ArticleCell2024
Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders.
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Article in Cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8citing papers in PubMed
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Who cites it
8 citing papers in PubMed.
- Genomic structural variations distinguishing archaic and modern humans are associated with neurodevelopment.iScience · 2026Article
- Neuroinflammation as molecular landscape of post-operative delirium revealed by live human brain multi-omics profiling.Molecular psychiatry · 2026Article
- Knowledge-guided contextual gene set analysis with large language models.Bioinformatics (Oxford, England) · 2026Article
- High-fidelity rare structural variant detection with HiFiRE3 reduced representation via restriction enzyme ends.bioRxiv : the preprint server for biology · 2026Article
- Glial Contribution to the Pathogenesis of Post-Operative Delirium Revealed by Multi-omic Analysis of Brain Tissue from Neurosurgery Patients.bioRxiv : the preprint server for biology · 2025Article
- Cutting-edge AI tools revolutionizing scientific research in life sciences.Biotechnologia · 2025Review
- Artificial intelligence in systemic diagnostics: Applications in psychiatry, cardiology, dermatology and oral pathology.Bioinformation · 2025Article
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Authors and funding
38 authors.
Bo ZhouDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: bozhou@alumni.stanford.edu.
Joseph G ArthurDepartment of Statistics, Stanford University, Stanford, CA 94305, USA.
Hanmin GuoDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Statistics, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
Taeyoung KimSchool of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea.
Yiling HuangDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Reenal PattniDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Tao WangDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Soumya KunduDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
Jay X J LuoDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
HoJoon LeeDivision of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
Daniel C NachunDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Carolin PurmannDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Emma M MonteDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Annika K WeimerDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Ping-Ping QuDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Minyi ShiDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Lixia JiangDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Xinqiong YangDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
John F FullardCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jaroslav BendlCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Kiran GirdharCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Minsu KimSchool of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea.
Xi ChenDepartment of Statistics, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
PsychENCODE Consortium
William J GreenleafDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Laramie DuncanDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.
Hanlee P JiDivision of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
Xiang ZhuDepartment of Statistics, Stanford University, Stanford, CA 94305, USA; Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
Giltae SongSchool of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea; Center for Artificial Intelligence Research, Pusan National University, Busan 46241, South Korea.
Stephen B MontgomeryDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA.
Dean PalejevInstitute of Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.
Heinrich Zu DohnaDepartment of Biology, American University of Beirut, Beirut 11-0236, Lebanon.
Panos RoussosCenter for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA; Mental Illness Research Education and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY 10468, USA.
Anshul KundajeDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
Joachim F HallmayerDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.
Michael P SnyderDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Wing H WongDepartment of Statistics, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA. Electronic address: whwong@stanford.edu.
Alexander E UrbanDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: aeurban@stanford.edu.
Funding
Penn State Clinical and Translational Science InstituteUL1TR002014 · NCATS · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · PI KRASCHNEWSKI, JENNIFER L. · 2016 to 2025
$33.7MSpecial EquipmentP50HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2014 to 2018
$15.2MUnderstanding the molecular mechanisms that contribute to neuropsychiatric symptoms in Alzheimer DiseaseR01AG067025 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI FINKBEINER, STEVEN M, HAROUTUNIAN, VAHRAM · 2019 to 2023
$11.8MHigher Order Chromatin and Genetic Risk for Alzheimer's DiseaseR01AG050986 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ROUSSOS, PANAGIOTIS · 2015 to 2025
$11.2MIntegrated, cell type specific functional genomics analyses of regulatory sequence elements and their dynamic interaction networks in neuropsychiatric brain tissuesU01MH116529 · NIMH · STANFORD UNIVERSITY · PI HALLMAYER, JOACHIM F, SNYDER, MICHAEL P. · 2019 to 2022
$7.0MMolecular Profiling of SchizophreniaR01MH110921 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI CHESS, ANDREW J, ROUSSOS, PANAGIOTIS · 2016 to 2020
$6.9MThe 3D genome in transcriptional regulation across the postnatal life span, with implications for schizophrenia and bipolar disorderU01MH116442 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, DRACHEVA, STELLA · 2018 to 2022
$5.9MMultiethnic genomic epigenomic and transcriptomic fine-mapping and functional validation analysis of schizophrenia and bipolar disorder risk lociR01MH125246 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ROUSSOS, PANAGIOTIS · 2021 to 2025
$5.0MRisk genetic variants and cis regulation of gene expression in Bipolar DisorderR01MH109677 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ROUSSOS, PANAGIOTIS · 2016 to 2020
$4.6MStatistical Models for Genome Sequencing and AssociationR01HG006137 · NHGRI · UNIVERSITY OF PENNSYLVANIA · PI JI, HANLEE P, ZHANG, NANCY R · 2011 to 2022
$4.3MMapping Molecular and Phenotypic Interactions in Alzheimers DiseaseR01AG066490 · NIA · STANFORD UNIVERSITY · PI MONTGOMERY, STEPHEN · 2020 to 2024
$3.6MIdentifying causal genetic variants and molecular mechanisms impacting mental healthR01MH125244 · NIMH · STANFORD UNIVERSITY · PI KUNDAJE, ANSHUL, MONTGOMERY, STEPHEN · 2021 to 2025
$3.0MBLRD VA I01 BX002395NCATS NIH HHS UL1 TR002014NHGRI NIH HHS P50 HG007735NHGRI NIH HHS R01 HG006137NHGRI NIH HHS R01 HG010359NHGRI NIH HHS U01 HG010963NIA NIH HHS R01 AG050986NIA NIH HHS R01 AG066490NIA NIH HHS R01 AG067025NIGMS NIH HHS T32 GM096982NIMH NIH HHS K01 MH129758NIMH NIH HHS R01 MH109677NIMH NIH HHS R01 MH110921NIMH NIH HHS R01 MH116529NIMH NIH HHS R01 MH125244NIMH NIH HHS R01 MH125246NIMH NIH HHS U01 MH116442NIMH NIH HHS U01 MH116529NINDS NIH HHS R01 NS128028NINDS NIH HHS UG3 NS132146
Abstract
Complex structural variations (cxSVs) are often overlooked in genome analyses due to detection challenges. We developed ARC-SV, a probabilistic and machine-learning-based method that enables accurate detection and reconstruction of cxSVs from standard datasets. By applying ARC-SV across 4,262 genomes representing all continental populations, we identified cxSVs as a significant source of natural human genetic variation. Rare cxSVs have a propensity to occur in neural genes and loci that underwent rapid human-specific evolution, including those regulating corticogenesis. By performing single-nucleus multiomics in postmortem brains, we discovered cxSVs associated with differential gene expression and chromatin accessibility across various brain regions and cell types. Additionally, cxSVs detected in brains of psychiatric cases are enriched for linkage with psychiatric GWAS risk alleles detected in the same brains. Furthermore, our analysis revealed significantly decreased brain-region- and cell-type-specific expression of cxSV genes, specifically for psychiatric cases, implicating cxSVs in the molecular etiology of major neuropsychiatric disorders.
Indexed as
BrainGenome, HumanMental DisordersChromatinGenetic VariationGenome-Wide Association StudyGenomic Structural VariationHumansMachine LearningTissue DonorsChromatinARC-SVcomplex structural variationcxSVsGTExhuman evolutionpopulation geneticsPsychENCODEpsychiatric geneticssingle-cell multiomicsstructural variation
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