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Armengol L, Villatoro S, González JR, Pantano L, García-Aragonés M, Rabionet R, Cáceres M, Estivill X. Identification of copy number variants defining genomic differences among major human groups. PLoS One 2009; 4:e7230. [PMID: 19789632 PMCID: PMC2747275 DOI: 10.1371/journal.pone.0007230] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 08/20/2009] [Indexed: 12/14/2022] Open
Abstract
Background Understanding the genetic contribution to phenotype variation of human groups is necessary to elucidate differences in disease predisposition and response to pharmaceutical treatments in different human populations. Methodology/Principal Findings We have investigated the genome-wide profile of structural variation on pooled samples from the three populations studied in the HapMap project by comparative genome hybridization (CGH) in different array platforms. We have identified and experimentally validated 33 genomic loci that show significant copy number differences from one population to the other. Interestingly, we found an enrichment of genes related to environment adaptation (immune response, lipid metabolism and extracellular space) within these regions and the study of expression data revealed that more than half of the copy number variants (CNVs) translate into gene-expression differences among populations, suggesting that they could have functional consequences. In addition, the identification of single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium with the copy number alleles allowed us to detect evidences of population differentiation and recent selection at the nucleotide variation level. Conclusions Overall, our results provide a comprehensive view of relevant copy number changes that might play a role in phenotypic differences among major human populations, and generate a list of interesting candidates for future studies.
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Affiliation(s)
- Lluís Armengol
- Genetic Causes of Disease Group, Genes and Disease Program, Center for Genomic Regulation (CRG-UPF) and CIBERESP, Barcelona, Catalonia, Spain
- Quantitative Genomic Medicine Laboratories (qGenomics), Barcelona, Catalonia, Spain
| | - Sergi Villatoro
- Genetic Causes of Disease Group, Genes and Disease Program, Center for Genomic Regulation (CRG-UPF) and CIBERESP, Barcelona, Catalonia, Spain
| | - Juan R. González
- Center for Research in Environmental Epidemiology (CREAL), Barcelona, Catalonia, Spain
| | - Lorena Pantano
- Genetic Causes of Disease Group, Genes and Disease Program, Center for Genomic Regulation (CRG-UPF) and CIBERESP, Barcelona, Catalonia, Spain
| | - Manel García-Aragonés
- Genetic Causes of Disease Group, Genes and Disease Program, Center for Genomic Regulation (CRG-UPF) and CIBERESP, Barcelona, Catalonia, Spain
| | - Raquel Rabionet
- Genetic Causes of Disease Group, Genes and Disease Program, Center for Genomic Regulation (CRG-UPF) and CIBERESP, Barcelona, Catalonia, Spain
| | - Mario Cáceres
- Genetic Causes of Disease Group, Genes and Disease Program, Center for Genomic Regulation (CRG-UPF) and CIBERESP, Barcelona, Catalonia, Spain
| | - Xavier Estivill
- Genetic Causes of Disease Group, Genes and Disease Program, Center for Genomic Regulation (CRG-UPF) and CIBERESP, Barcelona, Catalonia, Spain
- Genetics Unit, Department of Health and Experimental Life Sciences, Pompeu Fabra University (UPF), Barcelona, Catalonia, Spain
- National Genotyping Center (CeGen) Barcelona Genotyping Node, Center for Genomic Regulation (CRG-UPF), Barcelona, Catalonia, Spain
- * E-mail:
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