Population genetics of immune-related multilocus CNV in Native Americans

Luciana Zuccherato, Silvana Schneider, Eduardo Tarazona-Santos, Robert J Hardwick, Douglas Berg, Helen Bogle, Mateus Gouveia, Lee Machado, Moara Machado, Fernanda Rodrigues-Soares, Giordano Soares-Souza, Diego Togni, Roxana Zamudio, Robert Gilman, Denise Duarte, Edward J Hollox, Maira R Rodrigues

Research output: Contribution to journalArticle

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 , 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 SNPs studied in the same populations.
Original languageEnglish
JournalJournal of the Royal Society Interface
Volume14
Issue number128
DOIs
Publication statusPublished - 29 Mar 2017

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American Indians
population genetics
loci
population structure
assortative mating
genotype
founder effect
homozygosity
inbreeding
natural selection
gene frequency
methodology
genomics
genetic variation

Keywords

  • Amerindians
  • Immunity
  • genomic structural variation
  • population structure
  • profiled likelihood

Cite this

Zuccherato, L., Schneider, S., Tarazona-Santos, E., Hardwick, R. J., Berg, D., Bogle, H., ... Rodrigues, M. R. (2017). Population genetics of immune-related multilocus CNV in Native Americans. Journal of the Royal Society Interface, 14(128). https://doi.org/10.1098/rsif.2017.0057
Zuccherato, Luciana ; Schneider, Silvana ; Tarazona-Santos, Eduardo ; Hardwick, Robert J ; Berg, Douglas ; Bogle, Helen ; Gouveia, Mateus ; Machado, Lee ; Machado, Moara ; Rodrigues-Soares, Fernanda ; Soares-Souza, Giordano ; Togni, Diego ; Zamudio, Roxana ; Gilman, Robert ; Duarte, Denise ; Hollox, Edward J ; Rodrigues, Maira R. / Population genetics of immune-related multilocus CNV in Native Americans. In: Journal of the Royal Society Interface. 2017 ; Vol. 14, No. 128.
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Zuccherato, L, Schneider, S, Tarazona-Santos, E, Hardwick, RJ, Berg, D, Bogle, H, Gouveia, M, Machado, L, Machado, M, Rodrigues-Soares, F, Soares-Souza, G, Togni, D, Zamudio, R, Gilman, R, Duarte, D, Hollox, EJ & Rodrigues, MR 2017, 'Population genetics of immune-related multilocus CNV in Native Americans', Journal of the Royal Society Interface, vol. 14, no. 128. https://doi.org/10.1098/rsif.2017.0057

Population genetics of immune-related multilocus CNV in Native Americans. / Zuccherato, Luciana; Schneider, Silvana; Tarazona-Santos, Eduardo; Hardwick, Robert J; Berg, Douglas; Bogle, Helen; Gouveia, Mateus; Machado, Lee; Machado, Moara; Rodrigues-Soares, Fernanda; Soares-Souza, Giordano; Togni, Diego; Zamudio, Roxana; Gilman, Robert; Duarte, Denise; Hollox, Edward J; Rodrigues, Maira R.

In: Journal of the Royal Society Interface, Vol. 14, No. 128, 29.03.2017.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Population genetics of immune-related multilocus CNV in Native Americans

AU - Zuccherato, Luciana

AU - Schneider, Silvana

AU - Tarazona-Santos, Eduardo

AU - Hardwick, Robert J

AU - Berg, Douglas

AU - Bogle, Helen

AU - Gouveia, Mateus

AU - Machado, Lee

AU - Machado, Moara

AU - Rodrigues-Soares, Fernanda

AU - Soares-Souza, Giordano

AU - Togni, Diego

AU - Zamudio, Roxana

AU - Gilman, Robert

AU - Duarte, Denise

AU - Hollox, Edward J

AU - Rodrigues, Maira R

PY - 2017/3/29

Y1 - 2017/3/29

N2 - 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 , 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 SNPs studied in the same populations.

AB - 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 , 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 SNPs studied in the same populations.

KW - Amerindians

KW - Immunity

KW - genomic structural variation

KW - population structure

KW - profiled likelihood

U2 - 10.1098/rsif.2017.0057

DO - 10.1098/rsif.2017.0057

M3 - Article

VL - 14

JO - Journal of the Royal Society Interface

JF - Journal of the Royal Society Interface

SN - 1742-5689

IS - 128

ER -

Zuccherato L, Schneider S, Tarazona-Santos E, Hardwick RJ, Berg D, Bogle H et al. Population genetics of immune-related multilocus CNV in Native Americans. Journal of the Royal Society Interface. 2017 Mar 29;14(128). https://doi.org/10.1098/rsif.2017.0057