Global diversity, population stratification, and selection of human copy-number variation.
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ABSTRACT:
SUBMITTER: Sudmant PH
PROVIDER: S-EPMC4568308 | biostudies-literature | 2015 Sep
REPOSITORIES: biostudies-literature
Publications
Global diversity, population stratification, and selection of human copy-number variation.
Sudmant Peter H PH Mallick Swapan S Nelson Bradley J BJ Hormozdiari Fereydoun F Krumm Niklas N Huddleston John J Coe Bradley P BP Baker Carl C Nordenfelt Susanne S Bamshad Michael M Jorde Lynn B LB Posukh Olga L OL Sahakyan Hovhannes H Watkins W Scott WS Yepiskoposyan Levon L Abdullah M Syafiq MS Bravi Claudio M CM Capelli Cristian C Hervig Tor T Wee Joseph T S JT Tyler-Smith Chris C van Driem George G Romero Irene Gallego IG Jha Aashish R AR Karachanak-Yankova Sena S Toncheva Draga D Comas David D Henn Brenna B Kivisild Toomas T Ruiz-Linares Andres A Sajantila Antti A Metspalu Ene E Parik Jüri J Villems Richard R Starikovskaya Elena B EB Ayodo George G Beall Cynthia M CM Di Rienzo Anna A Hammer Michael F MF Khusainova Rita R Khusnutdinova Elza E Klitz William W Winkler Cheryl C Labuda Damian D Metspalu Mait M Tishkoff Sarah A SA Dryomov Stanislav S Sukernik Rem R Patterson Nick N Reich David D Eichler Evan E EE
Science (New York, N.Y.) 20150806 6253
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 pinpoin ...[more]
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Project description:Copy number variants (CNVs) affect both disease and normal phenotypic variation but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrate accurate estimation of absolute copy number for duplications as small as 1.9 kbp, ranging from 0-48 copies. We identified 4.1 million ‘singly unique nucleotide’ (SUN) positions informative in distinguishing specific copies, and use them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.
2010-09-24 | GSE24334 | GEO
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