Global diversity, population stratification, and selection of human copy-number variation
Open accessAbstract
Duplications and deletions in the human genome: Duplications and deletions can lead to variation in copy number for genes and genomic loci among humans. Such variants can reveal evolutionary patterns and have implications for human health. Sudmant et al. examined copy-number variation across 236 individual genomes from 125 human populations. Deletions were under more selection, whereas duplications showed more population-specific structure. Interestingly, Oceanic populations retain large duplications postulated to have originated in an ancient Denisovan lineage. Science , this issue 10.1126/science.aab3761
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TAD boundaries are significantly less likely (P < 0.02) to be affected by known deletion and duplication polymorphisms derived from genomes of healthy human populations.
“Interestingly, TAD boundaries are significantly less likely (P < 0.02) to be affected by known deletion and duplication polymorphisms derived from genomes of healthy human populations25–27 (Extended Data Fig. 2d).”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [27]
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References 58 · Cited by 345
- Authors
- Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., Jorde, L. B., Posukh, O. L., Sahakyan, H., Watkins, W. S., Yepiskoposyan, L., Abdullah, M. S., Bravi, C. M., Capelli, C., Hervig, T., Wee, J. T. S., Tyler-Smith, C., van Driem, G., Romero, I. G., Jha, A. R., Karachanak-Yankova, S., Toncheva, D., Comas, D., Henn, B., Kivisild, T., Ruiz-Linares, A., Sajantila, A., Metspalu, E., Parik, J., Villems, R., Starikovskaya, E. B., Ayodo, G., Beall, C. M., Di Rienzo, A., Hammer, M. F., Khusainova, R., Khusnutdinova, E., Klitz, W., Winkler, C., Labuda, D., Metspalu, M., Tishkoff, S. A., Dryomov, S., Sukernik, R., Patterson, N., Reich, D., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- Broad Institute (US)
- Howard Hughes Medical Institute (US)
- University of Utah (US)
- Russian Academy of Sciences (RU)
- Institute of Molecular Biology (AM)
- Raja Isteri Pengiran Anak Saleha Hospital (BN)
- Laboratorio 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.
- University of Oxford (GB)
- University of Bergen (NO)
- National Cancer Centre Singapore (SG)
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
- Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland.
- University of Chicago (US)
- Medical University of Sofia (BG)
- Consejo Superior de Investigaciones Científicas (ES)
- Stony Brook University (US)
- University of Cambridge (GB)
- Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK.
- University of Helsinki (FI)
- Estonian Biocentre (EE)
- Center for Global Health and Child Development, Kisumu 40100, Kenya.
- Case Western Reserve University (US)
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
- University of Arizona (US)
- Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.
- University of California, Berkeley (US)
- Frederick National Laboratory for Cancer Research (US)
- Centre Hospitalier Universitaire Sainte-Justine (CA)
- University of Pennsylvania (US)
- Corresponding author
- Eichler, Evan E.
- ORCID
- Sudmant, Peter H.
- Mallick, Swapan
- Nelson, Bradley J.
- Hormozdiari, Fereydoun
- Krumm, Niklas
- Huddleston, John
- Coe, Bradley P.
- Bamshad, Michael
- Jorde, Lynn B.
- Posukh, Olga L.
- Sahakyan, Hovhannes
- Watkins, W. Scott
- Yepiskoposyan, Levon
- Abdullah, M. Syafiq
- Capelli, Cristian
- Hervig, Tor
- Wee, Joseph T. S.
- Romero, Irene Gallego
- Jha, Aashish R.
- Karachanak-Yankova, Sena
- Toncheva, Draga
- Comas, David
- Henn, Brenna
- Kivisild, Toomas
- Sajantila, Antti
- Metspalu, Ene
- Villems, Richard
- Starikovskaya, Elena B.
- Ayodo, George
- Beall, Cynthia M.
- Hammer, Michael F.
- Khusainova, Rita
- Winkler, Cheryl
- Labuda, Damian
- Metspalu, Mait
- Tishkoff, Sarah A.
- Sukernik, Rem
- Patterson, Nick
- Eichler, Evan E.
- Venue
- Science
- Published
- 2015-09-11
- Volume
- 349
- Issue
- 6253
- Pages
- aab3761-aab3761
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4568308
- OpenAlex
- W2124429242
- Cited by
- 345
- References
- 58
- Citations by year
- 2026: 14 · 2025: 18 · 2024: 25 · 2023: 10 · 2022: 29 · 2021: 35 · 2020: 44 · 2019: 32 · 2018: 39 · 2017: 48 · 2016: 47 · 2015: 3
- FWCI
- 31.39
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (acceptedVersion)
- EPubDev Repository (submittedVersion)
- Americanae (AECID Library) (submittedVersion, other-oa)
- Bern Open Repository and Information System (University of Bern) (submittedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion)
- Conicet (submittedVersion, cc-by-nc-sa)
- RUNE (Research UNE) (submittedVersion)
- Funders
- NSF (BCS-1032255, 924726, 1153911)
- NIH (2R01HG002385, 11631, 5DP1ES022577 05, 1R01DK104339-01, 1R01GM113657-01)
- Howard Hughes Medical Institute
- National Cancer Institute
- Simons Foundation
- Paul G. Allen Family Foundation
- Wellcome Trust (98051)
- European Research Council (FP7 - 26213)
- Ministry of Education and Science, Russian Federation (14.Z50.31.0010)
- Intramural Research Program of the NIH
- Center for Cancer Research
- ENA (PRJEB9586, ERP010710)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- copy number variation, positive selection, genomic duplication, genomic deletions, single nucleotide variants
- MeSH terms
- Animals, Humans, Phylogeny, Population, Selection, Genetic, Hominidae, Genome, Human, Sequence Deletion, Evolution, Molecular, Gene Duplication, Polymorphism, Single Nucleotide, Black People, Native Hawaiian or Pacific Islander, Native Hawaiian or Other Pacific Islander, DNA Copy Number Variations
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