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Title: Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
Authors: Colonna, V
Ayub, Q
Chen, Y
Pagani, L
Luisi, P
Pybus, M
Garrison, E
Xue, Y
Tyler-Smith, C
Abecasis, GR
Auton, A
Brooks, LD
Depristo, MA
Durbin, RM
Handsaker, RE
Kang, HM
Marth, GT
McVean, G
Altshuler, DM
Bentley, DR
Chakravarti, A
Clark, AG
Donnelly, P
Eichler, EE
Flicek, P
Gabriel, SB
Gibbs, RA
Green, ED
Hurles, ME
Knoppers, BM
Korbel, JO
Lander, ES
Lee, C
Lehrach, H
Mardis, ER
McVean, GA
Nickerson, DA
Schmidt, JP
Sherry, ST
Wang, J
Wilson, RK
Dinh, H
Kovar, C
Lee, S
Lewis, L
Muzny, D
Reid, J
Wang, M
Fang, X
Guo, X
Jian, M
Jiang, H
Jin, X
Li, G
Li, J
Li, Y
Li, Z
Liu, X
Lu, Y
Ma, X
Su, Z
Tai, S
Tang, M
Wang, B
Wang, G
Wu, H
Wu, R
Yin, Y
Zhang, W
Zhao, J
Zhao, M
Zheng, X
Zhou, Y
Gupta, N
Clarke, L
Leinonen, R
Smith, RE
Zheng-Bradley, X
Grocock, R
Humphray, S
James, T
Kingsbury, Z
Sudbrak, R
Albrecht, MW
Amstislavskiy, VS
Borodina, TA
Lienhard, M
Mertes, F
Sultan, M
Timmermann, B
Yaspo, ML
Fulton, L
Fulton, R
Weinstock, GM
Balasubramaniam, S
Burton, J
Danecek, P
Keane, TM
Kolb-Kokocinski, A
McCarthy, S
Keywords: selective sweep;Levenshtein distance;standing variation;lactase persistence;functional annotation cluster
Issue Date: 30-Jun-2014
Publisher: BMC Springer Nature
Citation: Colonna, V., Ayub, Q., Chen, Y. et al. and the 1000 Genomes Project Consortium. (2014) 'Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences', Genome Biology, 15 (6), R88, pp. 1 - 14. doi: 10.1186/gb-2014-15-6-r88.
Abstract: Copyright © 2014 Colonna et al. Background: Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. Results: We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. Conclusions: We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.
Description: Data availability: The 1000 Genomes phase I integrated callset used in this study is publicly available at [The 1000 Genomes Project.]. For a list of samples used in this study, refer to Table S1 in Additional file 1. Additional files: Additional file 1: This file contains supplementary Tables ST1 to ST4 ( Additional file 2: This file contains supplementary Figures F1 to F16 ( Additional file 3: Full list of participants and institutions in the 1000 Genomes Project (
ISSN: 1474-7596
Appears in Collections:Dept of Life Sciences Research Papers

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