ArticleCell reports2020
Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex.
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Article in Cell reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers, 4 of them syntheses that pooled it.
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105citing papers in PubMed, 4 pooled it
7.7field-weighted citation impact, top 2% of its field
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Who cites it
105 citing papers in PubMed, 4 syntheses or guidelines pooled it, 149 citations in OpenAlex.
- Integrating cell-type-specific gene expression and genome-wide associations identifies risk genes for schizophrenia.Molecular psychiatry · 2026Pooled it
- Genome-wide association meta-analysis of age at onset of walking in over 70,000 infants of European ancestry.Nature human behaviour · 2025Pooled it
- Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance.Genome medicine · 2021Pooled it
- Brain-based sex differences in autism spectrum disorder across the lifespan: A systematic review of structural MRI, fMRI, and DTI findings.NeuroImage. Clinical · 2021Pooled it
- Article
- Dynamic neuro-immune regulation of psychiatric risk loci in human neurons.Nature communications · 2026Article
- Identification of hub genes involved in early-onset schizophrenia: from genetic susceptibility to predicted regulated gene expression.Molecular psychiatry · 2026Article
- Co-expression-based models improve eQTL predictions for transcriptome-wide association studies and highlight new schizophrenia-associated genes.Nature genetics · 2026Article
- Regional sex differences in human cortical anatomy vary in their morphometric bases and overlap with sex chromosomal and gonadal influences.Nature communications · 2026Article
- Decomposing the genetic risk of autism spectrum disorder into discrete molecular subtypes underlie clinical heterogeneity based on transcriptome profile.Journal of translational medicine · 2026Article
- Genetic Risk and Resilience for Schizophrenia Stratified by Perinatal Gene Expression Predict Adult Cognitive Performance.bioRxiv : the preprint server for biology · 2026Article
- Spatial transcriptomics implicates the thalamus and cortex in autism and schizophrenia.bioRxiv : the preprint server for biology · 2026Article
- Spatiotemporal analysis of autism gene enrichment implicates cortex, thalamus, and hypothalamus.bioRxiv : the preprint server for biology · 2026Article
- Transcriptomic analysis in autism spectrum disorder suggests three molecular subtypes with distinct phenotypic profiles and functional pathways.Communications biology · 2026Article
- Linking rare variants to cell-type function in profound autism with brain transcriptomics and foundation models.Cell genomics · 2026Review
- Molecular dynamics of Brodmann Area 22 in development and autism.bioRxiv : the preprint server for biology · 2026Article
- Perinatal brain developmental transition revealed by transcriptomic and proteomic analyses of Bama miniature pigs.Nature communications · 2026Article
- Co-occurrence of rare variants implicates gene pairs in cytoskeletal pathways and is associated with increased severity in autism spectrum disorder.Genome biology · 2026Article
- Single-Cell Gene Module Inference Reveals Alternative Polyadenylation Dynamics Associated with Autism.International journal of molecular sciences · 2026Article
- Targeted BDNF upregulation via upstream open reading frame disruption.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
45 more citing papers are in PubMed but not listed here.
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Authors and funding
33 authors at 14 institutions in 6 countries.
Donna M WerlingDepartment of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA.
Sirisha PochareddyDepartment of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
Jinmyung ChoiDepartment of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
Joon-Yong AnDepartment of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Republic of Korea; School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul 02841, Republic of Korea.
Brooke SheppardDepartment of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Minshi PengDepartment of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Zhen LiDepartment of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurosciences, University of California, San Diego, San Diego, CA 92093, USA.
Claudia DastmalchiDepartment of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Gabriel SantpereDepartment of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Neurogenomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.
André M M SousaDepartment of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
Andrew T N TebbenkampDepartment of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
Navjot KaurDepartment of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
Forrest O GuldenDepartment of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
Michael S BreenSeaver Autism Center for Research and Treatment, 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; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Lindsay LiangDepartment of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Michael C GilsonDepartment of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Xuefang ZhaoCenter for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02142, USA.
Shan DongDepartment of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Lambertus KleiDepartment of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
A Ercument CicekDepartment of Computer Engineering, Bilkent University, Ankara 06800, Turkey; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Joseph D BuxbaumSeaver Autism Center for Research and Treatment, 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; Mindich Child Health and Development Institute, 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.
Homa Adle-BiassetteDepartment of Pathology, Lariboisière Hospital, APHP, Biobank BB-0033-00064, and Université de Paris, 75006 Paris, France.
Jean-Leon ThomasDepartment of Neurology, Yale University School of Medicine, New Haven, CT 06511, USA; UMRS1127, Sorbonne Université, Institut du Cerveau et de la Moelle Épinière, 75013 Paris, France.
Kimberly A AldingerCenter for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA.
Diana R O'DayDepartment of Pediatrics, University of Washington, Seattle, WA 98105, USA.
Ian A GlassDepartment of Pediatrics, University of Washington, Seattle, WA 98105, USA.
Noah A ZaitlenDepartment of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
Michael E TalkowskiCenter for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02142, USA.
Kathryn RoederDepartment of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Matthew W StateDepartment of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA.
Bernie DevlinDepartment of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
Stephan J SandersDepartment of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: stephan.sanders@ucsf.edu.
Nenad SestanDepartment of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Comparative Medicine, Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA. Electronic address: nenad.sestan@yale.edu.
University of California, San Francisco · USYale University · USBroad Institute · USCarnegie Mellon University · USUniversity of Pittsburgh · USUniversity of Washington · USAllen Institute for Brain Science · USBilkent University · TRBrotman Baty Institute · USChild Health and Development Institute · USNeurosciences Institute · USUniversitat Pompeu Fabra · ESUniversité Paris Cité · FRUniversity of Wisconsin–Madison · US
Funding
Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9MLABORATORY OF DEVELOPMENTAL BIOLOGYR24HD000836 · NICHD · UNIVERSITY OF WASHINGTON · PI Ian Amos Glass · 1995 to 2026
$16.9M Functional Genomics of Human Brain DevelopmentP50MH106934 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD · 2014 to 2019
$7.9MCis-Regulatory Epigenome Mappings in SchizophreniaU01MH103392 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, SKLAR, PAMELA · 2014 to 2017
$7.6MClinical Diagnostic Sequencing of Structural VariationR01HD081256 · NICHD · MASSACHUSETTS GENERAL HOSPITAL · PI TALKOWSKI, MICHAEL E · 2015 to 2025
$7.2MTranscriptional and Epigenetic Signatures of Human Brain Development and AutismU01MH103339 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD, STATE, MATTHEW W. · 2014 to 2017
$6.5M1/2 Cell Type and Region-Specific Regulatory Networks in Human Brain Development and DisordersU01MH116488 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD · 2018 to 2022
$6.5MMethods for Genome-wide Association Studies in Admixed PopulationsR01HG006399 · NHGRI · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI PRICE, ALKES L · 2011 to 2024
$6.3M2/3-Identifying regulatory mutations that influence neuropsychiatric diseaseU01MH105575 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI STATE, MATTHEW W. · 2014 to 2018
$5.7MScalable tool and comprehensive maps to interpret structural variation across the neuropsychiatric spectrumR01MH115957 · NIMH · BROAD INSTITUTE, INC. · PI TALKOWSKI, MICHAEL E · 2019 to 2025
$5.4MGenetics Association in Schizophrenia and Other DisordersR37MH057881 · NIMH · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI DEVLIN, BERNIE · 2013 to 2022
$5.4MOptimizing imputation for diverse populations in a distributed frameworkU01HG009080 · NHGRI · STANFORD UNIVERSITY · PI KENNY, EIMEAR ELIZABETH · 2016 to 2020
$5.2MNCATS NIH HHS UL1 TR001863NCI NIH HHS R01 CA227237NHGRI NIH HHS R01 HG006399NHGRI NIH HHS U01 HG009080NHLBI NIH HHS K25 HL121295NICHD NIH HHS R01 HD081256NICHD NIH HHS R01 HD096326NICHD NIH HHS R24 HD000836NIDCR NIH HHS R03 DE025665NIMH NIH HHS P50 MH106934NIMH NIH HHS R01 MH057881NIMH NIH HHS R01 MH094714NIMH NIH HHS R01 MH105472NIMH NIH HHS R01 MH105898NIMH NIH HHS R01 MH109901NIMH NIH HHS R01 MH109904NIMH NIH HHS R01 MH110926NIMH NIH HHS R01 MH110928NIMH NIH HHS R01 MH115957NIMH NIH HHS R21 MH102791NIMH NIH HHS R21 MH103877NIMH NIH HHS R21 MH105881NIMH NIH HHS R37 MH057881NIMH NIH HHS U01 MH103339NIMH NIH HHS U01 MH103340NIMH NIH HHS U01 MH103346NIMH NIH HHS U01 MH103365NIMH NIH HHS U01 MH103392NIMH NIH HHS U01 MH105575NIMH NIH HHS U01 MH106874NIMH NIH HHS U01 MH111662NIMH NIH HHS U01 MH116488
Abstract
Gene expression levels vary across developmental stage, cell type, and region in the brain. Genomic variants also contribute to the variation in expression, and some neuropsychiatric disorder loci may exert their effects through this mechanism. To investigate these relationships, we present BrainVar, a unique resource of paired whole-genome and bulk tissue RNA sequencing from the dorsolateral prefrontal cortex of 176 individuals across prenatal and postnatal development. Here we identify common variants that alter gene expression (expression quantitative trait loci [eQTLs]) constantly across development or predominantly during prenatal or postnatal stages. Both "constant" and "temporal-predominant" eQTLs are enriched for loci associated with neuropsychiatric traits and disorders and colocalize with specific variants. Expression levels of more than 12,000 genes rise or fall in a concerted late-fetal transition, with the transitional genes enriched for cell-type-specific genes and neuropsychiatric risk loci, underscoring the importance of cataloging developmental trajectories in understanding cortical physiology and pathology.
Indexed as
Base SequenceBrainComputational BiologyDatabases, GeneticExome SequencingGenetic Predisposition to DiseaseGenetic VariationGenome-Wide Association StudyGenomicsHumansPhenotypePolymorphism, Single NucleotidePrefrontal CortexQuantitative Trait LociSequence Analysis, RNATranscriptomeBrainVarDLPFCdorsolateral prefrontal cortexfetal transitionLOC101926933 RP11-298I3.1 AL132780.1 ENSG00000257285mTORprenatal eQTLPsychENCODERHEBL1
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