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Balancing selection in the human genome: detection, causes and consequences

Grant number: 12/18010-0
Support type:Regular Research Grants
Duration: May 01, 2013 - October 31, 2015
Field of knowledge:Biological Sciences - Genetics
Principal Investigator:Diogo Meyer
Grantee:Diogo Meyer
Home Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Assoc. researchers: Aida Andrés ; Bruce Spencer Weir ; Eduardo José Melo dos Santos ; Emmanouil Dermitzakis ; Joao Farias Guerreiro ; Jorge Macedo Rocha ; Regina Célia Mingroni Netto


Abstract Balancing selection refers to a class of selective regimes that increase genetic variation with respect to neutral expectations. Forms of balancing selection include heterozygote advantage, frequency-dependent selection, and selection which varies over space or time. Although the analysis of genomic data has brought rapid progress to our understanding of how demography and selection interact, our understanding of balancing selection remains comparatively limited. In the present study we investigate this form of selection using several approaches, with the goal of understanding four main questions. (a) How widespread is balancing selection, and what are its targets? Most scans for selected genes focused on targets of directional selection, but lacked power to detect cases of balancing selection. We propose to use the low coverage sequencing data of 12 human populations made available by the 1000 genomes project to scan the genome for targets of balancing selection. (b) What is the effect of balancing selection on regions near the selected gene? Strong balancing selection is expected to increase linked variation, with the potential of increasing the frequency of linked deleterious variants. Using sequencing data for 12 human populations, we will test this hypothesis by surveying the patterns of polymorphism in regions of the genome close to genes under balancing selection. (c) How does balancing selection shape population differentiation? Although theory predicts that balancing selection will reduce interpopulation differentiation, recent results suggest the opposite may be happening, with selective regimes involving host-pathogen coevolution resulting in high differentiation. Using data from 29 populations with dense genotype data and 12 sequenced populations, in addition to dense genotype data we will generate for four Amerindian populations, we will test this hypothesis by examining genetic differentiation at the loci under the strongest balancing selection yet documented, the classical HLA loci. (d) What is the timescale of balancing selection, and how do selection and admixture interact? Although selection at HLA loci is widely accepted, it is not clear whether it has shaped the recent history of human populations. Using two admixed Brazilian populations, we will compare ancestry proportions in genes under balancing selection (including the strongly selected classical HLA loci) to genomewide averages. Differences in ancestry proportions in recently admixed populations are indicative of recent selection. (AU)

Scientific publications (10)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
AGUIAR, VITOR R. C.; CESAR, JONATAS; DELANEAU, OLIVIER; DERMITZAKIS, EMMANOUIL T.; MEYER, DIOGO. Expression estimation and eQTL mapping for HLA genes with a personalized pipeline. PLOS GENETICS, v. 15, n. 4 APR 2019. Web of Science Citations: 0.
BRANDT, DEBORA Y. C.; CESAR, JONATAS; GOUDET, JEROME; MEYER, DIOGO. The Effect of Balancing Selection on Population Differentiation: A Study with HLA Genes. G3-GENES, GENOMES, GENETICS, v. 8, n. 8, p. 2805-2815, AUG 2018. Web of Science Citations: 3.
LEMES, RENAN B.; NUNES, KELLY; CARNAVALLI, JULIANA E. P.; KIMURA, LILIAN; MINGRONI-NETTO, REGINA C.; MEYER, DIOGO; OTTO, PAULO A. Inbreeding estimates in human populations: Applying new approaches to an admixed Brazilian isolate. PLoS One, v. 13, n. 4 APR 24 2018. Web of Science Citations: 4.
BITARELLO, BARBARA D.; DE FILIPPO, CESARE; TEIXEIRA, JOAO C.; SCHMIDT, JOSHUA M.; KLEINERT, PHILIP; MEYER, DIOGO; ANDRES, AIDA M. Signatures of Long-Term Balancing Selection in Human Genomes. GENOME BIOLOGY AND EVOLUTION, v. 10, n. 3, p. 939-955, MAR 2018. Web of Science Citations: 10.
MEYER, DIOGO; AGUIAR, VITOR R. C.; BITARELLO, BARBARA D.; BRANDT, DEBORA Y. C.; NUNES, KELLY. A genomic perspective on HLA evolution. IMMUNOGENETICS, v. 70, n. 1, p. 5-27, JAN 2018. Web of Science Citations: 19.
KIMURA, LILIAN; NUNES, KELLY; INES MACEDO-SOUZA, LUCIA; ROCHA, JORGE; MEYER, DIOGO; MINGRONI-NETTO, REGINA CELIA. Inferring paternal history of rural African-derived Brazilian populations from Y chromosomes. AMERICAN JOURNAL OF HUMAN BIOLOGY, v. 29, n. 2, SI MAR-APR 2017. Web of Science Citations: 3.
NUNES, KELLY; PIOVEZAN, BRUNO; TORRES, MARGARETH A.; PONTES, GERLANDIA N.; KIMURA, LILIAN; CARNAVALLI, JULIANA E. P.; MINGRONI NETTO, REGINA CELIA; MORAES, MARIA ELISA; MEYER, DIOGO. Population variation of HLA genes in rural communities in Brazil, the Quilombos from the Vale do Ribeira, Sao Paulo - Brazil. HUMAN IMMUNOLOGY, v. 77, n. 6, p. 447-448, JUN 2016. Web of Science Citations: 3.
NUNES, KELLY; ZHENG, XIUWEN; TORRES, MARGARETH; MORAES, MARIA ELISA; PIOVEZAN, BRUNO Z.; PONTES, GERLANDIA N.; KIMURA, LILIAN; CARNAVALLI, JULIANA E. P.; MINGRONI NETTO, REGINA C.; MEYER, DIOGO. HLA imputation in an admixed population: An assessment of the 1000 Genomes data as a training set. HUMAN IMMUNOLOGY, v. 77, n. 3, p. 307-312, MAR 2016. Web of Science Citations: 12.
FRANCISCO, RODRIGO DOS SANTOS; BUHLER, STEPHANE; NUNES, JOSE MANUEL; BITARELLO, BARBARA DOMINGUES; FRANCA, GUSTAVO STARVAGGI; MEYER, DIOGO; SANCHEZ-MAZAS, ALICIA. HLA supertype variation across populations: new insights into the role of natural selection in the evolution of HLA-A and HLA-B polymorphisms. IMMUNOGENETICS, v. 67, n. 11-12, p. 651-663, NOV 2015. Web of Science Citations: 12.
BRANDT, DEBORA Y. C.; AGUIAR, VITOR R. C.; BITARELLO, BARBARA D.; NUNES, KELLY; GOUDET, JEROME; MEYER, DIOGO. Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data. G3-GENES, GENOMES, GENETICS, v. 5, n. 5, p. 931-941, MAY 1 2015. Web of Science Citations: 34.

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