ArticleNature communications2020
Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations.
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Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 1 of them a synthesis that pooled it.
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56citing papers in PubMed, 1 pooled it
11.5field-weighted citation impact, top 1% of its field
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Who cites it
56 citing papers in PubMed, 1 synthesis or guideline pooled it, 85 citations in OpenAlex.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- An electronic health record (EHR) phenotype algorithm to identify patients with attention deficit hyperactivity disorders (ADHD) and psychiatric comorbidities.Journal of neurodevelopmental disorders · 2022Trial
- Identification of rare maternal copy number variants by genome-wide analysis of noninvasive prenatal screening data in 113,017 pregnant women.Annals of medicine · 2026Article
- Whole genome sequencing of 1427 Mexican individuals from the oriGen cohort.Nature communications · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Advancing risk gene discovery across the allele frequency spectrum.HGG advances · 2026Review
- Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants.Genome biology · 2026Article
- Discovery of BEND4 as a novel single-gene prognostic marker and therapeutic target for adverse AML.NPJ precision oncology · 2026Article
- Copy Number Variants and Their Association With Intracerebral Hemorrhage Risk: A Case-Control Study.Annals of clinical and translational neurology · 2026Article
- Copy Number Variation Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Copy Number Variant Architecture of Child Psychopathology and Cognitive Development in the ABCD Study.The American journal of psychiatry · 2025Article
- Assessing the diagnostic impact of blood transcriptome profiling in a pediatric cohort previously assessed by genome sequencing.NPJ genomic medicine · 2025Article
- Diversity and consequences of structural variation in the human genome.Nature reviews. Genetics · 2025Review
- Identification of Transdiagnostic Childhood Externalizing Pathology Within an Electronic Medical Records Database and Application to the Analysis of Rare Copy Number Variation.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2025Article
- Contribution of copy number variations to education, socioeconomic status and cognition from a genome-wide study of 305,401 subjects.Molecular psychiatry · 2025Article
- Genome-wide association testing beyond SNPs.Nature reviews. Genetics · 2025Review
- LCAT in Cancer Biology: Embracing Epigenetic Regulation, Immune Interactions, and Therapeutic Implications.International journal of molecular sciences · 2025Review
- Germline copy number variants and endometrial cancer risk.Human genetics · 2024Article
- Rare copy number variant analysis in case-control studies using snp array data: a scalable and automated data analysis pipeline.BMC bioinformatics · 2024Article
Corrections and comments
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Authors and funding
41 authors at 6 institutions in 3 countries.
Yun Rose LiThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Joseph T GlessnerThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Bradley P CoeDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, 98195, USA.
Jin LiThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Maede MohebnasabThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.ORCID http://orcid.org/0000-0001-6623-9514
Xiao ChangThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
John ConnollyThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Charlly KaoThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Zhi WeiDepartment of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, 07102, USA.ORCID http://orcid.org/0000-0001-6059-4267
Jonathan BradfieldThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Cecilia KimThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Cuiping HouThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Munir KhanThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Frank MentchThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Haijun QiuThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Marina BakayThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Christopher CardinaleThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.ORCID http://orcid.org/0000-0001-7513-8977
Maria LemmaThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Debra AbramsThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Andrew Bridglall-JhingoorThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Meckenzie BehrThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Shanell HarrisonThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
George OtienoThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Alexandria ThomasThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Fengxiang WangThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Rosetta ChiavacciThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Lawrence WuThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Dexter HadleyHelen Diller Comprehensive Family Cancer Center and Department of Radiation Oncology, University of California San Francisco, San Francisco, California, 94143, USA.
Elizabeth GoldmuntzDepartment of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104, USA.ORCID http://orcid.org/0000-0003-2936-4396
Josephine EliaDepartment of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104, USA.
John MarisDepartment of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104, USA.
Robert GrundmeierCenter for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Marcella DevotoDepartment of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104, USA.
Brendan KeatingThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Michael MarchThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.ORCID http://orcid.org/0000-0001-9173-6862
Renata PellagrinoThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Struan F A GrantThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.ORCID http://orcid.org/0000-0003-2025-5302
Patrick M A SleimanThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
Mingyao LiDepartment of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, 19104, USA.ORCID http://orcid.org/0000-0003-2422-9494
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, 98195, USA.ORCID http://orcid.org/0000-0002-8246-4014
Hakon HakonarsonThe Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA. hakonarson@email.chop.edu.ORCID http://orcid.org/0000-0003-2814-7461
Children's Hospital of Philadelphia · USHoward Hughes Medical Institute · USNew Jersey Institute of Technology · USUniversity of California, San Francisco · USUniversity of Pennsylvania · USUniversity of Washington · US
Funding
Translational Research Support CoreP30ES013508 · NIEHS · UNIVERSITY OF PENNSYLVANIA · PI Rebecca A Simmons · 2006 to 2026
$35.3MIntegrative Analysis of a GWAS Repository with EMRs from over 40,000 ChildrenU01HG006830 · NHGRI · CHILDREN'S HOSP OF PHILADELPHIA · PI HAKONARSON, HAKON · 2012 to 2014
$3.7MCrowd-Assisted Deep Learning (CrADLe) Digital Curation to Translate Big Data into Precision MedicineU01LM012675 · NLM · UNIVERSITY OF CENTRAL FLORIDA · PI HADLEY, DEXTER D · 2017 to 2020
$2.1MNHGRI NIH HHS U01 HG006830NIEHS NIH HHS P30 ES013508NLM NIH HHS U01 LM012675
Abstract
Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution (P < 1 × 10
Indexed as
DNA Copy Number VariationsComparative Genomic HybridizationDatabases, GeneticGenetic LociGenetic Predisposition to DiseaseGenome, HumanGenome-Wide Association StudyHumansMolecular Sequence AnnotationPolymorphism, Single NucleotideWhite People
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