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  The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure

Barquera, R., Hernández-Zaragoza, D. I., Bravo-Acevedo, A., Arrieta-Bolaños, E., Clayton, S., Acuña-Alonzo, V., et al. (2020). The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure. Human Immunology, 2020.06.008. doi:10.1016/j.humimm.2020.06.008.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-ACD5-8 Version Permalink: http://hdl.handle.net/21.11116/0000-0006-ACD6-7
Genre: Journal Article

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 Creators:
Barquera, Rodrigo1, Author              
Hernández-Zaragoza, Diana Iraíz, Author
Bravo-Acevedo, Alicia, Author
Arrieta-Bolaños, Esteban, Author
Clayton, Stephen1, Author              
Acuña-Alonzo, Víctor, Author
Martínez-Álvarez, Julio César, Author
López-Gil, Concepción, Author
Adalid-Sáinz, Carmen, Author
Vega-Martínez, María del Rosario, Author
Escobedo-Ruíz, Araceli, Author
Juárez-Cortés, Eva Dolores, Author
Immel, Alexander1, Author              
Pacheco-Ubaldo, Hanna, Author
González-Medina, Liliana, Author
Lona-Sánchez, Abraham, Author
Lara-Riegos, Julio, Author
Sánchez-Fernández, María Guadalupe de Jesús, Author
Díaz-López, Rosario, Author
Guizar-López, Gregorio Ulises, Author
Medina-Escobedo, Carolina Elizabeth, AuthorArrazola-García, María Araceli, AuthorMontiel-Hernández, Gustavo Daniel, AuthorHernández-Hernández, Ofelia, Authorla Cruz, Ramos-de, AuthorRocío, Flor del, AuthorJuárez-Nicolás, Francisco, AuthorPantoja-Torres, Jorge Arturo, AuthorRodríguez-Munguía, Tirzo Jesús, AuthorJuárez-Barreto, Vicencio, AuthorDelgado-Aguirre, Héctor, AuthorEscutia-González, Ariadna Berenice, AuthorGoné-Vázquez, Isis, AuthorBenítez-Arvizu, Gamaliel, AuthorArellano-Prado, Francia Paulina, AuthorGarcía-Arias, Víctor Eduardo, AuthorRodríguez-López, Marla Estefanía, AuthorMéndez-Mani, Patricia, AuthorGarcía-Álvarez, Raquel, AuthorGonzález-Martínez, Marisela del Rocío, AuthorAquino-Rubio, Guadalupe, AuthorEscareño-Montiel, Néstor, AuthorVázquez-Castillo, Tannya Verónica, AuthorUribe-Duarte, María Guadalupe, AuthorRuíz-Corral, María de Jesús, AuthorOrtega-Yáñez, Andrea, AuthorBernal-Felipe, Natalia, AuthorGómez-Navarro, Benjamín, AuthorArriaga-Perea, Agustín Jericó, AuthorMartínez-Bezies, Virginia, AuthorMacías-Medrano, Rosa María, AuthorAguilar-Campos, Jesús Abraham, AuthorSolís-Martínez, Raúl, AuthorSerrano-Osuna, Ricardo, AuthorSandoval-Sandoval, Mario J., AuthorJaramillo-Rodríguez, Yolanda, AuthorSalgado-Adame, Antonio, AuthorJuárez-de la Cruz, Federico, AuthorNovelo-Garza, Bárbara, AuthorPavón-Vargas, María de los Ángeles, AuthorSalgado-Galicia, Norma, AuthorBortolini, Maria Cátira, AuthorGallo, Carla, AuthorBedoya, Gabriel, AuthorRothhammer, Francisco, AuthorGonzález-José, Rolando, AuthorRuiz-Linares, Andrés, AuthorCanizales-Quinteros, Samuel, AuthorRomero-Hidalgo, Sandra, AuthorKrause, Johannes2, Author              Zúñiga, Joaquín, AuthorYunis, Edmond J., AuthorBekker-Méndez, Carolina, AuthorGranados, Julio, Author more..
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2MHAAM, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2541699              

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Free keywords: HLA, Immunogenetics, Population genetics, Genetic substructure, Admixture, Latin American populations, Mexico
 Abstract: We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) allele groups and alleles by PCR-SSP based typing in a total of 15,318 mixed ancestry Mexicans from all the states of the country divided into 78 sample sets, providing information regarding allelic and haplotypic frequencies and their linkage disequilibrium, as well as admixture estimates and genetic substructure. We identified the presence of 4268 unique HLA extended haplotypes across Mexico and find that the ten most frequent (HF > 1%) HLA haplotypes with significant linkage disequilibrium (Δ’≥0.1) in Mexico (accounting for 20% of the haplotypic diversity of the country) are of primarily Native American ancestry (A*02~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*08~DQB1*04, A*68~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*14~DQB1*03:01, A*24~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*04~DQB1*03:02, A*02~B*40:02~DRB1*04~DQB1*03:02, A*68~B*35~DRB1*04~DQB1*03:02, A*02~B*15:01~DRB1*04~DQB1*03:02). Admixture estimates obtained by a maximum likelihood method using HLA-A/-B/-DRB1 as genetic estimators revealed that the main genetic components in Mexico as a whole are Native American (ranging from 37.8% in the northern part of the country to 81.5% in the southeastern region) and European (ranging from 11.5% in the southeast to 62.6% in northern Mexico). African admixture ranged from 0.0 to 12.7% not following any specific pattern. We were able to detect three major immunogenetic clusters correlating with genetic diversity and differential admixture within Mexico: North, Central and Southeast, which is in accordance with previous reports using genome-wide data. Our findings provide insights into the population immunogenetic substructure of the whole country and add to the knowledge of mixed ancestry Latin American population genetics, important for disease association studies, detection of demographic signatures on population variation and improved allocation of public health resources.

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Language(s): eng - English
 Dates: 2020-07-08
 Publication Status: Published online
 Pages: 14
 Publishing info: -
 Table of Contents: 1 Introduction

2 Subjects, materials and methods
2.1 Subjects
2.2 HLA typing
2.3 Statistical analysis
2.3.1 HLA allelic and haplotypic diversity
2.3.2 Admixture proportions calculations
2.3.3 Genetic diversity and genetic substructure assessment

3 Results
3.1 HLA allele groups
3.2 Haplotypic diversity
3.3 Admixture estimates
3.4 Genetic diversity and genetic substructure assessment

4 Discussion
4.1 Admixture estimates in Mexican populations and immunogenetic
diversity
4.2 The Native American immunogenetic component in Mexican
populations
4.3 Implications of the study of alleles and haplotypes of the HLA system in Mexican populations and final considerations

5 Conclusion
 Rev. Method: Peer
 Identifiers: DOI: 10.1016/j.humimm.2020.06.008
Other: shh2655
 Degree: -

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Title: Human Immunology
Source Genre: Journal
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Publ. Info: New York, N.Y. : Elsevier
Pages: - Volume / Issue: - Sequence Number: 2020.06.008 Start / End Page: - Identifier: ISSN: 0198-8859
CoNE: https://pure.mpg.de/cone/journals/resource/954925492912