Integration of Multimodal Data for Deciphering Brain Disorders

Chen, Jingqi; Dong, Guiying; Song, Liting; Zhao, Xingzhong; Cao, Jixin; Luo, Xingfang; Feng, Jianfeng; Zhao, Xing‐Ming

doi:10.1146/annurev-biodatasci-092820-020354

Cited by 6 publications

(7 citation statements)

References 66 publications

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“…The Zhangjiang International Brain Biobank collects matched genomic, transcriptomic, metabolic, and neuroimaging data for six brain disorder cohorts and utilizes an international team of scientists from biology, medicine, computer science, physics, statistics, and mathematics to mine the accumulated data. This understandably includes gut microbiomes since the human gut has more than 1000 types of bacteria, which have been proven to be associated with brain health [14].…”

Section: Npd Phenotypic Complexity and Overlap Between Npds And Comor...mentioning

confidence: 99%

“…How many of these alterations are present in an individual with an NPD? Utilizing fast-developing areas such as artificial intelligence to analyze hidden data patterns in data-driven mining, data noise reduction techniques, and meta-analyses, it is hoped that further insights can be gained by such additional fundamental research [14]. Major challenges remain, however, regarding the extreme complexity and high levels of disease heterogeneity associated with the low penetrance of specific gene mutations, multiple genetic-epigenetic and environmental interactions, and the influence of stochastic evolutionary processes which render most individual molecular mechanisms less than useful for clinical prediction [14].…”

Section: Has the Time Arrived For A New Research Paradigm?mentioning

confidence: 99%

“…Utilizing fast-developing areas such as artificial intelligence to analyze hidden data patterns in data-driven mining, data noise reduction techniques, and meta-analyses, it is hoped that further insights can be gained by such additional fundamental research [14]. Major challenges remain, however, regarding the extreme complexity and high levels of disease heterogeneity associated with the low penetrance of specific gene mutations, multiple genetic-epigenetic and environmental interactions, and the influence of stochastic evolutionary processes which render most individual molecular mechanisms less than useful for clinical prediction [14]. It has been suggested that there might be no clear causative relationships at the molecular level within a complex biosystem and it is likely that stochastic genome alterations have a random probability distribution or pattern that may be analyzed statistically, but may not be predicted precisely [16,17].…”

Section: Has the Time Arrived For A New Research Paradigm?mentioning

confidence: 99%

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A Unifying Hypothesis for the Genome Dynamics Proposed to Underlie Neuropsychiatric Phenotypes

Gericke

2024

Genes

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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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Section: Npd Phenotypic Complexity and Overlap Between Npds And Comor...mentioning

confidence: 99%

Section: Has the Time Arrived For A New Research Paradigm?mentioning

confidence: 99%

Section: Has the Time Arrived For A New Research Paradigm?mentioning

confidence: 99%

See 1 more Smart Citation

A Unifying Hypothesis for the Genome Dynamics Proposed to Underlie Neuropsychiatric Phenotypes

Gericke

2024

Genes

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show abstract

“…The Zhangjiang International Brain Biobank collects matched genomic, transcriptomic, metabolic, and neuroimaging data for six brain disorder cohorts and utilizes an international team of scientists from biology, medicine, computer science, physics, statistics, and mathematics to mine the accumulated data. This understandably includes gut microbiomes since the human gut has in excess of 1,000 types of bacteria, which have been proven to be associated with brain health [14].…”

Section: Phenotypic Complexity Overlap Between Npds and Comorbidities...mentioning

confidence: 99%

A Unifying Hypothesis for the Genome Dynamics Proposed to Underly Neuropsychiatric Phenotypes

Gericke

2024

Preprint

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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 microRNA’s, 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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“…The Shanghai Autism Early Developmental (SAED) Cohort was established with the support of several foundations, including major projects of the Shanghai Science and Technology Commission, the Natural Science Foundation of China, and the Science and Technology Commission of Shanghai Municipality. Some of the data also represent important parts of the Zhangjiang International Brain Biobank [ 4 ]. Unique biological samples serially collected throughout pregnancy and childhood with early screening, diagnostic assessments, and re-assessments to identify antenatal, perinatal, and early postnatal risk and protective factors.…”

Section: Why Was the Cohort Set Up?mentioning

confidence: 99%

Shanghai Autism Early Development: An Integrative Chinese ASD Cohort

et al. 2022

Self Cite

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6-12 years, the prevalence of ASD in China was reported to be 0.7% in 2020 [3]. The mission to improve the screening, diagnosis, rehabilitation, and assistance of ASD children aged 0-6 years has been listed in the national strategic deployments for the next decade, including the Outline for the Development of Children in China (2021-2030) and the China Brain Project 2030.Although ASD is highly heritable, the biological underpinnings and development over the lifespan remain largely unclear due to its heterogeneity. To address these challenges, large-scale sample collections focusing on the early developmental period of ASD are essential, as these are critical for identifying ways of screening high-risk Why Was the Cohort Set Up?Autism spectrum disorder (ASD) is a child neurodevelopmental disorder, the onset of which is generally within 3 years of age, and often leads to lifelong impaired social and cognitive functions, which impose significant mental pressure and economic burdens on the family and society. In 2012, the incidence data released by the World Health Organization showed that the global prevalence of ASD was ~0.625% [1], and the latest report from the Centers for Disease Control and Prevention show that the incidence of ASD in the USA had reached 2.3% in 2021 [2]. According to a nationwide survey of over 120,000 children aged www.neurosci.cn www.springer.com/12264 Yuan Dai, Yuqi Liu contributed equally to this work.

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Integration of Multimodal Data for Deciphering Brain Disorders

Cited by 6 publications

References 66 publications

A Unifying Hypothesis for the Genome Dynamics Proposed to Underlie Neuropsychiatric Phenotypes

A Unifying Hypothesis for the Genome Dynamics Proposed to Underlie Neuropsychiatric Phenotypes

A Unifying Hypothesis for the Genome Dynamics Proposed to Underly Neuropsychiatric Phenotypes

Shanghai Autism Early Development: An Integrative Chinese ASD Cohort

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