ArticleScience (New York, N.Y.)2015
Global diversity, population stratification, and selection of human copy-number variation.
Abstract readComparative Study
In one paragraph
Article in Science (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
217citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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.
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.
Who cites it
217 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Copy Number Variants in Alzheimer's Disease.Journal of Alzheimer's disease : JAD · 2017Pooled it
- Structural variant detection across sequencing technologies.Nature biotechnology · 2026Article
- scTransMIL bridges patient-level disease states and single-cell transcriptomics for cancer screening and heterogeneity inference.Nature communications · 2026Article
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Buffering of gene dosage response curves for human complex traits.Cell genomics · 2026Article
- A genomic study of trichotillomania and excoriation disorder in families.Translational psychiatry · 2026Article
- A phenome-wide association study of CNVs genotyped from genome sequencing read depth in the UK Biobank.American journal of human genetics · 2026Article
- Pangenome variation analysis uncovers the impacts of SNP-independent structural variations in modern European cattle breeding.iMetaOmics · 2026Article
- Article
- Admixture-driven structural variation diversity and its functional implications.National science review · 2026Article
- Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye-Aye (Daubentonia madagascariensis).American journal of primatology · 2025Review
- The Landscape of Structural Variation in Aye-Ayes (Daubentonia madagascariensis).Genome biology and evolution · 2025Article
- IMGTNAR genomics and bioinformatics · 2025Article
- Diversity of U1 Small Nuclear RNAs and Diagnostic Methods for Their Mutations.Cancer science · 2025Article
- Article
- Copy Number Variation Shapes Structural Genomic Diversity Associated With Ecological Adaptation in the Wild Tomato Solanum chilense.Molecular biology and evolution · 2025Article
- Population-level gene copy number variations reveal distinct genetic properties of different Malus species.BMC genomics · 2025Article
- Pangenome discovery of missing autism variants.medRxiv : the preprint server for health sciences · 2025Article
- Diversity and consequences of structural variation in the human genome.Nature reviews. Genetics · 2025Review
157 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
51 authors.
Peter H SudmantDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Swapan MallickBroad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Bradley J NelsonDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Fereydoun HormozdiariDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Niklas KrummDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
John HuddlestonDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Bradley P CoeDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Carl BakerDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Susanne NordenfeltBroad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Michael BamshadDepartment of Pediatrics, University of Washington, Seattle, WA 98119, USA.
Lynn B JordeDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
Olga L PosukhInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Novosibirsk State University, Novosibirsk 630090, Russia.
Hovhannes SahakyanEstonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
W Scott WatkinsDepartment of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
Levon YepiskoposyanLaboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
M Syafiq AbdullahRaja Isteri Pengiran Anak Saleha (RIPAS) Hospital, Bandar Seri Begawan, Brunei Darussalam.
Claudio M BraviLaboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), Centro Científico y Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET) and Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), La Plata B1906APO, Argentina.
Cristian CapelliDepartment of Zoology, University of Oxford, Oxford OX1 3PS, UK.
Tor HervigDepartment of Clinical Science, University of Bergen, Bergen 5021, Norway.
Joseph T S WeeNational Cancer Centre Singapore, Singapore.
Chris Tyler-SmithWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
George van DriemInstitute of Linguistics, University of Bern, Bern CH-3012, Switzerland.
Irene Gallego RomeroDepartment of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
Aashish R JhaDepartment of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
Sena Karachanak-YankovaDepartment of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
Draga TonchevaDepartment of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
David ComasInstitut de Biologia Evolutiva [Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra (CSIC-UPF)], Departament de Ciències Experimentals i de la Salut, UPF, Barcelona 08003, Spain.
Brenna HennDepartment of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA.
Toomas KivisildDivision of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK.
Andres Ruiz-LinaresDepartment of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK.
Antti SajantilaUniversity of Helsinki, Department of Forensic Medicine, Helsinki 00014, Finland.
Ene MetspaluEstonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. University of Tartu, Department of Evolutionary Biology, Tartu 5101, Estonia.
Jüri ParikEstonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.
Richard VillemsEstonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.
Elena B StarikovskayaLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
George AyodoCenter for Global Health and Child Development, Kisumu 40100, Kenya.
Cynthia M BeallDepartment of Anthropology, Case Western Reserve University, Cleveland, OH 44106-7125, USA.
Anna Di RienzoDepartment of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
Michael F HammerArizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA.
Rita KhusainovaInstitute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia.
Elza KhusnutdinovaInstitute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia.
William KlitzIntegrative Biology, University of California, Berkeley, CA 94720-3140, USA.
Cheryl WinklerBasic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Incorporated, Frederick National Laboratory, Frederick, MD 21702, USA.
Damian LabudaCentre Hospitalier Universitaire (CHU) Sainte-Justine, Département de Pédiatrie, Université de Montréal, QC H3T 1C5, Canada.
Mait MetspaluEstonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.
Sarah A TishkoffDepartments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
Stanislav DryomovLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
Rem SukernikLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Altai State University, Barnaul 656000, Russia.
Nick PattersonBroad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
David ReichBroad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
Evan E EichlerDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. eee@gs.washington.edu.
Funding
Translational Research Support CoreP30ES013508 · NIEHS · UNIVERSITY OF PENNSYLVANIA · PI Rebecca A Simmons · 2006 to 2026
$35.3MUniversity of Washington Medical Scientist Training Program: MD/PhDT32GM007266 · NIGMS · UNIVERSITY OF WASHINGTON · PI HORWITZ, MARSHALL S. · 1985 to 2023
$30.4MSequence and Assembly of Segmental DuplicationsR01HG002385 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2001 to 2026
$13.3MGenetic adaptations to high altitudeR01HL119577 · NHLBI · UNIVERSITY OF CHICAGO · PI DI RIENZO, ANNA · 2014 to 2023
$4.9MIntegrative Genomics of Body Size and Metabolism in Ethnically Diverse AfricansR01GM113657 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI TISHKOFF, SARAH ANNE · 2015 to 2019
$2.8MAfrican Odyssey: An Integrative Genomics Analysis of Complex Physiologic TraitsDP1ES022577 · NIEHS · UNIVERSITY OF PENNSYLVANIA · PI TISHKOFF, SARAH ANNE · 2012 to 2013
$1.6MIntegrative nutrigenomic and metabolomic analyses of Africans with variable dietsR01DK104339 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI TISHKOFF, SARAH ANNE · 2015 to 2018
$1.4MEuropean Research Council 261213Howard Hughes Medical InstituteIntramural NIH HHSNCCDPHP CDC HHS 5DP1ES022577 05NHGRI NIH HHS 2R01HG002385NHGRI NIH HHS R01 HG002385NHLBI NIH HHS R01 HL119577NIDDK NIH HHS 1R01DK104339-01NIDDK NIH HHS R01 DK104339NIEHS NIH HHS DP1 ES022577NIEHS NIH HHS P30 ES013508NIGMS NIH HHS 1R01GM113657-01NIGMS NIH HHS R01 GM113657NIGMS NIH HHS T32 GM007266PHS HHS HHSN26120080001EWellcome TrustWellcome Trust 098051
Abstract
In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.
Indexed as
DNA Copy Number VariationsEvolution, MolecularGene DuplicationSequence DeletionAnimalsBlack PeopleGenome, HumanHominidaeHumansNative Hawaiian or Pacific IslanderPhylogenyPolymorphism, Single NucleotidePopulationSelection, Genetic
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
Read underepoch 390
Registered trials
None linked
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.