Evidence map›Paper›PMID 25217958›Full record

ArticleNature genetics2014

Refining analyses of copy number variation identifies specific genes associated with developmental delay.

Bradley P Coe, Kali Witherspoon, Jill A Rosenfeld, Bregje W M van Bon, Anneke T Vulto-van Silfhout, Paolo Bosco, Kathryn L Friend, Carl Baker, Serafino Buono, Lisenka E L M Vissers and 28 more

Abstract read
In one paragraph

Article in Nature genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 379 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
379citing papers in PubMed, 2 pooled it
–field-weighted citation impact
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

379 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
  2. MYT1L: A systematic review of genetic variation encompassing schizophrenia and autism.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2020
    Pooled it
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  19. Behavioral and Prefrontal Circuit Deficits in a Newly DevelopedBiological psychiatry global open science · 2026
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319 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

38 authors.

Bradley P CoeDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
Kali WitherspoonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
Jill A RosenfeldSignature Genomics Laboratories, LLC, PerkinElmer, Inc., Spokane, Washington, USA.ORCID 0000000156647987
Bregje W M van Bon1] Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands. [2] SA Pathology, North Adelaide, South Australia, Australia.
Anneke T Vulto-van SilfhoutDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
Paolo BoscoIRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy.
Kathryn L FriendSA Pathology, North Adelaide, South Australia, Australia.
Carl BakerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
Serafino BuonoIRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy.
Lisenka E L M VissersDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
Janneke H Schuurs-HoeijmakersDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
Alex HoischenDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
Rolph PfundtDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
Nik KrummDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
Gemma L CarvillDepartment of Pediatrics, University of Washington, Seattle, Washington, USA.
Deana LiRepresenting the Autism Phenome Project, MIND Institute, University of California, Davis, Sacramento, California, USA.
David AmaralRepresenting the Autism Phenome Project, MIND Institute, University of California, Davis, Sacramento, California, USA.
Natasha Brown1] Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia. [2] Barwon Child Health Unit, Barwon Health, Geelong, Victoria, Australia.
Paul J Lockhart1] Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia. [2] Murdoch Childrens Research Institute, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.ORCID 0000000325318413
Ingrid E SchefferFlorey Institute, University of Melbourne, Austin Health and Royal Children's Hospital, Melbourne, Victoria, Australia.
Antonino AlbertiIRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy.
Marie ShawSA Pathology, North Adelaide, South Australia, Australia.
Rosa PettinatoIRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy.
Raymond TervoDivision of Developmental and Behavioral Pediatrics, Mayo Clinic, Rochester, Minnesota, USA.
Nicole de LeeuwDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
Margot R F ReijndersDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.ORCID 0000000263797147
Beth S TorchiaSignature Genomics Laboratories, LLC, PerkinElmer, Inc., Spokane, Washington, USA.
Hilde Peeters1] Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium. [2] Leuven Autism Research (LAuRes), Leuven, Belgium.
Brian J O'Roak1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2].
Marco Fichera1] IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy. [2].
Jayne Y Hehir-KwaDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
Jay ShendureDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
Heather C MeffordDepartment of Pediatrics, University of Washington, Seattle, Washington, USA.
Eric Haan1] SA Pathology, North Adelaide, South Australia, Australia. [2] School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia.
Jozef Gécz1] SA Pathology, North Adelaide, South Australia, Australia. [2] Robinson Institute, University of Adelaide, Adelaide, South Australia, Australia.ORCID 0000000278846861
Bert B A de VriesDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
Corrado RomanoIRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Associazione Oasi Maria Santissima, Troina, Italy.
Evan E Eichler1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, Seattle, Washington, USA.

Funding

University of Washington Medical Scientist Training Program: MD/PhDT32GM007266 · NIGMS · UNIVERSITY OF WASHINGTON · PI HORWITZ, MARSHALL S. · 1985 to 2023
$30.4M
Sporadic Mutations and Autism Spectrum DisordersR01MH101221 · NIMH · UNIVERSITY OF WASHINGTON · PI EICHLER, EVAN · 2013 to 2025
$9.2M
An epigenomic approach to identifying noncoding mutations in epilepsyK99NS089858 · NINDS · UNIVERSITY OF WASHINGTON · PI CARVILL, GEMMA LOUISE · 2014 to 2015
$182k
Howard Hughes Medical InstituteNIGMS NIH HHS T32 GM007266NIMH NIH HHS MH101221NIMH NIH HHS R01 MH101221NINDS NIH HHS K99 NS089858Wellcome Trust
6 · The paper itself

Abstract

Copy number variants (CNVs) are associated with many neurocognitive disorders; however, these events are typically large, and the underlying causative genes are unclear. We created an expanded CNV morbidity map from 29,085 children with developmental delay in comparison to 19,584 healthy controls, identifying 70 significant CNVs. We resequenced 26 candidate genes in 4,716 additional cases with developmental delay or autism and 2,193 controls. An integrated analysis of CNV and single-nucleotide variant (SNV) data pinpointed 10 genes enriched for putative loss of function. Follow-up of a subset of affected individuals identified new clinical subtypes of pediatric disease and the genes responsible for disease-associated CNVs. These genetic changes include haploinsufficiency of SETBP1 associated with intellectual disability and loss of expressive language and truncations of ZMYND11 in individuals with autism, aggression and complex neuropsychiatric features. This combined CNV and SNV approach facilitates the rapid discovery of new syndromes and genes involved in neuropsychiatric disease despite extensive genetic heterogeneity.

Indexed as

DNA Copy Number VariationsAutistic DisorderBase SequenceCarrier ProteinsCell Cycle ProteinsChildChromosome MappingComparative Genomic HybridizationCo-Repressor ProteinsDevelopmental DisabilitiesDNA-Binding ProteinsFemaleGenetic Association StudiesGenetic Predisposition to DiseaseHaploinsufficiencyHumansCarrier ProteinsCell Cycle ProteinsCo-Repressor ProteinsDNA-Binding ProteinsNuclear ProteinsSETBP1 protein, humanZMYND11 protein, human

Identifiers

PMID25217958
PMCPMC4177294

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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.