Evidence map›Paper›PMID 32296054›Full record

ArticleNature communications2020

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia.

Matthew Halvorsen, Ruth Huh, Nikolay Oskolkov, Jia Wen, Sergiu Netotea, Paola Giusti-Rodriguez, Robert Karlsson, Julien Bryois, Björn Nystedt, Adam Ameur and 10 more

Erratum issuedOpen access · goldAbstract read
In one paragraph

Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 45 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
45citing papers in PubMed, 2 pooled it
9.5field-weighted citation impact, top 2% 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

45 citing papers in PubMed, 2 syntheses or guidelines pooled it, 88 citations in OpenAlex.

  1. A Systematic Review on the Genetic Contribution to Tinnitus.Journal of the Association for Research in Otolaryngology : JARO · 2024
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors at 5 institutions in 2 countries.

Matthew Halvorsen *Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
Ruth Huh *Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA.
Nikolay Oskolkov *Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 22362, Lund, Sweden.ORCID http://orcid.org/0000-0001-5326-8893
Jia Wen *Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.ORCID http://orcid.org/0000-0003-3273-7704
Sergiu NetoteaDepartment of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, 41258, Göteborg, Sweden.
Paola Giusti-RodriguezDepartment of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.ORCID http://orcid.org/0000-0002-1921-1305
Robert KarlssonDepartment of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177, Stockholm, Sweden.ORCID http://orcid.org/0000-0002-8949-2587
Julien BryoisDepartment of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177, Stockholm, Sweden.
Björn NystedtDepartment of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 75237, Uppsala, Sweden.ORCID http://orcid.org/0000-0001-7809-7664
Adam AmeurDepartment of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185, Uppsala, Sweden.ORCID http://orcid.org/0000-0001-6085-6749
Anna K KählerDepartment of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177, Stockholm, Sweden.
NaEshia AncaladeDepartment of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
Martilias FarrellDepartment of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.ORCID http://orcid.org/0000-0002-9520-6209
James J CrowleyDepartment of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
Yun LiDepartment of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
Patrik K E MagnussonDepartment of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177, Stockholm, Sweden.ORCID http://orcid.org/0000-0002-7315-7899
Ulf GyllenstenDepartment of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185, Uppsala, Sweden.
Christina M HultmanDepartment of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177, Stockholm, Sweden.
Patrick F SullivanDepartment of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA. patrick.sullivan@ki.se.
Jin P SzatkiewiczDepartment of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA. jin_szatkiewicz@med.unc.edu.ORCID http://orcid.org/0000-0002-4898-7401
University of North Carolina at Chapel Hill · USKarolinska Institutet · SEUppsala University · SELund University · SEScience for Life Laboratory · SE

Funding

A Large-Scale Schizophrenia Association Study in SwedenR01MH077139 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI SULLIVAN, PATRICK F · 2007 to 2018
$9.9M
Preclinical CoreP50HD103573 · NICHD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Mark D Shen · 2020 to 2026
$9.7M
Preclinical CoreU54HD079124 · NICHD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI PIVEN, JOSEPH · 2013 to 2019
$8.0M
Finding causal variants within schizophrenia risk lociR01MH106611 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI SZATKIEWICZ, JIN PENG · 2015 to 2019
$3.3M
OCD: Novel Comparative Genomic Approaches to Identify Disease and Treatment MechanismsR01MH110427 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI CROWLEY, JAMES JOSEPH · 2016 to 2021
$3.0M
Interpreting GWAS associations in schizophrenia using genome-wide chromatin mappingK01MH109772 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI GIUSTI, PAOLA · 2016 to 2019
$621k
Finding single-gene copy number variants in schizophreniaR21MH104831 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI CROWLEY, JAMES JOSEPH, SZATKIEWICZ, JIN PENG · 2014 to 2015
$418k
Emotion-Modulated Psychophysiology of Autism Spectrum DisordersR21MH085254 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI BENNING, STEPHEN D, DICHTER, GABRIEL S · 2009 to 2010
$416k
NICHD NIH HHS P50 HD103573NICHD NIH HHS U54 HD079124NIMH NIH HHS K01 MH109772NIMH NIH HHS R01 MH077139NIMH NIH HHS R01 MH106611NIMH NIH HHS R01 MH110427NIMH NIH HHS R21 MH085254NIMH NIH HHS R21 MH104831
6 · The paper itself

Abstract

Despite considerable progress in schizophrenia genetics, most findings have been for large rare structural variants and common variants in well-imputed regions with few genes implicated from exome sequencing. Whole genome sequencing (WGS) can potentially provide a more complete enumeration of etiological genetic variation apart from the exome and regions of high linkage disequilibrium. We analyze high-coverage WGS data from 1162 Swedish schizophrenia cases and 936 ancestry-matched population controls. Our main objective is to evaluate the contribution to schizophrenia etiology from a variety of genetic variants accessible to WGS but not by previous technologies. Our results suggest that ultra-rare structural variants that affect the boundaries of topologically associated domains (TADs) increase risk for schizophrenia. Alterations in TAD boundaries may lead to dysregulation of gene expression. Future mechanistic studies will be needed to determine the precise functional effects of these variants on biology.

Indexed as

BrainExomeGenome, HumanGenome-Wide Association StudyHigh-Throughput Nucleotide SequencingHumansMaleNervous SystemQuality ControlSchizophreniaSequence Analysis, DNA

Identifiers

PMID32296054
PMCPMC7160146
OpenAlexW3017004584

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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.