Supplementary material from "Population genetics of immune-related multilocus copy number variation in Native Americans"
Posted on 2017-03-14 - 10:00
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.
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W. Zuccherato, Luciana; Schneider, Silvana; Tarazona-Santos, Eduardo; J. Hardwick, Robert; E. Berg, Douglas; Bogle, Helen; et al. (2017). Supplementary material from "Population genetics of immune-related multilocus copy number variation in Native Americans". The Royal Society. Collection. https://doi.org/10.6084/m9.figshare.c.3716284.v1
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AUTHORS (17)
LW
Luciana W. Zuccherato
SS
Silvana Schneider
ET
Eduardo Tarazona-Santos
RJ
Robert J. Hardwick
DE
Douglas E. Berg
HB
Helen Bogle
MG
Mateus H. Gouveia
LR
Lee R. Machado
MM
Moara Machado
FR
Fernanda Rodrigues-Soares
GS
Giordano B. Soares-Souza
DT
Diego L. Togni
RZ
Roxana Zamudio
RG
Robert H. Gilman
DD
Denise Duarte
EJ
Edward J. Hollox
MR
Maíra R. Rodrigues