinal and renal abnormalities, autoimmune disease, variable cognitive delays, behavioural phenotypes and psychiatric illness - all far extending the original description of DiGeorge syndrome. Management requires a multidisciplinary approach involving paediatrics, general medicine, surgery, psychiatry, psychology, interventional therapies (physical, occupational, speech, language and behavioural) and genetic counselling. Although common, lack of recognition of the condition and/or lack of familiarity with genetic testing methods, together with the wide variability of clinical presentation, delays diagnosis. Early diagnosis, preferably prenatally or neonatally, could improve outcomes, thus stressing the importance of universal screening. Equally important, 22q11.2DS has become a model for understanding rare and frequent congenital anomalies, medical conditions, psychiatric and developmental disorders, and may provide a platform to better understand these disorders while affording opportunities for translational strategies across the lifespan for both patients with 22q11.2DS and those with these associated features in the general population.
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