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Gericke GS. A Unifying Hypothesis for the Genome Dynamics Proposed to Underlie Neuropsychiatric Phenotypes. Genes (Basel) 2024; 15:471. [PMID: 38674405 PMCID: PMC11049865 DOI: 10.3390/genes15040471] [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: 03/17/2024] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
The sheer number of gene variants and the extent of the observed clinical and molecular heterogeneity recorded in neuropsychiatric disorders (NPDs) could be due to the magnified downstream effects initiated by a smaller group of genomic higher-order alterations in response to endogenous or environmental stress. Chromosomal common fragile sites (CFS) are functionally linked with microRNAs, gene copy number variants (CNVs), sub-microscopic deletions and duplications of DNA, rare single-nucleotide variants (SNVs/SNPs), and small insertions/deletions (indels), as well as chromosomal translocations, gene duplications, altered methylation, microRNA and L1 transposon activity, and 3-D chromosomal topology characteristics. These genomic structural features have been linked with various NPDs in mostly isolated reports and have usually only been viewed as areas harboring potential candidate genes of interest. The suggestion to use a higher level entry point (the 'fragilome' and associated features) activated by a central mechanism ('stress') for studying NPD genetics has the potential to unify the existing vast number of different observations in this field. This approach may explain the continuum of gene findings distributed between affected and unaffected individuals, the clustering of NPD phenotypes and overlapping comorbidities, the extensive clinical and molecular heterogeneity, and the association with certain other medical disorders.
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Xiao T, Dong X, Lu Y, Zhou W. High-Resolution and Multidimensional Phenotypes Can Complement Genomics Data to Diagnose Diseases in the Neonatal Population. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:204-215. [PMID: 37197647 PMCID: PMC10110825 DOI: 10.1007/s43657-022-00071-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 05/19/2023]
Abstract
Advances in genomic medicine have greatly improved our understanding of human diseases. However, phenome is not well understood. High-resolution and multidimensional phenotypes have shed light on the mechanisms underlying neonatal diseases in greater details and have the potential to optimize clinical strategies. In this review, we first highlight the value of analyzing traditional phenotypes using a data science approach in the neonatal population. We then discuss recent research on high-resolution, multidimensional, and structured phenotypes in neonatal critical diseases. Finally, we briefly introduce current technologies available for the analysis of multidimensional data and the value that can be provided by integrating these data into clinical practice. In summary, a time series of multidimensional phenome can improve our understanding of disease mechanisms and diagnostic decision-making, stratify patients, and provide clinicians with optimized strategies for therapeutic intervention; however, the available technologies for collecting multidimensional data and the best platform for connecting multiple modalities should be considered.
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Affiliation(s)
- Tiantian Xiao
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai, 201102 China
- Department of Neonatology, Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610000 China
| | - Xinran Dong
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
| | - Yulan Lu
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
| | - Wenhao Zhou
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai, 201102 China
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
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3
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Dai Y, Liu Y, Zhang L, Ren T, Wang H, Yu J, Liu X, Chen Z, Deng L, Tao M, Tan H, Huang CC, Zhang J, Luo Q, Feng J, Cao M, Li F. Shanghai Autism Early Development: An Integrative Chinese ASD Cohort. Neurosci Bull 2022; 38:1603-1607. [PMID: 35739378 PMCID: PMC9723093 DOI: 10.1007/s12264-022-00904-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/14/2022] [Indexed: 02/07/2023] Open
Affiliation(s)
- Yuan Dai
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Yuqi Liu
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Lingli Zhang
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Tai Ren
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Hui Wang
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Juehua Yu
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China ,grid.414902.a0000 0004 1771 3912Center for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032 China
| | - Xin Liu
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Zilin Chen
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Lin Deng
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Minyi Tao
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Hangyu Tan
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Chu-Chung Huang
- grid.22069.3f0000 0004 0369 6365Key Laboratory of Brain Functional Genomics (Ministry of Education), Affiliated Mental Health Center, School of Psychology and Cognitive Science, East China Normal University, Shanghai, 200062 China ,grid.410642.5Shanghai Changning Mental Health Center, Shanghai, 200335 China
| | - Jiaying Zhang
- grid.20513.350000 0004 1789 9964State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875 China ,grid.20513.350000 0004 1789 9964Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, 100875 China ,grid.20513.350000 0004 1789 9964IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875 China
| | - Qiang Luo
- grid.8547.e0000 0001 0125 2443National Clinical Research Center for Aging and Medicine at Huashan Hospital, Fudan University, Shanghai, 200433 China ,grid.8547.e0000 0001 0125 2443Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China ,grid.8547.e0000 0001 0125 2443State Key Laboratory of Medical Neurobiology and Ministry of Education Frontiers Center for Brain Science, Institutes of Brain Science and Human Phenome Institute, Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Fudan University, Shanghai, 200433 China
| | - Jianfeng Feng
- grid.8547.e0000 0001 0125 2443Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China ,grid.8547.e0000 0001 0125 2443Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Fudan University, Shanghai, 200433 China
| | - Miao Cao
- grid.8547.e0000 0001 0125 2443Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China ,grid.8547.e0000 0001 0125 2443Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Fudan University, Shanghai, 200433 China
| | - Fei Li
- grid.16821.3c0000 0004 0368 8293Department of Developmental and Behavioral Pediatric and Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and Ministry of Education-Shanghai Key Laboratory for Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
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Gupta C, Chandrashekar P, Jin T, He C, Khullar S, Chang Q, Wang D. Bringing machine learning to research on intellectual and developmental disabilities: taking inspiration from neurological diseases. J Neurodev Disord 2022; 14:28. [PMID: 35501679 PMCID: PMC9059371 DOI: 10.1186/s11689-022-09438-w] [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: 10/19/2021] [Accepted: 04/07/2022] [Indexed: 12/31/2022] Open
Abstract
Intellectual and Developmental Disabilities (IDDs), such as Down syndrome, Fragile X syndrome, Rett syndrome, and autism spectrum disorder, usually manifest at birth or early childhood. IDDs are characterized by significant impairment in intellectual and adaptive functioning, and both genetic and environmental factors underpin IDD biology. Molecular and genetic stratification of IDDs remain challenging mainly due to overlapping factors and comorbidity. Advances in high throughput sequencing, imaging, and tools to record behavioral data at scale have greatly enhanced our understanding of the molecular, cellular, structural, and environmental basis of some IDDs. Fueled by the "big data" revolution, artificial intelligence (AI) and machine learning (ML) technologies have brought a whole new paradigm shift in computational biology. Evidently, the ML-driven approach to clinical diagnoses has the potential to augment classical methods that use symptoms and external observations, hoping to push the personalized treatment plan forward. Therefore, integrative analyses and applications of ML technology have a direct bearing on discoveries in IDDs. The application of ML to IDDs can potentially improve screening and early diagnosis, advance our understanding of the complexity of comorbidity, and accelerate the identification of biomarkers for clinical research and drug development. For more than five decades, the IDDRC network has supported a nexus of investigators at centers across the USA, all striving to understand the interplay between various factors underlying IDDs. In this review, we introduced fast-increasing multi-modal data types, highlighted example studies that employed ML technologies to illuminate factors and biological mechanisms underlying IDDs, as well as recent advances in ML technologies and their applications to IDDs and other neurological diseases. We discussed various molecular, clinical, and environmental data collection modes, including genetic, imaging, phenotypical, and behavioral data types, along with multiple repositories that store and share such data. Furthermore, we outlined some fundamental concepts of machine learning algorithms and presented our opinion on specific gaps that will need to be filled to accomplish, for example, reliable implementation of ML-based diagnosis technology in IDD clinics. We anticipate that this review will guide researchers to formulate AI and ML-based approaches to investigate IDDs and related conditions.
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Affiliation(s)
- Chirag Gupta
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Pramod Chandrashekar
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ting Jin
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chenfeng He
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Saniya Khullar
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Qiang Chang
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Neurology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA. .,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA. .,Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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