1. The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure
- Author
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Barquera, R., https://orcid.org/0000-0003-0518-4518, Hernández-Zaragoza, D., Bravo-Acevedo, A., Arrieta-Bolaños, E., Clayton, S., Acuña-Alonzo, V., Martínez-Álvarez, J., López-Gil, C., Adalid-Sáinz, C., Vega-Martínez, M., Escobedo-Ruíz, A., Juárez-Cortés, E., Immel, A., Pacheco-Ubaldo, H., González-Medina, L., Lona-Sánchez, A., Lara-Riegos, J., Sánchez-Fernández, M., Díaz-López, R., Guizar-López, G., Medina-Escobedo, C., Arrazola-García, M., Montiel-Hernández, G., Hernández-Hernández, O., la Cruz, R., Rocío, F., Juárez-Nicolás, F., Pantoja-Torres, J., Rodríguez-Munguía, T., Juárez-Barreto, V., Delgado-Aguirre, H., Escutia-González, A., Goné-Vázquez, I., Benítez-Arvizu, G., Arellano-Prado, F., García-Arias, V., Rodríguez-López, M., Méndez-Mani, P., García-Álvarez, R., González-Martínez, M., Aquino-Rubio, G., Escareño-Montiel, N., Vázquez-Castillo, T., Uribe-Duarte, M., Ruíz-Corral, M., Ortega-Yáñez, A., Bernal-Felipe, N., Gómez-Navarro, B., Arriaga-Perea, A., Martínez-Bezies, V., Macías-Medrano, R., Aguilar-Campos, J., Solís-Martínez, R., Serrano-Osuna, R., Sandoval-Sandoval, M., Jaramillo-Rodríguez, Y., Salgado-Adame, A., Juárez-de la Cruz, F., Novelo-Garza, B., Pavón-Vargas, M., Salgado-Galicia, N., Bortolini, M., Gallo, C., Bedoya, G., Rothhammer, F., González-José, R., Ruiz-Linares, A., Canizales-Quinteros, S., Romero-Hidalgo, S., Krause, J., https://orcid.org/0000-0001-9144-3920, Zúñiga, J., Yunis, E., Bekker-Méndez, C., Granados, J., Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, and Fudan University [Shanghai]-School of Life Sciences
- Subjects
0301 basic medicine ,musculoskeletal diseases ,media_common.quotation_subject ,Immunology ,Population ,[SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology ,Medizin ,Library science ,LATIN AMERICAN POPULATIONS ,Polymorphism, Single Nucleotide ,Linkage Disequilibrium ,MEXICO ,Major Histocompatibility Complex ,purl.org/becyt/ford/1 [https] ,03 medical and health sciences ,0302 clinical medicine ,Gene Frequency ,HLA Antigens ,immune system diseases ,Political science ,POPULATION GENETICS ,Humans ,Immunology and Allergy ,education ,skin and connective tissue diseases ,purl.org/becyt/ford/1.6 [https] ,Mexico ,Biological sciences ,Alleles ,ComputingMilieux_MISCELLANEOUS ,media_common ,education.field_of_study ,Genome, Human ,DNA ,General Medicine ,GENETIC SUBSTRUCTURE ,purl.org/pe-repo/ocde/ford#3.01.03 [https] ,3. Good health ,ADMIXTURE ,HLA ,Genetics, Population ,030104 developmental biology ,Haplotypes ,Research council ,IMMUNOGENETICS ,Genetic structure ,030215 immunology ,Diversity (politics) - 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. Fil: Barquera, Rodrigo. Max Planck Institute For The Science Of Human History; Alemania. Instituto Nacional de Antropología E Historia. Escuela Nacional de Antropología E Historia; México Fil: Hernández Zaragoza, Diana Iraíz. Técnicas Genéticas Aplicadas A la Clínica (tgac); México. Instituto Nacional de Antropología E Historia. Escuela Nacional de Antropología E Historia; México Fil: Bravo Acevedo, Alicia. Instituto Mexicano del Seguro Social; México Fil: Arrieta Bolaños, Esteban. Universitat Essen; Alemania Fil: Clayton, Stephen. Max Planck Institute For The Science Of Human History; Alemania Fil: Acuña Alonzo, Víctor. Instituto Nacional de Antropología E Historia, Mexico; México Fil: Martínez Álvarez, Julio César. Instituto Mexicano del Seguro Social; México Fil: López Gil, Concepción. Instituto Mexicano del Seguro Social; México Fil: Adalid Sáinz, Carmen. Instituto Mexicano del Seguro Social; México Fil: Vega Martínez, María del Rosario. Hospital Central Sur de Alta Especialidad; México Fil: Escobedo Ruíz, Araceli. Instituto Mexicano del Seguro Social; México Fil: Juárez Cortés, Eva Dolores. Instituto Mexicano del Seguro Social; México Fil: Immel, Alexander. Max Planck Institute For The Science Of Human History; Alemania. Christian Albrechts Universitat Zu Kiel; Alemania Fil: Pacheco Ubaldo, Hanna. Instituto Nacional de Antropología E Historia. Escuela Nacional de Antropología E Historia; México Fil: González Medina, Liliana. Instituto Nacional de Antropología E Historia. Escuela Nacional de Antropología E Historia; México Fil: Lona Sánchez, Abraham. Instituto Nacional de Antropología E Historia. Escuela Nacional de Antropología E Historia; México Fil: Lara Riegos, Julio. Universidad Autónoma de Yucatán; México Fil: Sánchez Fernández, María Guadalupe de Jesús. Instituto Mexicano del Seguro Social; México Fil: Díaz López, Rosario. Hospital Central Militar, Mexico City; México Fil: Guizar López, Gregorio Ulises. Hospital Central Militar, Mexico City; México Fil: Medina Escobedo, Carolina Elizabeth. Instituto Mexicano del Seguro Social; México Fil: Arrazola García, María Araceli. Instituto Mexicano del Seguro Social; México Fil: Montiel Hernández, Gustavo Daniel. Instituto Nacional de Antropología E Historia. Escuela Nacional de Antropología E Historia; México Fil: Hernández Hernández, Ofelia. Técnicas Genéticas Aplicadas a la Clínica ; México Fil: Ramos de la Cruz, Flor del Rocío. Instituto Mexicano del Seguro Social; México Fil: Juárez Nicolás, Francisco. Instituto Nacional de Pediatría; México Fil: Pantoja Torres, Jorge Arturo. Instituto Mexicano del Seguro Social; México Fil: Rodríguez Munguía, Tirzo Jesús. Hospital General Norberto Treviño Zapata; México Fil: Juárez Barreto, Vicencio. Hospital Infantil de Mexico Federico Gomez; México Fil: Gonzalez-Jose, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina
- Published
- 2020
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