Global diversity, population stratification, and selection of human copy-number variation

Peter H. Sudmant, Swapan Mallick, Bradley J. Nelson, Fereydoun Hormozdiari, Niklas Krumm, John Huddleston, Bradley P. Coe, Carl Baker, Susanne Nordenfelt, Michael Bamshad, Lynn B. Jorde, Olga L. Posukh, Hovhannes Sahakyan, W. Scott Watkins, Levon Yepiskoposyan, M. Syafiq Abdullah, Claudio M. Bravi, Cristian Capelli, Tor Hervig, Joseph T S WeeChris Tyler-Smith, George Van Driem, Irene Gallego Romero, Aashish R. Jha, Sena Karachanak-Yankova, Draga Toncheva, David Comas, Brenna Henn, Toomas Kivisild, Andres Ruiz-Linares, Antti Sajantila, Ene Metspalu, Jüri Parik, Richard Villems, Elena B. Starikovskaya, George Ayodo, Cynthia M. Beall, Anna Di Rienzo, Michael F Hammer, Rita Khusainova, Elza Khusnutdinova, William Klitz, Cheryl Winkler, Damian Labuda, Mait Metspalu, Sarah A. Tishkoff, Stanislav Dryomov, Rem Sukernik, Nick Patterson, David Reich, Evan E. Eichler

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131 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberaab3761
JournalScience
Volume349
Issue number6253
DOIs
StatePublished - Sep 11 2015

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Population
Base Pairing
Population Genetics
Human Genome
Nucleotides
DNA

ASJC Scopus subject areas

  • General

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Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., ... Eichler, E. E. (2015). Global diversity, population stratification, and selection of human copy-number variation. Science, 349(6253), [aab3761]. https://doi.org/10.1126/science.aab3761

Global diversity, population stratification, and selection of human copy-number variation. / Sudmant, Peter H.; Mallick, Swapan; Nelson, Bradley J.; Hormozdiari, Fereydoun; Krumm, Niklas; Huddleston, John; Coe, Bradley P.; Baker, Carl; Nordenfelt, Susanne; Bamshad, Michael; Jorde, Lynn B.; Posukh, Olga L.; Sahakyan, Hovhannes; Watkins, W. Scott; Yepiskoposyan, Levon; Abdullah, M. Syafiq; Bravi, Claudio M.; Capelli, Cristian; Hervig, Tor; Wee, Joseph T S; Tyler-Smith, Chris; Van Driem, George; Romero, Irene Gallego; Jha, Aashish R.; Karachanak-Yankova, Sena; Toncheva, Draga; Comas, David; Henn, Brenna; Kivisild, Toomas; Ruiz-Linares, Andres; Sajantila, Antti; Metspalu, Ene; Parik, Jüri; Villems, Richard; Starikovskaya, Elena B.; Ayodo, George; Beall, Cynthia M.; Di Rienzo, Anna; Hammer, Michael F; Khusainova, Rita; Khusnutdinova, Elza; Klitz, William; Winkler, Cheryl; Labuda, Damian; Metspalu, Mait; Tishkoff, Sarah A.; Dryomov, Stanislav; Sukernik, Rem; Patterson, Nick; Reich, David; Eichler, Evan E.

In: Science, Vol. 349, No. 6253, aab3761, 11.09.2015.

Research output: Contribution to journalArticle

Sudmant, PH, Mallick, S, Nelson, BJ, Hormozdiari, F, Krumm, N, Huddleston, J, Coe, BP, Baker, C, Nordenfelt, S, Bamshad, M, Jorde, LB, Posukh, OL, Sahakyan, H, Watkins, WS, Yepiskoposyan, L, Abdullah, MS, Bravi, CM, Capelli, C, Hervig, T, Wee, JTS, Tyler-Smith, C, Van Driem, G, Romero, IG, Jha, AR, Karachanak-Yankova, S, Toncheva, D, Comas, D, Henn, B, Kivisild, T, Ruiz-Linares, A, Sajantila, A, Metspalu, E, Parik, J, Villems, R, Starikovskaya, EB, Ayodo, G, Beall, CM, Di Rienzo, A, Hammer, MF, Khusainova, R, Khusnutdinova, E, Klitz, W, Winkler, C, Labuda, D, Metspalu, M, Tishkoff, SA, Dryomov, S, Sukernik, R, Patterson, N, Reich, D & Eichler, EE 2015, 'Global diversity, population stratification, and selection of human copy-number variation', Science, vol. 349, no. 6253, aab3761. https://doi.org/10.1126/science.aab3761
Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J et al. Global diversity, population stratification, and selection of human copy-number variation. Science. 2015 Sep 11;349(6253). aab3761. https://doi.org/10.1126/science.aab3761
Sudmant, Peter H. ; Mallick, Swapan ; Nelson, Bradley J. ; Hormozdiari, Fereydoun ; Krumm, Niklas ; Huddleston, John ; Coe, Bradley P. ; Baker, Carl ; Nordenfelt, Susanne ; Bamshad, Michael ; Jorde, Lynn B. ; Posukh, Olga L. ; Sahakyan, Hovhannes ; Watkins, W. Scott ; Yepiskoposyan, Levon ; Abdullah, M. Syafiq ; Bravi, Claudio M. ; Capelli, Cristian ; Hervig, Tor ; Wee, Joseph T S ; Tyler-Smith, Chris ; Van Driem, George ; Romero, Irene Gallego ; Jha, Aashish R. ; Karachanak-Yankova, Sena ; Toncheva, Draga ; Comas, David ; Henn, Brenna ; Kivisild, Toomas ; Ruiz-Linares, Andres ; Sajantila, Antti ; Metspalu, Ene ; Parik, Jüri ; Villems, Richard ; Starikovskaya, Elena B. ; Ayodo, George ; Beall, Cynthia M. ; Di Rienzo, Anna ; Hammer, Michael F ; Khusainova, Rita ; Khusnutdinova, Elza ; Klitz, William ; Winkler, Cheryl ; Labuda, Damian ; Metspalu, Mait ; Tishkoff, Sarah A. ; Dryomov, Stanislav ; Sukernik, Rem ; Patterson, Nick ; Reich, David ; Eichler, Evan E. / Global diversity, population stratification, and selection of human copy-number variation. In: Science. 2015 ; Vol. 349, No. 6253.
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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.",
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AU - Mallick, Swapan

AU - Nelson, Bradley J.

AU - Hormozdiari, Fereydoun

AU - Krumm, Niklas

AU - Huddleston, John

AU - Coe, Bradley P.

AU - Baker, Carl

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AU - Bamshad, Michael

AU - Jorde, Lynn B.

AU - Posukh, Olga L.

AU - Sahakyan, Hovhannes

AU - Watkins, W. Scott

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AU - Bravi, Claudio M.

AU - Capelli, Cristian

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AU - Van Driem, George

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AU - Toncheva, Draga

AU - Comas, David

AU - Henn, Brenna

AU - Kivisild, Toomas

AU - Ruiz-Linares, Andres

AU - Sajantila, Antti

AU - Metspalu, Ene

AU - Parik, Jüri

AU - Villems, Richard

AU - Starikovskaya, Elena B.

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AU - Tishkoff, Sarah A.

AU - Dryomov, Stanislav

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AU - Patterson, Nick

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