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Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

التفاصيل البيبلوغرافية
العنوان: Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
المؤلفون: 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
المساهمون: Molecular Dynamics, Biomimetics, Urban and Regional Studies Institute, Nanomedicine & Drug Targeting, Artificial Intelligence, Micromechanics, Molecular Cell Biology, Van Swinderen Institute for Particle Physics and G, Archaeology of Northwestern Europe, Polymer Chemistry and Bioengineering, Christianity and the History of Ideas, Scientific Visualization and Computer Graphics, Chemical Technology, Macromolecular Chemistry & New Polymeric Materials, Bernoulli Institute, Surfaces and Thin Films, Hemelrijk group, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Falcao Salles lab, Synthetic Organic Chemistry, Psychometrics and Statistics, Bio-inspired systems and circuits, Advanced Production Engineering, Drug Design, The 1000 Genomes Project Consortium, Faculteit Medische Wetenschappen/UMCG, Wellcome Trust, Consiglio Nazionale delle Ricerche, EMBO, 1000 Genomes Project Consortium
المصدر: Genome Biology, 15(6):R88. BMC
Recercat. Dipósit de la Recerca de Catalunya
instname
Genome Biology
CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
GenomeBiology.com (Lond., Print) 15 (2014). doi:10.1186/gb-2014-15-6-r88
info:cnr-pdr/source/autori:Colonna, Vincenza; Ayub, Qasim; Chen, Yuan; Pagani, Luca; Luisi, Pierre; Pybus, Marc; Garrison, Erik; Xue, Yali; Tyler-Smith, Chris/titolo:Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences/doi:10.1186%2Fgb-2014-15-6-r88/rivista:GenomeBiology.com (Lond., Print)/anno:2014/pagina_da:/pagina_a:/intervallo_pagine:/volume:15
Genome Biology : Biology for the Post-Genomic Era
Digital.CSIC. Repositorio Institucional del CSIC
Genome biology
سنة النشر: 2014
مصطلحات موضوعية: Historia y Arqueología, lactase persistence, POSITIVE SELECTION, BALANCING SELECTION, SOFT SWEEP, Biología, standing variation, Population, Biology, Balancing selection, Genome, Polymorphism, Single Nucleotide, Genètica de poblacions humanes, Ciencias Biológicas, purl.org/becyt/ford/1 [https], selective sweep, functional annotation cluster, Genética y Herencia, HUMANIDADES, Genetic drift, Gene Frequency, INDEL Mutation, Humans, Selection, Genetic, education, purl.org/becyt/ford/1.6 [https], Selection (genetic algorithm), education.field_of_study, purl.org/becyt/ford/6 [https], Genome, Human, Research, Genetic Drift, Levenshtein distance, Selecció natural, Sequence Analysis, DNA, Human genetics, Otras Historia y Arqueología, Evolutionary biology, Human genome, purl.org/becyt/ford/6.1 [https], Selective sweep, Genètica humana -- Variació, CIENCIAS NATURALES Y EXACTAS
الوصف: It contains associated material.-- The 1000 Genomes Project Consortium
[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. © 2014 Colonna et al.
This work was supported by The Wellcome Trust (098051), an Italian National Research Council (CNR) short-term mobility fellowship from the 2013 program to VC, and an EMBO Short Term Fellowship ASTF 324–2010 to VC.
وصف الملف: Print-Electronic; application/pdf
اللغة: English
تدمد: 1474-7596
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6661b65b2e9464a1bffd586a856b1386
https://research.rug.nl/en/publications/0d833a56-8eb8-4c58-a06e-7daade1712d5
حقوق: OPEN
رقم الأكسشن: edsair.doi.dedup.....6661b65b2e9464a1bffd586a856b1386
قاعدة البيانات: OpenAIRE
الوصف
تدمد:14747596