Evidence map›Paper›PMID 30087329›Full record

ArticleNature communications2018

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.

Julien Bryois, Melanie E Garrett, Lingyun Song, Alexias Safi, Paola Giusti-Rodriguez, Graham D Johnson, Annie W Shieh, Alfonso Buil, John F Fullard, Panos Roussos and 11 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
117citing papers in PubMed, 3 pooled it
16.1field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

117 citing papers in PubMed, 3 syntheses or guidelines pooled it, 185 citations in OpenAlex.

  1. Pooled it
  2. Pooled it
  3. Pooled it
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  18. AnFrontiers in genetics · 2025
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  19. Review
  20. A practical guide to sequencing in neuropsychiatric research.NPP - digital psychiatry and neuroscience · 2025
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57 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors at 9 institutions in 3 countries.

Julien BryoisDepartment of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden.ORCID http://orcid.org/0000-0002-4747-2166
Melanie E GarrettDuke Molecular Physiology Institute, Durham, NC, 27701, USA.
Lingyun SongCenter for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
Alexias SafiCenter for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
Paola Giusti-RodriguezDepartment of Genetics, University of North Carolina, Chapel Hill, NC, 27599-7264, USA.ORCID http://orcid.org/0000-0002-1921-1305
Graham D JohnsonCenter for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.ORCID http://orcid.org/0000-0003-0723-4697
Annie W ShiehDepartment of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
Alfonso BuilResearch Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Roskilde, 4000, Denmark.
John F FullardDepartment of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Panos RoussosDepartment of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.ORCID http://orcid.org/0000-0002-4640-6239
Pamela SklarDepartment of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Schahram AkbarianDepartment of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.ORCID http://orcid.org/0000-0001-7700-0891
Vahram HaroutunianDepartment of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.ORCID http://orcid.org/0000-0001-5860-2512
Craig A StockmeierDepartment of Psychiatry and Human Behavior, Center for Psychiatric Neuroscience, University of Mississippi Medical Center, Jackson, MS, 39216, USA.ORCID http://orcid.org/0000-0003-1861-1013
Gregory A WrayCenter for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
Kevin P WhiteDepartment of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
Chunyu LiuDepartment of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
Timothy E ReddyCenter for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.ORCID http://orcid.org/0000-0002-7629-061X
Allison Ashley-KochDuke Molecular Physiology Institute, Durham, NC, 27701, USA.
Patrick F SullivanDepartment of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden. pfsulliv@med.unc.edu.ORCID http://orcid.org/0000-0002-6619-873X
Gregory E CrawfordCenter for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. greg.crawford@duke.edu.ORCID http://orcid.org/0000-0001-6106-2772
Duke University · USIcahn School of Medicine at Mount Sinai · USJames J. Peters VA Medical Center · USSUNY Upstate Medical University · USUniversity of North Carolina at Chapel Hill · USKarolinska Institutet · SESankt Hans Hospital · DKUniversity of Chicago · USUniversity of Mississippi Medical Center · US

Funding

VESICULAR LOCALIZATION AND FUNCTION OF PRESENILIN 1 FRAGMENTP50AG005138 · NIA · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI SEWELL, MARGARET · 1985 to 2019
$37.9M
QUANTITATIVE ANALYSIS OF MICROVASCULAR CHANGES IN THE AGING BRAINP01AG002219 · NIA · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI HAROUTUNIAN, VAHRAM · 1985 to 2009
$19.2M
White Matter Abnormalities in SchizophreniaP50MH066392 · NIMH · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI O'DONOVAN, MICHAEL J · 2002 to 2012
$18.6M
Project 5: In vivo measurement of GABA transmission in healthy controls & subjectP50MH084053 · NIMH · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI LEWIS, DAVID A · 2008 to 2012
$11.5M
International Cohort Collection for Bipolar DisorderR01MH085542 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI SMOLLER, JORDAN W · 2008 to 2012
$10.7M
Functional Genomics of Human Brain DevelopmentP50MH106934 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD · 2014 to 2019
$7.9M
Cis-Regulatory Epigenome Mappings in SchizophreniaU01MH103392 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, SKLAR, PAMELA · 2014 to 2017
$7.6M
Transcriptional and Epigenetic Signatures of Human Brain Development and AutismU01MH103339 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD, STATE, MATTHEW W. · 2014 to 2017
$6.5M
Center for Psychiatric NeuroscienceP30GM103328 · NIGMS · UNIVERSITY OF MISSISSIPPI MED CTR · PI STOCKMEIER, CRAIG ALLEN · 2013 to 2017
$5.5M
Genetics Association in Schizophrenia and Other DisordersR37MH057881 · NIMH · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI DEVLIN, BERNIE · 2013 to 2022
$5.4M
Genetic variants affect brain gene expression and risks of psychiatric disordersU01MH103340 · NIMH · UPSTATE MEDICAL UNIVERSITY · PI LIU, CHUNYU, RZHETSKY, ANDREY · 2014 to 2017
$4.3M
Src mediates molecular alterations leading to NMDAR hypofunction in schizophreniaR01MH075916 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI BORGMANN-WINTER, KARIN, HAHN, CHANG-GYU · 2006 to 2019
$3.3M
BLRD VA I01 BX002395NIA NIH HHS P01 AG002219NIA NIH HHS P50 AG005138NIGMS NIH HHS P30 GM103328NIMH NIH HHS HHSN271201300031CNIMH NIH HHS K01 MH109772NIMH NIH HHS P50 MH066392NIMH NIH HHS P50 MH084053NIMH NIH HHS P50 MH106934NIMH NIH HHS R01 MH075916NIMH NIH HHS R01 MH080405NIMH NIH HHS R01 MH085542NIMH NIH HHS R01 MH093725NIMH NIH HHS R01 MH094714NIMH NIH HHS R01 MH097276NIMH NIH HHS R01 MH105472NIMH NIH HHS R01 MH105898NIMH NIH HHS R01 MH110920NIMH 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 MH109528U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) P30GM103328Vetenskapsrådet (Swedish Research Council) D0886501
6 · The paper itself

Abstract

Schizophrenia genome-wide association studies have identified >150 regions of the genome associated with disease risk, yet there is little evidence that coding mutations contribute to this disorder. To explore the mechanism of non-coding regulatory elements in schizophrenia, we performed ATAC-seq on adult prefrontal cortex brain samples from 135 individuals with schizophrenia and 137 controls, and identified 118,152 ATAC-seq peaks. These accessible chromatin regions in the brain are highly enriched for schizophrenia SNP heritability. Accessible chromatin regions that overlap evolutionarily conserved regions exhibit an even higher heritability enrichment, indicating that sequence conservation can further refine functional risk variants. We identify few differences in chromatin accessibility between cases and controls, in contrast to thousands of age-related differential accessible chromatin regions. Altogether, we characterize chromatin accessibility in the human prefrontal cortex, the effect of schizophrenia and age on chromatin accessibility, and provide evidence that our dataset will allow for fine mapping of risk variants.

Indexed as

Genome-Wide Association StudyQuantitative Trait LociAgedAged, 80 and overBrainChromatinFemaleGene Expression ProfilingHigh-Throughput Nucleotide SequencingHumansMaleMiddle AgedPolymorphism, Single NucleotidePrefrontal CortexRiskSchizophreniaChromatin

Identifiers

PMID30087329
PMCPMC6081462
OpenAlexW2886367104

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.