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Population genetics of immune-related multilocus copy number variation in Native Americans

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dc.contributor.author Zuccherato, L. W.
dc.contributor.author Schneider, S.
dc.contributor.author Tarazona-Santos, E.
dc.contributor.author Hardwick, R. J.
dc.contributor.author Berg, D. E.
dc.contributor.author Bogle, H.
dc.contributor.author Gouveia, M. H.
dc.contributor.author Machado, L. R.
dc.contributor.author Machado, M.
dc.contributor.author Rodrigues-Soares, F.
dc.contributor.author Soares-Souza, G. B.
dc.contributor.author Togni, D. L.
dc.contributor.author Zamudio, R.
dc.contributor.author Gilman, R. H.
dc.contributor.author Duarte, D.
dc.contributor.author Hollox, E. J.
dc.contributor.author Rodrigues, M. R.
dc.date.accessioned 2019-01-25T16:36:28Z
dc.date.available 2019-01-25T16:36:28Z
dc.date.issued 2017
dc.identifier.uri https://hdl.handle.net/20.500.12866/4844
dc.description.abstract While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy-Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f, which quantifies the departure of homozygosity from the Hardy-Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1, FCGR3A, FCGR3B and FCGR2C) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations. en_US
dc.language.iso eng
dc.publisher The Royal Society
dc.relation.ispartof urn:issn:1742-5662
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject disease en_US
dc.subject history en_US
dc.subject Science & Technology - Other Topics en_US
dc.subject Amerindians en_US
dc.subject ccl3l1 en_US
dc.subject f-statistics en_US
dc.subject fcgr3b en_US
dc.subject genomic structural variation en_US
dc.subject hiv load en_US
dc.subject human genome en_US
dc.subject immunity en_US
dc.subject locus en_US
dc.subject population structure en_US
dc.subject profiled-likelihood en_US
dc.subject reconstitution en_US
dc.subject sub-saharan africans en_US
dc.title Population genetics of immune-related multilocus copy number variation in Native Americans en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1098/rsif.2017.0057


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