Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance

 

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dc.contributor.author Choudhury, Ananyo
dc.contributor.author Hazelhurst, Scott
dc.contributor.author Meintjes, Ayton
dc.contributor.author Achinike-Oduaran, Ovokeraye
dc.contributor.author Aron, Shaun
dc.contributor.author Gamieldien, Junaid
dc.contributor.author Jalali Sefid Dashti, Mahjoubeh
dc.contributor.author Mulder, Nicola
dc.contributor.author Tiffin, Nicki
dc.contributor.author Ramsay, Michèle
dc.date.accessioned 2015-07-30T04:11:19Z
dc.date.available 2015-07-30T04:11:19Z
dc.date.issued 2014-06-06
dc.identifier.citation Choudhury, A., Hazelhurst, S., Meintjes, A., Achinike-Oduaran, O., Aron, S., Gamieldien, J., ... & Ramsay, M. (2014). Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. BMC genomics, 15(1), 437.
dc.identifier.uri http://hdl.handle.net/11427/13629
dc.identifier.uri http://dx.doi.org/10.1186/1471-2164-15-437
dc.description.abstract Abstract Background Population differentiation is the result of demographic and evolutionary forces. Whole genome datasets from the 1000 Genomes Project (October 2012) provide an unbiased view of genetic variation across populations from Europe, Asia, Africa and the Americas. Common population-specific SNPs (MAF > 0.05) reflect a deep history and may have important consequences for health and wellbeing. Their interpretation is contextualised by currently available genome data. Results The identification of common population-specific (CPS) variants (SNPs and SSV) is influenced by admixture and the sample size under investigation. Nine of the populations in the 1000 Genomes Project (2 African, 2 Asian (including a merged Chinese group) and 5 European) revealed that the African populations (LWK and YRI), followed by the Japanese (JPT) have the highest number of CPS SNPs, in concordance with their histories and given the populations studied. Using two methods, sliding 50-SNP and 5-kb windows, the CPS SNPs showed distinct clustering across large genome segments and little overlap of clusters between populations. iHS enrichment score and the population branch statistic (PBS) analyses suggest that selective sweeps are unlikely to account for the clustering and population specificity. Of interest is the association of clusters close to recombination hotspots. Functional analysis of genes associated with the CPS SNPs revealed over-representation of genes in pathways associated with neuronal development, including axonal guidance signalling and CREB signalling in neurones. Conclusions Common population-specific SNPs are non-randomly distributed throughout the genome and are significantly associated with recombination hotspots. Since the variant alleles of most CPS SNPs are the derived allele, they likely arose in the specific population after a split from a common ancestor. Their proximity to genes involved in specific pathways, including neuronal development, suggests evolutionary plasticity of selected genomic regions. Contrary to expectation, selective sweeps did not play a large role in the persistence of population-specific variation. This suggests a stochastic process towards population-specific variation which reflects demographic histories and may have some interesting implications for health and susceptibility to disease.
dc.rights This is an Open Access article distributed under the terms of the Creative Commons Attribution License *
dc.rights.uri http://creativecommons.org/licenses/by/2.0 *
dc.source BMC Genomics en_ZA
dc.source.uri http://www.biomedcentral.com/bmcgenomics/
dc.subject.other Genomics en_ZA
dc.title Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance
dc.type Journal Article en_ZA
dc.date.updated 2015-01-15T17:56:13Z
dc.language.rfc3066 en
dc.rights.holder Choudhury et al.; licensee BioMed Central Ltd.
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department Department of Clinical Laboratory Sciences en_ZA
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uct.type.filetype Text
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dc.identifier.apacitation Choudhury, A., Hazelhurst, S., Meintjes, A., Achinike-Oduaran, O., Aron, S., Gamieldien, J., ... Ramsay, M. (2014). Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. <i>BMC Genomics</i>, http://hdl.handle.net/11427/13629 en_ZA
dc.identifier.chicagocitation Choudhury, Ananyo, Scott Hazelhurst, Ayton Meintjes, Ovokeraye Achinike-Oduaran, Shaun Aron, Junaid Gamieldien, Mahjoubeh Jalali Sefid Dashti, Nicola Mulder, Nicki Tiffin, and Michèle Ramsay "Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance." <i>BMC Genomics</i> (2014) http://hdl.handle.net/11427/13629 en_ZA
dc.identifier.vancouvercitation Choudhury A, Hazelhurst S, Meintjes A, Achinike-Oduaran O, Aron S, Gamieldien J, et al. Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. BMC Genomics. 2014; http://hdl.handle.net/11427/13629. en_ZA
dc.identifier.ris TY - Journal Article AU - Choudhury, Ananyo AU - Hazelhurst, Scott AU - Meintjes, Ayton AU - Achinike-Oduaran, Ovokeraye AU - Aron, Shaun AU - Gamieldien, Junaid AU - Jalali Sefid Dashti, Mahjoubeh AU - Mulder, Nicola AU - Tiffin, Nicki AU - Ramsay, Michèle AB - Abstract Background Population differentiation is the result of demographic and evolutionary forces. Whole genome datasets from the 1000 Genomes Project (October 2012) provide an unbiased view of genetic variation across populations from Europe, Asia, Africa and the Americas. Common population-specific SNPs (MAF > 0.05) reflect a deep history and may have important consequences for health and wellbeing. Their interpretation is contextualised by currently available genome data. Results The identification of common population-specific (CPS) variants (SNPs and SSV) is influenced by admixture and the sample size under investigation. Nine of the populations in the 1000 Genomes Project (2 African, 2 Asian (including a merged Chinese group) and 5 European) revealed that the African populations (LWK and YRI), followed by the Japanese (JPT) have the highest number of CPS SNPs, in concordance with their histories and given the populations studied. Using two methods, sliding 50-SNP and 5-kb windows, the CPS SNPs showed distinct clustering across large genome segments and little overlap of clusters between populations. iHS enrichment score and the population branch statistic (PBS) analyses suggest that selective sweeps are unlikely to account for the clustering and population specificity. Of interest is the association of clusters close to recombination hotspots. Functional analysis of genes associated with the CPS SNPs revealed over-representation of genes in pathways associated with neuronal development, including axonal guidance signalling and CREB signalling in neurones. Conclusions Common population-specific SNPs are non-randomly distributed throughout the genome and are significantly associated with recombination hotspots. Since the variant alleles of most CPS SNPs are the derived allele, they likely arose in the specific population after a split from a common ancestor. Their proximity to genes involved in specific pathways, including neuronal development, suggests evolutionary plasticity of selected genomic regions. Contrary to expectation, selective sweeps did not play a large role in the persistence of population-specific variation. This suggests a stochastic process towards population-specific variation which reflects demographic histories and may have some interesting implications for health and susceptibility to disease. DA - 2014-06-06 DB - OpenUCT DO - 10.1186/1471-2164-15-437 DP - University of Cape Town J1 - BMC Genomics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2014 T1 - Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance TI - Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance UR - http://hdl.handle.net/11427/13629 ER - en_ZA


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