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García-Vilchis B, Román-López TV, Ramírez-González D, López-Camaño XJ, Murillo-Lechuga V, Díaz-Téllez X, Sánchez-Moncada CI, Espinosa-Méndez IM, Zenteno-Morales D, Espinosa-Valdes ZX, Pradel-Jiménez S, Tapia-Atilano A, Zanabria-Pérez AV, Livas-Gangas F, Aldana-Assad O, Caballero-Sánchez U, Dominguez-Frausto CA, Rentería ME, Medina-Rivera A, Alcauter S, Ruiz-Contreras AE. TwinsMX: Exploring the Genetic and Environmental Influences on Health Traits in the Mexican Population. Twin Res Hum Genet 2024:1-12. [PMID: 38699821 DOI: 10.1017/thg.2024.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
TwinsMX registry is a national research initiative in Mexico that aims to understand the complex interplay between genetics and environment in shaping physical and mental health traits among the country's population. With a multidisciplinary approach, TwinsMX aims to advance our knowledge of the genetic and environmental mechanisms underlying ethnic variations in complex traits and diseases, including behavioral, psychometric, anthropometric, metabolic, cardiovascular and mental disorders. With information gathered from over 2800 twins, this article updates the prevalence of several complex traits; and describes the advances and novel ideas we have implemented such as magnetic resonance imaging. The future expansion of the TwinsMX registry will enhance our comprehension of the intricate interplay between genetics and environment in shaping health and disease in the Mexican population. Overall, this report describes the progress in the building of a solid database that will allow the study of complex traits in the Mexican population, valuable not only for our consortium, but also for the worldwide scientific community, by providing new insights of understudied genetically admixed populations.
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Affiliation(s)
- Brisa García-Vilchis
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Talia V Román-López
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Diego Ramírez-González
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Xanat J López-Camaño
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Vanessa Murillo-Lechuga
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Xóchitl Díaz-Téllez
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | | | - Ian M Espinosa-Méndez
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Diego Zenteno-Morales
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Zaida X Espinosa-Valdes
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sofia Pradel-Jiménez
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Andrea Tapia-Atilano
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ana V Zanabria-Pérez
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Federica Livas-Gangas
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Oscar Aldana-Assad
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Ulises Caballero-Sánchez
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Miguel E Rentería
- Mental Health & Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Sarael Alcauter
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Alejandra E Ruiz-Contreras
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Ochoa‐Avilés C, Ochoa‐Avilés A, Rivas‐Párraga R, Escandón S, Santos‐Jesus TD, Silva MDJ, Leão V, Salinas M, Vicuña Y, Baldeón L, Molina‐Cando MJ, Morillo D, Machuca M, Rodas C, Figueiredo C, Neira VA. Mother's smoking habits affects IL10 methylation but not asthma in Ecuadorian children. Mol Genet Genomic Med 2024; 12:e2438. [PMID: 38666495 PMCID: PMC11046467 DOI: 10.1002/mgg3.2438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024] Open
Abstract
There is no evidence evaluating the IL10 epigenetic upregulation among mestizo children in a high-altitude Andean city in Latin America. OBJECTIVE To identify polymorphisms and methylation profiles in the IL10 gene associated with asthma in children aged 5 to 11. METHODS A case-control study was conducted with asthmatic and non-asthmatic children aged 5 to 11 years in Cuenca-Ecuador. Data on allergic diseases and risk factors were collected through a questionnaire for parents. Atopy was measured by skin prick test (SPT) to relevant aeroallergens. Three IL10 single nucleotide polymorphisms were evaluated in all participants, and methylation analysis was performed in 54 participants. Association between risk factors, allergic diseases and genetic factors were estimated using multivariate logistic regression. RESULTS The results of polymorphisms showed no differences between cases and controls when comparing the SNPs rs3024495, rs3024496, rs1800896 allelic and genotypic frequencies. In the methylation analysis, no differences in the IL10 methylation profile were found between cases and controls; however, the multivariate analysis showed an association between the mother's smoking habits and the IL10 methylation profile. CONCLUSION Smoking habit could be essential as an environmental exposure factor in regulating gene expression in children with asthma.
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Affiliation(s)
- Cristina Ochoa‐Avilés
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | | | - Roque Rivas‐Párraga
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Biomass to Resources GroupUniversidad Regional Amazónica IkiamTenaNapoEcuador
| | - Samuel Escandón
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
| | - Talita Dos Santos‐Jesus
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | - Milca de J. Silva
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | - Valderiene Leão
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | - Marco Salinas
- Biomass to Resources GroupUniversidad Regional Amazónica IkiamTenaNapoEcuador
| | - Yosselin Vicuña
- Instituto de Investigación en Biomedicina Facultad de Ciencias MédicasUniversidad Central del EcuadorQuitoPichinchaEcuador
| | - Lucy Baldeón
- Instituto de Investigación en Biomedicina Facultad de Ciencias MédicasUniversidad Central del EcuadorQuitoPichinchaEcuador
| | - María José Molina‐Cando
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Facultad de MedicinaUniversidad Internacional del EcuadorQuitoPichinchaEcuador
| | - Diana Morillo
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Facultad de MedicinaUniversidad Internacional del EcuadorQuitoPichinchaEcuador
| | - Marcos Machuca
- Facultad de MedicinaUniversidad del AzuayCuencaAzuayEcuador
| | - Claudia Rodas
- Facultad de MedicinaUniversidad del AzuayCuencaAzuayEcuador
| | - Camila Figueiredo
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | - Vivian Alejandra Neira
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Facultad de MedicinaUniversidad del AzuayCuencaAzuayEcuador
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Bravo-Villagra KM, Muñoz-Valle JF, Baños-Hernández CJ, Cerpa-Cruz S, Navarro-Zarza JE, Parra-Rojas I, Aguilar-Velázquez JA, García-Arellano S, López-Quintero A. STAT4 Gene Variant rs7574865 Is Associated with Rheumatoid Arthritis Activity and Anti-CCP Levels in the Western but Not in the Southern Population of Mexico. Genes (Basel) 2024; 15:241. [PMID: 38397230 PMCID: PMC10887563 DOI: 10.3390/genes15020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Rheumatoid Arthritis (RA) is a multifactorial autoimmune disease. Currently, several genes play an important role in the development of the disease. The objective was to evaluate the association of the STAT4 rs7574865 and rs897200 gene variants with RA susceptibility, DAS28, RF, and anti-CCP in Western and Southern Mexico populations. Genotyping was performed on 476 samples (cases = 240; controls = 236) using the Taqman® system and qPCR probes. Disease activity was assessed using DAS28 and HAQ DI. CRP, ESR, RF, and anti-CCP were determined for clinical assessment. Our study showed there is a statistically significant association with susceptibility to RA for the rs7574865 variant in the Western population for the GT and TT genotypes. The same genotypes also showed a moderate-to-high activity according to DAS28 and positive anti-CCP compared to the control group. This association was not found in the Southern population. This work confirms the association of the rs7574865 variant with RA, as well as a moderate-to-high activity and positive anti-CCP in the Western population but not in the Southern population. No association of the rs897200 variant was found in any of the studied populations.
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Affiliation(s)
- Karla Mayela Bravo-Villagra
- Instituto de Nutrigenética y Nutrigenómica Traslacional, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
| | - José Francisco Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico; (J.F.M.-V.); (C.J.B.-H.); (S.G.-A.)
| | - Christian Johana Baños-Hernández
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico; (J.F.M.-V.); (C.J.B.-H.); (S.G.-A.)
| | - Sergio Cerpa-Cruz
- Antiguo Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44200, Mexico;
| | | | - Isela Parra-Rojas
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de Bravo 39086, Mexico;
| | - José Alonso Aguilar-Velázquez
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico; (J.F.M.-V.); (C.J.B.-H.); (S.G.-A.)
| | - Samuel García-Arellano
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico; (J.F.M.-V.); (C.J.B.-H.); (S.G.-A.)
| | - Andres López-Quintero
- Instituto de Nutrigenética y Nutrigenómica Traslacional, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
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Nava-Bringas TI, Manrique CMJ, González-Huerta NC, Morales-Hernández E, Miranda-Duarte A. COMT and SCN9A gene variants do not contribute to chronic low back pain in Mexican-Mestizo patients. Acta Neurochir (Wien) 2024; 166:73. [PMID: 38329587 DOI: 10.1007/s00701-024-05937-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/26/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND Chronic low back pain (CLBP) is a complex condition in which genetic factors play a role in its susceptibility. Catechol-O-methyltransferase (COMT) and sodium channel NaV1.7 (SCN9A) genes are implicated in pain perception. The aim is to analyze the association of COMT and SCN9A with CLBP and their interaction, in a Mexican-Mestizo population. METHODS A case-control study was conducted. Cases corresponded to adults of both sexes with CLBP. Controls were adults with no CLBP. Variants of SCN9A and COMT were genotyped. Allelic and genotypic frequencies and Hardy-Weinberg equilibrium (HWE) were calculated. Association was tested under codominant, dominant, and recessive models. Multifactor dimensionality reduction was developed to detect epistasis. RESULTS Gene variants were in HWE, and there was no association under different inheritance models in the whole sample. In women, in codominant and dominant models, a trend to a high risk was observed for AA of rs4680 of COMT (OR = 1.7 [0.5-5.3] and 1.6 [0.7-3.4]) and for TT of rs4633 (OR = 1.6 [0.7-3.7] and 1.6 [0.7-3.4]). In men, a trend to low risk was observed for AG genotype of rs4680 in the same models (OR = 0.6 [0.2-1.7] and 0.7 [0.3-1.7]), and for TC genotype of rs4633 in the codominant model (OR = 0.6 [0.2-1.7]). In the interaction analysis, a model of the SCN9A and COMT variants showed a CVC of 10/10; however, the TA was 0.4141. CONCLUSION COMT and SCN9A variants are not associated with CLBP in the analyzed Mexican-Mestizo population.
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Affiliation(s)
- Tania Inés Nava-Bringas
- Department of Orthopedic Rehabilitation, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", Av. México-Xochimilco 289, Colonia Arenal de Guadalupe, Tlalpan, 14389, Mexico City, Mexico
| | - Carlos Manuel Juaristi Manrique
- Department of Genomic Medicine, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", Av. México-Xochimilco 289, Colonia Arenal de Guadalupe, Tlalpan, 14389, Mexico City, Mexico
| | - Norma Celia González-Huerta
- Department of Genomic Medicine, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", Av. México-Xochimilco 289, Colonia Arenal de Guadalupe, Tlalpan, 14389, Mexico City, Mexico
| | - Eugenio Morales-Hernández
- Radiology Service, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", Av. México-Xochimilco 289, Colonia Arenal de Guadalupe, Tlalpan, 14389, Mexico City, Mexico
| | - Antonio Miranda-Duarte
- Department of Genomic Medicine, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", Av. México-Xochimilco 289, Colonia Arenal de Guadalupe, Tlalpan, 14389, Mexico City, Mexico.
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Sohail M, Moreno-Estrada A. The Mexican Biobank Project promotes genetic discovery, inclusive science and local capacity building. Dis Model Mech 2024; 17:dmm050522. [PMID: 38299665 PMCID: PMC10855211 DOI: 10.1242/dmm.050522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Diversifying genotype-phenotype databases is essential to understanding complex trait and disease etiology across different environments and genetic ancestries. The rise of biobanks across the world is helping reveal the genetic and environmental architecture of multiple disease traits but the diversity they capture remains limited. To help close this gap, the Mexican Biobank (MXB) Project was recently generated, and has already revealed fine-scale genetic ancestries and demographic histories across the country, and their impact on trait-relevant genetic variation. This will help guide future genetic epidemiology and public health efforts, and has also improved polygenic prediction for several traits in Mexican populations compared with using data from other genome-wide association studies, such as the UK Biobank. The MXB illustrates the importance of transnational initiatives and funding calls that prioritize local leadership and capacity building to move towards inclusive genomic science.
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Affiliation(s)
- Mashaal Sohail
- Genómica Computacional, Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), 62209 Cuernavaca, Morelos, México
| | - Andrés Moreno-Estrada
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), 36821 Irapuato, Guanajuato, México
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6
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Zollner L, Torres D, Briceno I, Gilbert M, Torres-Mejía G, Dennis J, Bolla MK, Wang Q, Hamann U, Lorenzo Bermejo J. Native American ancestry and breast cancer risk in Colombian and Mexican women: ruling out potential confounding through ancestry-informative markers. Breast Cancer Res 2023; 25:111. [PMID: 37784177 PMCID: PMC10544431 DOI: 10.1186/s13058-023-01713-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Latin American and Hispanic women are less likely to develop breast cancer (BC) than women of European descent. Observational studies have found an inverse relationship between the individual proportion of Native American ancestry and BC risk. Here, we use ancestry-informative markers to rule out potential confounding of this relationship, estimating the confounder-free effect of Native American ancestry on BC risk. METHODS AND STUDY POPULATION We used the informativeness for assignment measure to select robust instrumental variables for the individual proportion of Native American ancestry. We then conducted separate Mendelian randomization (MR) analyses based on 1401 Colombian women, most of them from the central Andean regions of Cundinamarca and Huila, and 1366 Mexican women from Mexico City, Monterrey and Veracruz, supplemented by sensitivity and stratified analyses. RESULTS The proportion of Colombian Native American ancestry showed a putatively causal protective effect on BC risk (inverse variance-weighted odds ratio [OR] = 0.974 per 1% increase in ancestry proportion, 95% confidence interval [CI] 0.970-0.978, p = 3.1 × 10-40). The corresponding OR for Mexican Native American ancestry was 0.988 (95% CI 0.987-0.990, p = 1.4 × 10-44). Stratified analyses revealed a stronger association between Native American ancestry and familial BC (Colombian women: OR = 0.958, 95% CI 0.952-0.964; Mexican women: OR = 0.973, 95% CI 0.969-0.978), and stronger protective effects on oestrogen receptor (ER)-positive BC than on ER-negative and triple-negative BC. CONCLUSIONS The present results point to an unconfounded protective effect of Native American ancestry on BC risk in both Colombian and Mexican women which appears to be stronger for familial and ER-positive BC. These findings provide a rationale for personalised prevention programmes that take genetic ancestry into account, as well as for future admixture mapping studies.
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Affiliation(s)
- Linda Zollner
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Ignacio Briceno
- Instituto de Genética Humana, Universidad de la Sabana, Bogotá, Colombia
| | - Michael Gilbert
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Gabriela Torres-Mejía
- Center for Population Health Research, National Institute of Public Health, Cuernavaca, Morelos, Mexico
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
| | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
- Department of Biostatistics for Precision Oncology, Institut de Cancérologie Strasbourg Europe, Strasbourg, France
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7
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Ziyatdinov A, Torres J, Alegre-Díaz J, Backman J, Mbatchou J, Turner M, Gaynor SM, Joseph T, Zou Y, Liu D, Wade R, Staples J, Panea R, Popov A, Bai X, Balasubramanian S, Habegger L, Lanche R, Lopez A, Maxwell E, Jones M, García-Ortiz H, Ramirez-Reyes R, Santacruz-Benítez R, Nag A, Smith KR, Damask A, Lin N, Paulding C, Reppell M, Zöllner S, Jorgenson E, Salerno W, Petrovski S, Overton J, Reid J, Thornton TA, Abecasis G, Berumen J, Orozco-Orozco L, Collins R, Baras A, Hill MR, Emberson JR, Marchini J, Kuri-Morales P, Tapia-Conyer R. Genotyping, sequencing and analysis of 140,000 adults from Mexico City. Nature 2023; 622:784-793. [PMID: 37821707 PMCID: PMC10600010 DOI: 10.1038/s41586-023-06595-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/31/2023] [Indexed: 10/13/2023]
Abstract
The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City1. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. We describe high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Indigenous American, European and African ancestry, with extensive admixture from Indigenous populations in central, southern and southeastern Mexico. Indigenous Mexican segments of the genome had lower levels of coding variation but an excess of homozygous loss-of-function variants compared with segments of African and European origin. We estimated ancestry-specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Indigenous Mexican ancestry at exome variants, all available through a public browser. Using whole-genome sequencing, we developed an imputation reference panel that outperforms existing panels at common variants in individuals with high proportions of central, southern and southeastern Indigenous Mexican ancestry. Our work illustrates the value of genetic studies in diverse populations and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States, where the Hispanic/Latino population is predominantly of Mexican descent.
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Affiliation(s)
| | - Jason Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| | - Jesús Alegre-Díaz
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | | | | | - Michael Turner
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Oxford Kidney Unit, Churchill Hospital, Oxford, UK
| | | | | | - Yuxin Zou
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Daren Liu
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Rachel Wade
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | - Alex Popov
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | - Alex Lopez
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | - Raul Ramirez-Reyes
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Rogelio Santacruz-Benítez
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Abhishek Nag
- Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | - Katherine R Smith
- Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | - Amy Damask
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Nan Lin
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | | | | | | | | | - Jaime Berumen
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | | | - Rory Collins
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Michael R Hill
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan R Emberson
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Pablo Kuri-Morales
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
- Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico.
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8
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Sohail M, Palma-Martínez MJ, Chong AY, Quinto-Cortés CD, Barberena-Jonas C, Medina-Muñoz SG, Ragsdale A, Delgado-Sánchez G, Cruz-Hervert LP, Ferreyra-Reyes L, Ferreira-Guerrero E, Mongua-Rodríguez N, Canizales-Quintero S, Jimenez-Kaufmann A, Moreno-Macías H, Aguilar-Salinas CA, Auckland K, Cortés A, Acuña-Alonzo V, Gignoux CR, Wojcik GL, Ioannidis AG, Fernández-Valverde SL, Hill AVS, Tusié-Luna MT, Mentzer AJ, Novembre J, García-García L, Moreno-Estrada A. Mexican Biobank advances population and medical genomics of diverse ancestries. Nature 2023; 622:775-783. [PMID: 37821706 PMCID: PMC10600006 DOI: 10.1038/s41586-023-06560-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/22/2023] [Indexed: 10/13/2023]
Abstract
Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories and complex trait architectures remain hidden owing to insufficient data1. To fill this gap, the Mexican Biobank project genotyped 6,057 individuals from 898 rural and urban localities across all 32 states in Mexico at a resolution of 1.8 million genome-wide markers with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Here, using ancestry deconvolution and inference of identity-by-descent segments, we inferred ancestral population sizes across Mesoamerican regions over time, unravelling Indigenous, colonial and postcolonial demographic dynamics2-6. We observed variation in runs of homozygosity among genomic regions with different ancestries reflecting distinct demographic histories and, in turn, different distributions of rare deleterious variants. We conducted genome-wide association studies (GWAS) for 22 complex traits and found that several traits are better predicted using the Mexican Biobank GWAS compared to the UK Biobank GWAS7,8. We identified genetic and environmental factors associating with trait variation, such as the length of the genome in runs of homozygosity as a predictor for body mass index, triglycerides, glucose and height. This study provides insights into the genetic histories of individuals in Mexico and dissects their complex trait architectures, both crucial for making precision and preventive medicine initiatives accessible worldwide.
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Affiliation(s)
- Mashaal Sohail
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico.
| | - María J Palma-Martínez
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Amanda Y Chong
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Consuelo D Quinto-Cortés
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Carmina Barberena-Jonas
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Santiago G Medina-Muñoz
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Aaron Ragsdale
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Luis Pablo Cruz-Hervert
- Instituto Nacional de Salud Pública (INSP), Cuernavaca, Mexico
- División de Estudios de Posgrado e Investigación, Facultad de Odontología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | | | | | | | - Andrés Jimenez-Kaufmann
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Hortensia Moreno-Macías
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Carlos A Aguilar-Salinas
- Division de Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Kathryn Auckland
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adrián Cortés
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | | | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Selene L Fernández-Valverde
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
- School of Biotechnology and Biomolecular Sciences and the RNA Institute, The University of New South Wales, Sydney, New South Wales, Australia
| | - Adrian V S Hill
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, University of Oxford, Oxford, UK
| | - María Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Alexander J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Andrés Moreno-Estrada
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico.
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Lázaro-Figueroa A, Reyes-Pérez P, Morelos-Figaredo E, Guerra-Galicia CM, Estrada-Bellmann I, Salinas-Barboza K, Matuk-Pérez Y, Gandarilla-Martínez NA, Caballero-Sánchez U, Flores-Ocampo V, Montés-Alcántara P, Espinosa-Méndez IM, Moral AZD, Gaspar-Martínez E, Vazquez-Guevara D, Rodríguez-Violante M, Inca-Martinez M, Mata IF, Alcauter S, Rentería ME, Medina-Rivera A, Ruiz-Contreras AE. MEX-PD: A National Network for the Epidemiological & Genetic Research of Parkinson's Disease. medRxiv 2023:2023.08.28.23294700. [PMID: 37693616 PMCID: PMC10491355 DOI: 10.1101/2023.08.28.23294700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background Parkinson's Disease (PD) has a complex etiology, involving genetic and environmental factors. Most of our current understanding of the disease comes from studies in populations with mostly European ancestry, representing challenges in generalizing findings to other populations with different genetic, social, and environmental contexts. There are scarce studies focused in Latin American populations. The Mexican population is genetically diverse because its admixture from Native American, European, and African ancestries, coupled with the unique environmental conditions, stressing the relevance of establishing genetic studies in this population. Thus, we have established the Mexican Parkinson's Research Network (MEX-PD), a consortium to research the clinical, genetical, environmental, and neurophysiological bases of the phenotypic diversity in Mexican PD patients. Objectives Describing how MEX-PD was established, the methods and instruments and presenting the first results. Methods Patients and controls were recruited from medical centers in 20 states of Mexico. Initial recruitment included neurological evaluation, cognitive assessment, and DNA collection. Results MEX-PD has registered 302 controls and 262 PD patients with a mean age of diagnosis of 61 years (SD=10.86). There were 19.8% PD patients identified with early onset. Levodopa was the most common pharmacological treatment. Conclusions MEX-PD contributes to understand PD nationally. The information gathered here will allow us to understand the prevalence of mental health, neurological symptoms, and cognitive function in the PD Mexican population and how genetical and environmental factors contributes to those outcomes. These will advocate for personalized treatments and improving quality of life in the Mexican population.
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Affiliation(s)
- Alejandra Lázaro-Figueroa
- Lab. Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias, Coord. Psicobiología y Neurociencias, Fac. Psicología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Paula Reyes-Pérez
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, México
| | | | | | - Ingrid Estrada-Bellmann
- Movement Disorders Clinic, Neurology Division, Internal Medicine Department, University Hospital “Dr. José E. González”, Universidad Autónoma de Nuevo León, Monterrey. Mexico
| | | | - Yamil Matuk-Pérez
- Facultad de Medicina, Universidad Autónoma de Querétaro. Unidad de Neurociencias, Hospital Ángeles Centro Sur
| | | | - Ulises Caballero-Sánchez
- Lab. Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias, Coord. Psicobiología y Neurociencias, Fac. Psicología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Victor Flores-Ocampo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, México
| | - Pablo Montés-Alcántara
- Lab. Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias, Coord. Psicobiología y Neurociencias, Fac. Psicología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | | | | | - Edith Gaspar-Martínez
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, México
| | | | - Mayela Rodríguez-Violante
- Laboratorio Clínico de Enfermedades Neurodegenerativas. Instituto Nacional de Neurología y Neurocirugía, Ciudad de Mexico, Mexico
| | | | - Ignacio F. Mata
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Sarael Alcauter
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, México
| | - Miguel E. Rentería
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Mental Health & Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, México
| | - Alejandra E. Ruiz-Contreras
- Lab. Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias, Coord. Psicobiología y Neurociencias, Fac. Psicología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
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10
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Cruz LA, Cooke Bailey JN, Crawford DC. Importance of Diversity in Precision Medicine: Generalizability of Genetic Associations Across Ancestry Groups Toward Better Identification of Disease Susceptibility Variants. Annu Rev Biomed Data Sci 2023; 6:339-356. [PMID: 37196357 PMCID: PMC10720270 DOI: 10.1146/annurev-biodatasci-122220-113250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Genome-wide association studies (GWAS) revolutionized our understanding of common genetic variation and its impact on common human disease and traits. Developed and adopted in the mid-2000s, GWAS led to searchable genotype-phenotype catalogs and genome-wide datasets available for further data mining and analysis for the eventual development of translational applications. The GWAS revolution was swift and specific, including almost exclusively populations of European descent, to the neglect of the majority of the world's genetic diversity. In this narrative review, we recount the GWAS landscape of the early years that established a genotype-phenotype catalog that is now universally understood to be inadequate for a complete understanding of complex human genetics. We then describe approaches taken to augment the genotype-phenotype catalog, including the study populations, collaborative consortia, and study design approaches aimed to generalize and then ultimately discover genome-wide associations in non-European descent populations. The collaborations and data resources established in the efforts to diversify genomic findings undoubtedly provide the foundations of the next chapters of genetic association studies with the advent of budget-friendly whole-genome sequencing.
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Affiliation(s)
- Lauren A Cruz
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA;
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA;
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA;
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
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11
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Arámburo-Gálvez JG, Figueroa-Salcido OG, Ramírez-Torres GI, Terán-Cabanillas E, Gracia-Valenzuela MH, Arvizu-Flores AA, Sánchez-Cárdenas CA, Mora-Melgem JA, Valdez-Zavala L, Cárdenas-Torres FI, Ontiveros N. Prevalence of Parent-Reported Food Allergy in a Mexican Pre-School Population. J Clin Med 2023; 12:5095. [PMID: 37568497 PMCID: PMC10420166 DOI: 10.3390/jcm12155095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
The magnitude and relevance of food allergies in the preschool population remain unknown in most regions of Mexico and Latin America. Thus, our aim was to estimate the parent-reported prevalence of food allergies in a Mexican preschool population and to characterize their clinical diagnosis and presentation. A cross-sectional survey was conducted in Culiacán City. A validated questionnaire was utilized. A total of 810 parents responded to the questionnaire (valid response rate, 40.7%). The estimated prevalence rates (95% CI) were: "physician-diagnosed Food Allergy (FA), ever" 5.30% (3.86-7.08); "immediate-type FA, ever" 2.96% (1.91-4.38); "immediate-type FA, current" 1.60% (0.86-2.73); and food-dependent anaphylaxis 1.11% (0.51-2.01). The main food allergens were milk (0.49%), strawberries (0.37%), egg, and soy (0.25% each). Atopic diseases and a family history of allergies were significantly associated with immediate-type FA. Among "immediate-type FA, current" cases, 76.9% required emergency room visits, but the prescription of epinephrine autoinjectors was reported in one case only. The food reactions occurred at home (92.35%), in a relative's house (38.5), and at restaurants (23%). Immediate-type FA reactions requiring emergency room visits are not uncommon among the studied population. Actions like proper anaphylaxis management and the prevention of cross-contamination of foods should be encouraged.
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Affiliation(s)
- Jesús Gilberto Arámburo-Gálvez
- Nutrition Sciences Postgraduate Program, Faculty of Nutrition Sciences, Autonomous University of Sinaloa, Culiacan 80010, Mexico; (J.G.A.-G.); (O.G.F.-S.); (E.T.-C.); (C.A.S.-C.); (J.A.M.-M.); (L.V.-Z.)
| | - Oscar Gerardo Figueroa-Salcido
- Nutrition Sciences Postgraduate Program, Faculty of Nutrition Sciences, Autonomous University of Sinaloa, Culiacan 80010, Mexico; (J.G.A.-G.); (O.G.F.-S.); (E.T.-C.); (C.A.S.-C.); (J.A.M.-M.); (L.V.-Z.)
- Integral Postgraduate Program in Biotechnology, Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Ciudad Universitaria, Culiacan 80010, Mexico
| | | | - Elí Terán-Cabanillas
- Nutrition Sciences Postgraduate Program, Faculty of Nutrition Sciences, Autonomous University of Sinaloa, Culiacan 80010, Mexico; (J.G.A.-G.); (O.G.F.-S.); (E.T.-C.); (C.A.S.-C.); (J.A.M.-M.); (L.V.-Z.)
| | - Martina Hilda Gracia-Valenzuela
- Department of Engineering, Technological National of Mexico, Technological Institute of the Yaqui Valley, Bacum 85276, Mexico;
| | - Aldo Alejandro Arvizu-Flores
- Postgraduate Program in Health Sciences, Faculty of Biological and Health Sciences, University of Sonora, Hermosillo 83000, Mexico;
| | - Cesar Antonio Sánchez-Cárdenas
- Nutrition Sciences Postgraduate Program, Faculty of Nutrition Sciences, Autonomous University of Sinaloa, Culiacan 80010, Mexico; (J.G.A.-G.); (O.G.F.-S.); (E.T.-C.); (C.A.S.-C.); (J.A.M.-M.); (L.V.-Z.)
| | - José Antonio Mora-Melgem
- Nutrition Sciences Postgraduate Program, Faculty of Nutrition Sciences, Autonomous University of Sinaloa, Culiacan 80010, Mexico; (J.G.A.-G.); (O.G.F.-S.); (E.T.-C.); (C.A.S.-C.); (J.A.M.-M.); (L.V.-Z.)
| | - Luisamaria Valdez-Zavala
- Nutrition Sciences Postgraduate Program, Faculty of Nutrition Sciences, Autonomous University of Sinaloa, Culiacan 80010, Mexico; (J.G.A.-G.); (O.G.F.-S.); (E.T.-C.); (C.A.S.-C.); (J.A.M.-M.); (L.V.-Z.)
| | - Feliznando Isidro Cárdenas-Torres
- Nutrition Sciences Postgraduate Program, Faculty of Nutrition Sciences, Autonomous University of Sinaloa, Culiacan 80010, Mexico; (J.G.A.-G.); (O.G.F.-S.); (E.T.-C.); (C.A.S.-C.); (J.A.M.-M.); (L.V.-Z.)
| | - Noé Ontiveros
- Clinical and Research Laboratory (LACIUS, U.N.), Department of Chemical, Biological, and Agricultural Sciences (DC-QB), Faculty of Biological and Health Sciences, University of Sonora, Navojoa 85880, Mexico
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12
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Cullina S, Wojcik GL, Shemirani R, Klarin D, Gorman BR, Sorokin EP, Gignoux CR, Belbin GM, Pyarajan S, Asgari S, Tsao PS, Damrauer SM, Abul-Husn NS, Kenny EE. Admixture mapping of peripheral artery disease in a Dominican population reveals a putative risk locus on 2q35. Front Genet 2023; 14:1181167. [PMID: 37600667 PMCID: PMC10432698 DOI: 10.3389/fgene.2023.1181167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Peripheral artery disease (PAD) is a form of atherosclerotic cardiovascular disease, affecting ∼8 million Americans, and is known to have racial and ethnic disparities. PAD has been reported to have a significantly higher prevalence in African Americans (AAs) compared to non-Hispanic European Americans (EAs). Hispanic/Latinos (HLs) have been reported to have lower or similar rates of PAD compared to EAs, despite having a paradoxically high burden of PAD risk factors; however, recent work suggests prevalence may differ between sub-groups. Here, we examined a large cohort of diverse adults in the BioMe biobank in New York City. We observed the prevalence of PAD at 1.7% in EAs vs. 8.5% and 9.4% in AAs and HLs, respectively, and among HL sub-groups, the prevalence was found at 11.4% and 11.5% in Puerto Rican and Dominican populations, respectively. Follow-up analysis that adjusted for common risk factors demonstrated that Dominicans had the highest increased risk for PAD relative to EAs [OR = 3.15 (95% CI 2.33-4.25), p < 6.44 × 10-14]. To investigate whether genetic factors may explain this increased risk, we performed admixture mapping by testing the association between local ancestry and PAD in Dominican BioMe participants (N = 1,813) separately from European, African, and Native American (NAT) continental ancestry tracts. The top association with PAD was an NAT ancestry tract at chromosome 2q35 [OR = 1.96 (SE = 0.16), p < 2.75 × 10-05) with 22.6% vs. 12.9% PAD prevalence in heterozygous NAT tract carriers versus non-carriers, respectively. Fine-mapping at this locus implicated tag SNP rs78529201 located within a long intergenic non-coding RNA (lincRNA) LINC00607, a gene expression regulator of key genes related to thrombosis and extracellular remodeling of endothelial cells, suggesting a putative link of the 2q35 locus to PAD etiology. Efforts to reproduce the signal in other Hispanic cohorts were unsuccessful. In summary, we showed how leveraging health system data helped understand nuances of PAD risk across HL sub-groups and admixture mapping approaches elucidated a putative risk locus in a Dominican population.
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Affiliation(s)
- Sinead Cullina
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Genevieve L. Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ruhollah Shemirani
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Derek Klarin
- VA Palo Alto Healthcare System, Palo Alto, CA, United States
- Division of Vascular Surgery, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Bryan R. Gorman
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, United States
- Booz Allen Hamilton, McLean, VA, United States
| | - Elena P. Sorokin
- Department of Genetics, Stanford University, Stanford, CA, United States
| | - Christopher R. Gignoux
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Colorado Center for Personalized Medicine, Aurora, CO, United States
| | - Gillian M. Belbin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Brigham Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Samira Asgari
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Philip S. Tsao
- VA Palo Alto Healthcare System, Palo Alto, CA, United States
| | - Scott M. Damrauer
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Noura S. Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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13
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Kopal J, Uddin LQ, Bzdok D. The end game: respecting major sources of population diversity. Nat Methods 2023; 20:1122-1128. [PMID: 36869122 DOI: 10.1038/s41592-023-01812-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
- Jakub Kopal
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montréal, Quebec, Canada
- Mila - Quebec Artificial Intelligence Institute, Montréal, Quebec, Canada
| | - Lucina Q Uddin
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Danilo Bzdok
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montréal, Quebec, Canada.
- Mila - Quebec Artificial Intelligence Institute, Montréal, Quebec, Canada.
- TheNeuro - Montreal Neurological Institute (MNI), McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Quebec, Canada.
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14
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Aguilar-Velázquez JA, Llamas-de-Dios BJ, Córdova-Mercado MF, Coronado-Ávila CE, Salas-Salas O, López-Quintero A, Ramos-González B, Rangel-Villalobos H. Accuracy of Eye and Hair Color Prediction in Mexican Mestizos from Monterrey City Based on ForenSeq TM DNA Signature Prep. Genes (Basel) 2023; 14:genes14051120. [PMID: 37239480 DOI: 10.3390/genes14051120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/14/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Forensic genomic systems allow simultaneously analyzing identity informative (iiSNPs), ancestry informative (aiSNPs), and phenotype informative (piSNPs) genetic markers. Among these kits, the ForenSeq DNA Signature prep (Verogen) analyzes identity STRs and SNPs as well as 24 piSNPs from the HIrisPlex system to predict the hair and eye color. We report herein these 24 piSNPs in 88 samples from Monterrey City (Northeast, Mexico) based on the ForenSeq DNA Signature prep. Phenotypes were predicted by genotype results with both Universal Analysis Software (UAS) and the web tool of the Erasmus Medical Center (EMC). We observed predominantly brown eyes (96.5%) and black hair (75%) phenotypes, whereas blue eyes, and blond and red hair were not observed. Both UAS and EMC showed high performance in eye color prediction (p ≥ 96.6%), but a lower accuracy was observed for hair color prediction. Overall, UAS hair color predictions showed better performance and robustness than those obtained with the EMC web tool (when hair shade is excluded). Although we employed a threshold (p > 70%), we suggest using the EMC enhanced approach to avoid the exclusion of a high number of samples. Finally, although our results are helpful to employ these genomic tools to predict eye color, caution is suggested for hair color prediction in Latin American (admixed) populations such as those studied herein, principally when no black color is predicted.
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Affiliation(s)
- José Alonso Aguilar-Velázquez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
- Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Blanca Jeannete Llamas-de-Dios
- Licenciatura en Ciencias Forenses, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Miranda Fabiola Córdova-Mercado
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Carolina Elena Coronado-Ávila
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Orlando Salas-Salas
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Andrés López-Quintero
- Instituto de Nutrigenética y Nutrigenómica Traslacional, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Benito Ramos-González
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCI-UdeG), Ocotlán 47820, Jalisco, Mexico
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15
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Villa-Islas V, Izarraras-Gomez A, Larena M, Campos EMP, Sandoval-Velasco M, Rodríguez-Rodríguez JE, Bravo-Lopez M, Moguel B, Fregel R, Garfias-Morales E, Medina Tretmanis J, Velázquez-Ramírez DA, Herrera-Muñóz A, Sandoval K, Nieves-Colón MA, Zepeda García Moreno G, Villanea FA, Medina EFV, Aguayo-Haro R, Valdiosera C, Ioannidis AG, Moreno-Estrada A, Jay F, Huerta-Sanchez E, Moreno-Mayar JV, Sánchez-Quinto F, Ávila-Arcos MC. Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 2023; 380:eadd6142. [PMID: 37167382 DOI: 10.1126/science.add6142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled "ghost" populations.
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Affiliation(s)
- Viridiana Villa-Islas
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Alan Izarraras-Gomez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Maximilian Larena
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Cuidad de México, Mexico
| | | | - Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Barbara Moguel
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
- Centro de Geociencias, UNAM Juriquilla, Juriquilla, Querétaro, México
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Ernesto Garfias-Morales
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | | | | | | | - Karla Sandoval
- Equity and Gender Office of the Centre for Research and Advanced Studies (CODIGO-C), CINVESTAV, Mexico City, Mexico
| | - Maria A Nieves-Colón
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | | | - Fernando A Villanea
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Cristina Valdiosera
- Departamento de Historia, Geografía y Comunicaciones, Universidad de Burgos, Burgos, Spain
- Department of History and Archaeology, La Trobe University, Melbourne, Australia
| | - Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Flora Jay
- Laboratoire Interdisciplinaire des Sciences du Numérique, Université Paris-Saclay, CNRS, INRIA, 91400 Orsay, France
| | | | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
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16
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Wagner JK, Yu JH, Fullwiley D, Moore C, Wilson JF, Bamshad MJ, Royal CD. Guidelines for genetic ancestry inference created through roundtable discussions. HGG Adv 2023; 4:100178. [PMID: 36798092 PMCID: PMC9926022 DOI: 10.1016/j.xhgg.2023.100178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
The use of genetic and genomic technology to infer ancestry is commonplace in a variety of contexts, particularly in biomedical research and for direct-to-consumer genetic testing. In 2013 and 2015, two roundtables engaged a diverse group of stakeholders toward the development of guidelines for inferring genetic ancestry in academia and industry. This report shares the stakeholder groups' work and provides an analysis of, commentary on, and views from the groundbreaking and sustained dialogue. We describe the engagement processes and the stakeholder groups' resulting statements and proposed guidelines. The guidelines focus on five key areas: application of genetic ancestry inference, assumptions and confidence/laboratory and statistical methods, terminology and population identifiers, impact on individuals and groups, and communication or translation of genetic ancestry inferences. We delineate the terms and limitations of the guidelines and discuss their critical role in advancing the development and implementation of best practices for inferring genetic ancestry and reporting the results. These efforts should inform both governmental regulation and self-regulation.
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Affiliation(s)
- Jennifer K. Wagner
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Joon-Ho Yu
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
| | - Duana Fullwiley
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
| | | | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
| | - Michael J. Bamshad
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
| | - Charmaine D. Royal
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
| | - Genetic Ancestry Inference Roundtable Participants
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
- The DNA Detectives, Dana Point, CA, USA
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
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17
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Cullina S, Wojcik GL, Shemirani R, Klarin D, Gorman BR, Sorokin EP, Gignoux CR, Belbin GM, Pyarajan S, Asgari S, Tsao PS, Damrauer SM, Abul-Husn NS, Kenny EE. Admixture Mapping of Peripheral Artery Disease in a Dominican Population Reveals a Novel Risk Locus on 2q35. medRxiv 2023:2023.03.27.23287788. [PMID: 37034679 PMCID: PMC10081406 DOI: 10.1101/2023.03.27.23287788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Peripheral artery disease (PAD) is a form of atherosclerotic cardiovascular disease, affecting ∼8 million Americans, and is known to have racial and ethnic disparities. PAD has been reported to have significantly higher prevalence in African Americans (AAs) compared to non-Hispanic European Americans (EAs). Hispanic/Latinos (HLs) have been reported to have lower or similar rates of PAD compared to EAs, despite having a paradoxically high burden of PAD risk factors, however recent work suggests prevalence may differ between sub-groups. Here we examined a large cohort of diverse adults in the Bio Me biobank in New York City (NYC). We observed the prevalence of PAD at 1.7% in EAs vs 8.5% and 9.4% in AAs and HLs, respectively; and among HL sub-groups, at 11.4% and 11.5% in Puerto Rican and Dominican populations, respectively. Follow-up analysis that adjusted for common risk factors demonstrated that Dominicans had the highest increased risk for PAD relative to EAs (OR=3.15 (95% CI 2.33-4.25), P <6.44×10 -14 ). To investigate whether genetic factors may explain this increased risk, we performed admixture mapping by testing the association between local ancestry (LA) and PAD in Dominican Bio Me participants (N=1,940) separately for European (EUR), African (AFR) and Native American (NAT) continental ancestry tracts. We identified a NAT ancestry tract at chromosome 2q35 that was significantly associated with PAD (OR=2.05 (95% CI 1.51-2.78), P <4.06×10 -6 ) with 22.5% vs 12.5% PAD prevalence in heterozygous NAT tract carriers versus non-carriers, respectively. Fine-mapping at this locus implicated tag SNP rs78529201 located within a long intergenic non-coding RNA (lincRNA) LINC00607 , a gene expression regulator of key genes related to thrombosis and extracellular remodeling of endothelial cells, suggesting a putative link of the 2q35 locus to PAD etiology. In summary, we showed how leveraging health systems data helped understand nuances of PAD risk across HL sub-groups and admixture mapping approaches elucidated a novel risk locus in a Dominican population.
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18
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Juárez-Luis J, Canseco-Ocaña M, Cid-Soto MA, Castro-Martínez XH, Martínez-Hernández A, Orozco L, Hernández-Zavala A, Córdova EJ. Single nucleotide variants in microRNA biosynthesis genes in Mexican individuals. Front Genet 2023; 14:1022912. [PMID: 36968598 PMCID: PMC10037310 DOI: 10.3389/fgene.2023.1022912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/02/2023] [Indexed: 03/08/2023] Open
Abstract
Background: MicroRNAs (miRNAs) are important regulators in a variety of biological processes, and their dysregulation is associated with multiple human diseases. Single nucleotide variants (SNVs) in genes involved in the processing of microRNAs may alter miRNA regulation and could present high allele heterogeneity in populations from different ethnic groups. Thus, the aim of this study was to genotype 15 SNVs in eight genes involved in the miRNA processing pathway in Mexican individuals and compare their frequencies across 21 populations from five continental groups.Methods: Genomic DNA was obtained from 399 healthy Mexican individuals. SNVs in AGO2 (rs2293939 and rs4961280), DGCR8 (rs720012), DICER (rs3742330 and rs13078), DROSHA (rs10719 and rs6877842), GEMIN3 (rs197388 and rs197414), GEMIN4 (rs7813, rs2740349, and rs4968104), TNRC6B (rs9611280), and XP05 (rs11077 and rs34324334) were genotyped using TaqMan probes. The minor allele frequency of each SNV was compared to those reported in the 1,000 Genomes database using chi-squared. Sankey plot was created in the SankeyMATIC package to visualize the frequency range of each variant in the different countries analyzed.Results: In Mexican individuals, all 15 SNVs were found in Hardy-Weinberg equilibrium, with frequencies ranging from 0.04 to 0.45. The SNVs rs4961280, rs2740349, rs34324334, and rs720012 in Mexican individuals had the highest minor allele frequencies worldwide, whereas the minor allele frequencies of rs197388, rs10719, rs197414, and rs1107 were among the lowest in Mexican individuals. The variants had high allele heterogeneity among the sub-continental populations, ranging from monomorphic, as was the case for rs9611280 and rs34324334 in African groups, to >0.50, which was the case for variants rs11077 and rs10719 in most of the populations. Importantly, the variants rs197388, rs720012, and rs197414 had FST values > 0.18, indicating a directional selective process. Finally, the SNVs rs13078 and rs10719 significantly correlated with both latitude and longitude.Conclusion: These data indicate the presence of high allelic heterogeneity in the worldwide distribution of the frequency of SNVs located in components of the miRNA processing pathway, which could modify the genetic susceptibility associated with human diseases in populations with different ancestry.
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Affiliation(s)
- Jesús Juárez-Luis
- Section of Research and Postgraduate, Superior School of Medicine, National Institute Polytechnique, Mexico City, Mexico
| | - Moisés Canseco-Ocaña
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Miguel Angel Cid-Soto
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Xochitl H. Castro-Martínez
- Genomics of Psychiatric and Neurogenerative diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Araceli Hernández-Zavala
- Section of Research and Postgraduate, Superior School of Medicine, National Institute Polytechnique, Mexico City, Mexico
| | - Emilio J. Córdova
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- *Correspondence: Emilio J. Córdova,
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Rivera-Paredez B, Hidalgo-Bravo A, León-Reyes G, Barajas-Olmos F, Martínez-Hernández A, Orozco L, Denova-Gutiérrez E, Salmerón J, Velázquez-Cruz R. The role of single nucleotide variant rs3819817 of the Histidine Ammonia-Lyase gene and 25-Hydroxyvitamin D on bone mineral density, adiposity markers, and skin pigmentation, in Mexican population. J Endocrinol Invest 2023:10.1007/s40618-023-02051-1. [PMID: 36862244 DOI: 10.1007/s40618-023-02051-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023]
Abstract
PURPOSE Vitamin D (VD) deficiency and osteoporosis have become a global public health problem. A variant in the Histidine Ammonia-Lyase (HAL) gene has been associated with VD levels and bone mineral density (BMD). However, whether this variant has an influence on VD levels and BMD in Mexican adults remain unclear. METHODS This cross-sectional analysis included 1,905 adults participating in the Health Worker Cohort Study and 164 indigenous postmenopausal women from the Metabolic Analysis in an Indigenous Sample (MAIS) cohort. The rs3819817 variant was genotyped by TaqMan probe assay. Total 25 hydroxyvitamin D levels were measured by DiaSorin Liaison. BMD at the different sites was assessed through dual-energy X-ray absorptiometry. Linear and logistic regression models were performed to evaluate the associations of interest. RESULTS The prevalence of VD deficiency was 41%, showing differences between sexes. Obesity and skin pigmentation were associated with lower levels of VD in males and females. rs3819817-T allele was associated with low levels of 25-hydroxyvitamin D, VD deficiency, and hip and femoral neck BMD values (g/cm2). We found two interactions with VD levels, one between adiposity and rs3819817-T allele (P = 0.017) and another between skin pigmentation and rs3819817-T allele (P = 0.019). In indigenous postmenopausal women, we observed higher VD levels in the southern region compared to the northern region (P < 0.001); however, we did not observe differences by genotype. CONCLUSION Our findings confirm that the genetic variant rs3819817 has an essential function in VD levels and BMD and suggests a role in skin pigmentation in the Mexican population.
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Affiliation(s)
- B Rivera-Paredez
- Centro de Investigación en Políticas, Población y Salud de la Facultad de Medicina de la Universidad Nacional Autónoma de México (UNAM), Mexico City, México
| | - A Hidalgo-Bravo
- Departamento de Genética, Instituto Nacional de Rehabilitación, Mexico City, México
| | - G León-Reyes
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - F Barajas-Olmos
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - A Martínez-Hernández
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - L Orozco
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - E Denova-Gutiérrez
- Centro de Investigación en Nutrición y Salud, Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México
| | - J Salmerón
- Centro de Investigación en Políticas, Población y Salud de la Facultad de Medicina de la Universidad Nacional Autónoma de México (UNAM), Mexico City, México
| | - R Velázquez-Cruz
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México.
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20
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Vázquez-Romo R, Millan-Catalan O, Ruíz-García E, Martínez-Gutiérrez AD, Alvarado-Miranda A, Campos-Parra AD, López-Camarillo C, Jacobo-Herrera N, López-Urrutia E, Guardado-Estrada M, Cantú de León D, Pérez-Plasencia C. Pathogenic variant profile in DNA damage response genes correlates with metastatic breast cancer progression-free survival in a Mexican-mestizo population. Front Oncol 2023; 13:1146008. [PMID: 37182128 PMCID: PMC10174330 DOI: 10.3389/fonc.2023.1146008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/14/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Metastatic breast cancer causes the most breast cancer-related deaths around the world, especially in countries where breast cancer is detected late into its development. Genetic testing for cancer susceptibility started with the BRCA 1 and 2 genes. Still, recent research has shown that variations in other members of the DNA damage response (DDR) are also associated with elevated cancer risk, opening new opportunities for enhanced genetic testing strategies. Methods We sequenced BRCA1/2 and twelve other DDR genes from a Mexican-mestizo population of 40 metastatic breast cancer patients through semiconductor sequencing. Results Overall, we found 22 variants -9 of them reported for the first time- and a strikingly high proportion of variations in ARID1A. The presence of at least one variant in the ARID1A, BRCA1, BRCA2, or FANCA genes was associated with worse progression-free survival and overall survival in our patient cohort. Discussion Our results reflected the unique characteristics of the Mexican-mestizo population as the proportion of variants we found differed from that of other global populations. Based on these findings, we suggest routine screening for variants in ARID1A along with BRCA1/2 in breast cancer patients from the Mexican-mestizo population.
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Affiliation(s)
- Rafael Vázquez-Romo
- Departamento de Cirugía de Tumores Mamarios, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
| | - Oliver Millan-Catalan
- Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
| | - Erika Ruíz-García
- Laboratorio de Medicina Traslacional y Departamento de Tumores Gastrointestinales, Instituto Nacional de Cancerología, CDMX, Mexico
| | | | - Alberto Alvarado-Miranda
- Departamento de Cirugía de Tumores Mamarios, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
| | - Alma D. Campos-Parra
- Dirección de Investigación, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, Mexico
| | - Nadia Jacobo-Herrera
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición, Salvador Zubirán (INCMNSZ), Ciudad de México, Mexico
| | - Eduardo López-Urrutia
- Laboratorio de Genómica, Unidad de Biomedicina, FES-IZTACALA, UNAM, Tlalnepantla, Mexico
| | - Mariano Guardado-Estrada
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - David Cantú de León
- Dirección de Investigación, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
- *Correspondence: David Cantú de León, ; Carlos Pérez-Plasencia,
| | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
- Laboratorio de Genómica, Unidad de Biomedicina, FES-IZTACALA, UNAM, Tlalnepantla, Mexico
- *Correspondence: David Cantú de León, ; Carlos Pérez-Plasencia,
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Cerrato-Izaguirre D, Chirino YI, Prada D, Quezada-Maldonado EM, Herrera LA, Hernández-Guerrero A, Alonso-Larraga JO, Herrera-Goepfert R, Oñate-Ocaña LF, Cantú-de-León D, Meneses-García A, Basurto-Lozada P, Robles-Espinoza CD, Camacho J, García-Cuellar CM, Sánchez-Pérez Y. Somatic Mutational Landscape in Mexican Patients: CDH1 Mutations and chr20q13.33 Amplifications Are Associated with Diffuse-Type Gastric Adenocarcinoma. Int J Mol Sci 2022; 23:11116. [PMID: 36232418 PMCID: PMC9570354 DOI: 10.3390/ijms231911116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 12/04/2022] Open
Abstract
The Hispanic population, compared with other ethnic groups, presents a more aggressive gastric cancer phenotype with higher frequency of diffuse-type gastric adenocarcinoma (GA); this could be related to the mutational landscape of GA in these patients. Using whole-exome sequencing, we sought to present the mutational landscape of GA from 50 Mexican patients who were treated at The Instituto Nacional de Cancerología from 2019 to 2020. We performed a comprehensive statistical analysis to explore the relationship of the genomic variants and clinical data such as tumor histology and presence of signet-ring cell, H. pylori, and EBV. We describe a potentially different mutational landscape between diffuse and intestinal GA in Mexican patients. Patients with intestinal-type GA tended to present a higher frequency of NOTCH1 mutations, copy number gains in cytobands 13.14, 10q23.33, and 12q25.1, and copy number losses in cytobands 7p12, 14q24.2, and 11q13.1; whereas patients with diffuse-type GA tended to present a high frequency of CDH1 mutations and CNV gains in cytobands 20q13.33 and 22q11.21. This is the first description of a mutational landscape of GA in Mexican patients to better understand tumorigenesis in Hispanic patients and lay the groundwork for discovering potential biomarkers and therapeutic targets.
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Affiliation(s)
- Dennis Cerrato-Izaguirre
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del I.P.N. (CINVESTAV), Avenida Instituto Politécnico Nacional No. 2508, Ciudad de México CP. 07360, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - Yolanda I. Chirino
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Iztacala, Tlalnepantla de Baz, Estado de México CP. 54090, Mexico
| | - Diddier Prada
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - Ericka Marel Quezada-Maldonado
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - Luis A Herrera
- Instituto Nacional de Medicina Genómica (INMEGEN), Periférico Sur No. 4809, Arenal Tepepan, Tlalpan, Ciudad de México CP. 14610, Mexico
| | - Angélica Hernández-Guerrero
- Servicio de Endoscopía, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - Juan Octavio Alonso-Larraga
- Servicio de Endoscopía, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - Roberto Herrera-Goepfert
- Departamento de Patología, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - Luis F. Oñate-Ocaña
- Subdirección de Investigación Clínica, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - David Cantú-de-León
- Dirección de Investigación, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - Abelardo Meneses-García
- Dirección General, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - Patricia Basurto-Lozada
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro CP. 76010, Mexico
| | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro CP. 76010, Mexico
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Javier Camacho
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del I.P.N. (CINVESTAV), Avenida Instituto Politécnico Nacional No. 2508, Ciudad de México CP. 07360, Mexico
| | - Claudia M. García-Cuellar
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
| | - Yesennia Sánchez-Pérez
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), San Fernando No. 22, Tlalpan, Ciudad de México CP. 14080, Mexico
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Roldan-Marin R, Rangel-Gamboa L, Vega-Memije ME, Hernández-Doño S, Ruiz-Gómez D, Granados J. Human leukocyte antigen Class II alleles associated with acral lentiginous melanoma in Mexican Mestizo patients: A case-control study. Indian J Dermatol Venereol Leprol 2022; 88:608-614. [PMID: 35138055 DOI: 10.25259/ijdvl_627_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/01/2021] [Indexed: 12/24/2022]
Abstract
Background Melanoma is an aggressive cutaneous cancer. Acral lentiginous melanoma is a melanoma subtype arising on palms, soles, and nail-units. The incidence, prevalence and prognosis differ among populations. The link between expression of major histocompatibility complex Class II alleles and melanoma progression is known. However, available studies report variable results regarding the association of melanoma with specific HLA Class II loci. Aims The aim of the study was to determine HLA Class II allele frequencies in acral lentiginous melanoma patients and healthy Mexican Mestizo individuals. Methods Eighteen patients with acral lentiginous melanoma and 99 healthy controls were recruited. HLA Class II typing was performed based on the sequence-specific oligonucleotide method. Results Three alleles were associated with increased susceptibility to develop acral lentiginous melanoma, namely: HLA-DRB1*13:01; pC = 0.02, odds ratio = 6.1, IC95% = 1.4-25.5, HLA-DQA1*01:03; pC = 0.001, odds ratio = 9.3, IC95% = 2.7-31.3 and HLA-DQB1*02:02; pC = 0.01, odds ratio = 3.7, IC95% = 1.4-10.3. Limitations The small sample size was a major limitation, although it included all acral lentiginous melanoma patients seen at the dermatology department of Dr. Manuel Gea González General Hospital during the study period. Conclusion HLA-DRB1*13:01, HLA-DQB1*02:02 and HLA-DQA*01:03 alleles are associated with increased susceptibility to develop acral lentiginous melanoma in Mexican Mestizo patients.
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Affiliation(s)
- Rodrigo Roldan-Marin
- OncoDermatology Clinic, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico
| | - Lucia Rangel-Gamboa
- Ecology of Pathogenic Agents, Division of Research, General Hospital Dr. Manuel Gea González, Mexico
| | | | - Susana Hernández-Doño
- Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Daniela Ruiz-Gómez
- Department of Internal Medicine, Fundación Clínica Médica Sur A.C, Mexico
| | - Julio Granados
- Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
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23
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Khan AT, Gogarten SM, McHugh CP, Stilp AM, Sofer T, Bowers ML, Wong Q, Cupples LA, Hidalgo B, Johnson AD, McDonald MLN, McGarvey ST, Taylor MR, Fullerton SM, Conomos MP, Nelson SC. Recommendations on the use and reporting of race, ethnicity, and ancestry in genetic research: Experiences from the NHLBI TOPMed program. Cell Genom 2022; 2:100155. [PMID: 36119389 PMCID: PMC9481067 DOI: 10.1016/j.xgen.2022.100155] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
How race, ethnicity, and ancestry are used in genomic research has wide-ranging implications for how research is translated into clinical care and incorporated into public understanding. Correlation between race and genetic ancestry contributes to unresolved complexity for the scientific community, as illustrated by heterogeneous definitions and applications of these variables. Here, we offer commentary and recommendations on the use of race, ethnicity, and ancestry across the arc of genetic research, including data harmonization, analysis, and reporting. While informed by our experiences as researchers affiliated with the NHLBI Trans-Omics for Precision Medicine (TOPMed) program, these recommendations are applicable to basic and translational genomic research in diverse populations with genome-wide data. Moving forward, considerable collaborative effort will be required to ensure that race, ethnicity, and ancestry are described and used appropriately to generate scientific knowledge that yields broad and equitable benefit.
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Affiliation(s)
- Alyna T. Khan
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | | | - Caitlin P. McHugh
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
| | - Michael L. Bowers
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew D. Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Merry-Lynn N. McDonald
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stephen T. McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
- Department of Anthropology, Brown University, Providence, RI, USA
| | - Matthew R.G. Taylor
- Department of Medicine, Adult Medical Genetics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | | | - Sarah C. Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
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24
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Collen EJ, Johar AS, Teixeira JC, Llamas B. The immunogenetic impact of European colonization in the Americas. Front Genet 2022; 13:918227. [PMID: 35991555 PMCID: PMC9388791 DOI: 10.3389/fgene.2022.918227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.
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Affiliation(s)
- Evelyn Jane Collen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Evelyn Jane Collen, ; Bastien Llamas,
| | - Angad Singh Johar
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Culture History and Language, The Australian National University, Canberra, ACT, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
- Telethon Kids Institute, Indigenous Genomics Research Group, Adelaide, SA, Australia
- *Correspondence: Evelyn Jane Collen, ; Bastien Llamas,
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25
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Molina-Torres CA, Quinn FD, Castro-Garza J, Gómez-Velasco A, Ocampo-Candiani J, Bencomo-Alerm A, Sánchez-Pérez HJ, Muñoz-Jiménez S, Rendón A, Ansari A, Sharma M, Singh P, Vera-Cabrera L. Genetic Diversity of Mycobacterium tuberculosis Isolates From an Amerindian Population in Chiapas, México. Front Cell Infect Microbiol 2022; 12:875909. [PMID: 35909960 PMCID: PMC9326120 DOI: 10.3389/fcimb.2022.875909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
This is the first report of the genetic diversity of the Mycobacterium tuberculosis complex isolates found in a Mexican-Amerindian setting. In this study, we analyzed isolates collected from the Highlands region of Chiapas, Mexico, by using spoligotyping and whole-genome sequencing analyses. Seventy-three M. tuberculosis isolates were analyzed initially by spoligotyping; no new spoligotypes were identified. Nineteen percent of the isolates were identified as SIT53 (T1) (n = 14), followed by SIT42 (14%, n = 10, LAM9) and SIT119 (11%; n = 8, X1). SIT53, SIT42, and orphan isolates (16.4%, n = 12) constituted about 50% of the isolates studied and were subjected to whole-genome sequencing (WGS) analysis. Most SIT53 (10/12) isolates belonged to the Euro-American sub-lineage 4.8. Most SIT42 isolates (4/7) as .well as most orphan isolates (5/8) belonged to the lineage 4.3.3 LAM group. By comparing the single-nucleotide polymorphism (SNP) patterns of the SIT53 isolates, we found one clone (<7 SNPs) and four clustered isolates (<15 SNPs). In isolates from the SIT42 and orphan groups, we did not find any clones or clusters. This work demonstrates the success of sub-lineage 4.8 to predominate in Mexico and confirms the dominion of sub-lineage 4.3.3 in Central and South America.
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Affiliation(s)
- Carmen A. Molina-Torres
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Frederick D. Quinn
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Jorge Castro-Garza
- Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, Mexico
| | - Anaximandro Gómez-Velasco
- Departamento de Ecología Humana, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Unidad Mérida, Mérida, Mexico
| | - Jorge Ocampo-Candiani
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Alied Bencomo-Alerm
- Laboratorio de Micobacterias, Programa de Prevención y Control de la Tuberculosis, región Altos de Chiapas, Instituto de Salud del Estado de Chiapas, Secretaría de Salud (SSA), San Cristóbal de Las Casas, Mexico
| | | | - Sergio Muñoz-Jiménez
- Laboratorio de Micobacterias, Programa de Prevención y Control de la Tuberculosis, región Altos de Chiapas, Instituto de Salud del Estado de Chiapas, Secretaría de Salud (SSA), San Cristóbal de Las Casas, Mexico
| | - Adrián Rendón
- Centro de Investigación, Prevención y Tratamiento de Infecciones Respiratorias, Hospital Universitario, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Afzal Ansari
- Microbial Pathogenesis and Genomics Lab, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Mukul Sharma
- Microbial Pathogenesis and Genomics Lab, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Pushpendra Singh
- Microbial Pathogenesis and Genomics Lab, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Lucio Vera-Cabrera
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, Universidad Autónoma de Nuevo León, Monterrey, Mexico
- *Correspondence: Lucio Vera-Cabrera,
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26
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Castro-Jiménez TK, Gómez-Legorreta LC, López-Campa LA, Martínez-Torres V, Alvarado-Silva M, Posadas-Mondragón A, Díaz-Lima N, Angulo-Mendez HA, Mejía-Domínguez NR, Vaca-Paniagua F, Ávila-Moreno F, García-Cordero J, Cedillo-Barrón L, Aguilar-Ruíz SR, Bustos-Arriaga J. Variability in Susceptibility to Type I Interferon Response and Subgenomic RNA Accumulation Between Clinical Isolates of Dengue and Zika Virus From Oaxaca Mexico Correlate With Replication Efficiency in Human Cells and Disease Severity. Front Cell Infect Microbiol 2022; 12:890750. [PMID: 35800385 PMCID: PMC9254156 DOI: 10.3389/fcimb.2022.890750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Dengue and Zika viruses cocirculate annually in endemic areas of Mexico, causing outbreaks of different magnitude and severity every year, suggesting a continuous selection of Flavivirus variants with variable phenotypes of transmissibility and virulence. To evaluate if Flavivirus variants with different phenotypes cocirculate during outbreaks, we isolated dengue and Zika viruses from blood samples of febrile patients from Oaxaca City during the 2016 and 2019 epidemic years. We compared their replication kinetics in human cells, susceptibility to type I interferon antiviral response, and the accumulation of subgenomic RNA on infected cells. We observed correlations between type I interferon susceptibility and subgenomic RNA accumulation, with high hematocrit percentage and thrombocytopenia. Our results suggest that Flaviviruses that cocirculate in Oaxaca, Mexico, have variable sensitivity to the antiviral activity of type I interferons, and this phenotypic trait correlates with the severity of the disease.
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Affiliation(s)
- Tannya Karen Castro-Jiménez
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Laura Cristina Gómez-Legorreta
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Laura Alejandra López-Campa
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Valeria Martínez-Torres
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Marcos Alvarado-Silva
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Araceli Posadas-Mondragón
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | | | | | - Nancy R. Mejía-Domínguez
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Felipe Vaca-Paniagua
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Federico Ávila-Moreno
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Julio García-Cordero
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Leticia Cedillo-Barrón
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Sergio Roberto Aguilar-Ruíz
- Departamento de Biomedicina Experimental, Facultad de Medicina y Cirugía de la Universidad Autónoma ‘Benito Juárez’ de Oaxaca, Oaxaca, Mexico
| | - José Bustos-Arriaga
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
- *Correspondence: José Bustos-Arriaga,
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27
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Wu S, Wang M, Alqahtani A, Lou M, Stock W, Bhojwani D, Alachkar H. Hispanic ethnicity and the rs4880 variant in SOD2 are associated with elevated liver enzymes and bilirubin levels in children receiving asparaginase-containing chemotherapy for acute lymphoblastic leukemia. Biomed Pharmacother 2022; 150:113000. [PMID: 35658244 DOI: 10.1016/j.biopha.2022.113000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/11/2022] [Accepted: 04/17/2022] [Indexed: 01/29/2023] Open
Abstract
Asparaginase is an integral component of acute lymphoblastic leukemia (ALL)3 treatment. Hepatotoxicity related to asparaginase is one of the most common treatment-related toxicities in ALL therapy. Hispanic children are at higher risk of developing ALL, and toxicities from ALL therapy. The rs4880 variant in the superoxide dismutase 2 (SOD2)4 gene, a critical mitochondrial enzyme that protects cells against oxidative stress, was found to be associated with increased incidence of asparaginase-related hepatotoxicity in adult cohort of largely White non-Hispanics patients with ALL. The risk genotype (rs4880-CC) is more frequent among adult Hispanic patients with ALL. To assess the prevalence of hepatotoxicity and risk genotype among pediatric patients with ALL, particularly of Hispanic ethnicity, we conducted a prospective study of 143 pediatric patients with ALL (62.2% Hispanic). Bilirubin and hepatic transaminase levels were collected at different times during multiagent therapy including asparaginase treatment. Germline DNA blood samples were genotyped for the SOD2 rs4880. We found that the frequency of hepatotoxicity and the rs4880-CC risk genotype are higher in Hispanic patients than non-Hispanic. Patients with the CC genotype exhibit higher bilirubin and hepatic transaminase levels compared with patients with the TT and CT genotypes. In a multivariate Cox analysis, Hispanic ethnicity was identified as a strong predictor of hepatotoxicity (hazard ratio [HR] = 1.9, 95% confidence interval [95% CI] 1.0-3.5, p = 0.05). Altogether, these findings demonstrate that hepatotoxicity is highly prevalent among Hispanic pediatric patients with ALL, and those with rs4880-CC genotype.
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28
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Jurado-Camacho PA, Cid-Soto MA, Barajas-Olmos F, García-Ortíz H, Baca-Peynado P, Martínez-Hernández A, Centeno-Cruz F, Contreras-Cubas C, González-Villalpando ME, Saldaña-Álvarez Y, Salas-Martinez G, Mendoza-Caamal EC, González-Villalpando C, Córdova EJ, Orozco L. Exome Sequencing Data Analysis and a Case-Control Study in Mexican Population Reveals Lipid Trait Associations of New and Known Genetic Variants in Dyslipidemia-Associated Loci. Front Genet 2022; 13:807381. [PMID: 35669185 PMCID: PMC9164108 DOI: 10.3389/fgene.2022.807381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Plasma lipid levels are a major risk factor for cardiovascular diseases. Although international efforts have identified a group of loci associated with the risk of dyslipidemia, Latin American populations have been underrepresented in these studies.Objective: To know the genetic variation occurring in lipid-related loci in the Mexican population and its association with dyslipidemia.Methods: We searched for single-nucleotide variants in 177 lipid candidate genes using previously published exome sequencing data from 2838 Mexican individuals belonging to three different cohorts. With the extracted variants, we performed a case-control study. Logistic regression and quantitative trait analyses were implemented in PLINK software. We used an LD pruning using a 50-kb sliding window size, a 5-kb window step size and a r2 threshold of 0.1.Results: Among the 34251 biallelic variants identified in our sample population, 33% showed low frequency. For case-control study, we selected 2521 variants based on a minor allele frequency ≥1% in all datasets. We found 19 variants in 9 genes significantly associated with at least one lipid trait, with the most significant associations found in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster on chromosome 11. Notably, all 11 variants associated with hypertriglyceridemia were within this cluster; whereas variants associated with hypercholesterolemia were located at chromosome 2 and 19, and for low high density lipoprotein cholesterol were in chromosomes 9, 11, and 19. No significant associated variants were found for low density lipoprotein. We found several novel variants associated with different lipemic traits: rs3825041 in BUD13 with hypertriglyceridemia, rs7252453 in CILP2 with decreased risk to hypercholesterolemia and rs11076176 in CETP with increased risk to low high density lipoprotein cholesterol.Conclusions: We identified novel variants in lipid-regulation candidate genes in the Mexican population, an underrepresented population in genomic studies, demonstrating the necessity of more genomic studies on multi-ethnic populations to gain a deeper understanding of the genetic structure of the lipemic traits.
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Affiliation(s)
- Pedro A. Jurado-Camacho
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- Posgraduate in Biomedical Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Miguel A. Cid-Soto
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Humberto García-Ortíz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Paulina Baca-Peynado
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- Posgraduate in Biomedical Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - María Elena González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigación en Diabetes y Riesgo Cardiovascular, Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Yolanda Saldaña-Álvarez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Guadalupe Salas-Martinez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | | | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigación en Diabetes y Riesgo Cardiovascular, Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Emilio J. Córdova
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- *Correspondence: Emilio J. Córdova, ; Lorena Orozco,
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- *Correspondence: Emilio J. Córdova, ; Lorena Orozco,
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Zhang Z, Zhang Y, Wang Y, Zhao Z, Yang M, Zhang L, Zhou B, Xu B, Zhang H, Chen T, Dai W, Zhou Y, Shi S, Nielsen R, Li SC, Li S. The Tibetan-Yi region is both a corridor and a barrier for human gene flow. Cell Rep 2022; 39:110720. [PMID: 35476999 DOI: 10.1016/j.celrep.2022.110720] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 11/08/2021] [Accepted: 03/31/2022] [Indexed: 11/22/2022] Open
Abstract
The Tibetan-Yi Corridor (TYC) region between Tibet and the rest of east Asia has served as a crossroads for human migrations for thousands of years. The lack of whole-genome sequencing data specific to the TYC populations has hindered the understanding of the fundamental patterns of migration and divergence between humans in east Asia and southeast Asia. Here, we provide 248 individual whole genomes from the 16 TYC and 3 outgroup populations to elucidate historical relationships. We find that the Tibetan plateau forms an important barrier to gene flow, with a more Tibetan-like ancestry in northern populations and a southern east Asian-related ancestry in south populations. An isolated population, Achang, shows a prolonged isolation and genetic drift compared to other TYC populations. We also note that previous claims regarding the history and structure of TYC populations inferred by linguistics are incompatible with the genetic evidence.
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Castañeda-Partida L, Ocadiz-Delgado R, Sánchez-López JM, García-Villa E, Peñaloza-González JG, Velázquez-Aviña MM, Torres-Nava JR, Martín-Trejo JA, Solís-Labastida K, Guerra-Castillo FX, Bekker-Méndez VC, Rosales-García VH, Romero-Rodríguez D, Mojica-Espinoza R, Mendez-Tenorio A, Ramírez-Calzada CA, Álvarez-Ríos E, Mejía-Aranguré JM, Gariglio P. Global expression profiling of CD10 + /CD19 + pre-B lymphoblasts from Hispanic B-ALL patients correlates with comparative TARGET database analysis. Discov Oncol 2022; 13:28. [PMID: 35445848 PMCID: PMC9023642 DOI: 10.1007/s12672-022-00480-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/16/2022] [Indexed: 11/29/2022] Open
Abstract
Mexico City has one of the highest incidences of acute lymphoblastic leukemia (ALL) globally, with patients showing low survival, and high relapse rates. To gain more insight into the molecular features of B-ALL in Mexican children, we isolated CD10 + /CD19 + precursor B lymphoblasts from four bone marrow and nine peripheral blood samples of B-ALL patients using a fluorescence-activated cell sorting protocol. The global gene expression profile (BM vs PB) revealed 136 differentially expressed genes; 62 were upregulated (45.6%) and 74 were downregulated (54.4%). Pearson's correlation coefficient was calculated to determine the similarity between pre-B lymphoblast populations. We selected 26 highly significant genes and validated 21 by RT-qPCR (CNN3, STON2, CALN1, RUNX2, GADD45A, CDC45, CDC20, PLK1, AIDA, HCK, LY86, GPR65, PIK3CG, LILRB2, IL7R, TCL1A, DOCK1, HIST1H3G, PTPN14, CD72, and NT5E). The gene set enrichment analysis of the total expression matrix and the ingenuity pathway analysis of the 136 differentially expressed genes showed that the cell cycle was altered in the bone marrow with four overexpressed genes (PLK1, CDC20, CDC45, and GADD45A) and a low expression of IL7R and PIK3CG, which are involved in B cell differentiation. A comparative bioinformatics analysis of 15 bone marrow and 10 peripheral blood samples from Hispanic B-ALL patients collected by the TARGET program, corroborated the genes observed, except for PIK3CG. We conclude the Mexican and the Hispanic B-ALL patients studied present common driver alterations and histotype-specific mutations that could facilitate risk stratification and diagnostic accuracy and serve as potential therapeutic targets.
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Affiliation(s)
- Laura Castañeda-Partida
- Laboratorio de Genética Toxicológica, Biología. Facultad de Estudios Profesionales Iztacala (FESI), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla, Estado de México, Mexico
| | - Rodolfo Ocadiz-Delgado
- Laboratorio de Oncología Molecular, Departamento de Genética y Biología Molecular. Centro de Investigación y de Estudios Avanzados (Cinvestav), Ciudad de México, Mexico
| | | | - Enrique García-Villa
- Laboratorio de Oncología Molecular, Departamento de Genética y Biología Molecular. Centro de Investigación y de Estudios Avanzados (Cinvestav), Ciudad de México, Mexico
| | | | | | | | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología, Hospital de Pediatría. Centro Médico Nacional (CMN), "Siglo XXI" , Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Karina Solís-Labastida
- Servicio de Hematología, Hospital de Pediatría. Centro Médico Nacional (CMN), "Siglo XXI" , Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Francisco Xavier Guerra-Castillo
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología ''Dr. Daniel Mendez Hernández'', ''La Raza'', IMSS, Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología ''Dr. Daniel Mendez Hernández'', ''La Raza'', IMSS, Mexico City, Mexico
| | - Víctor Hugo Rosales-García
- Laboratorio de Citometría de Flujo, Laboratorios Nacionales de Servicios Experimentales, Centro de Investigación y de Estudios Avanzados (Cinvestav), Mexico City, Mexico
| | - Dámaris Romero-Rodríguez
- Unidad de Citometría, Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
| | - Raúl Mojica-Espinoza
- Unidad de Genotipificación y Análisis de Expresión, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Alfonso Mendez-Tenorio
- Laboratorio Biotecnología y Bioinformática Genómica, Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. MX, Mexico City, Mexico
| | - Crystel A Ramírez-Calzada
- Laboratorio Biotecnología y Bioinformática Genómica, Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. MX, Mexico City, Mexico
| | - Elízabeth Álvarez-Ríos
- Laboratorio de Oncología Molecular, Departamento de Genética y Biología Molecular. Centro de Investigación y de Estudios Avanzados (Cinvestav), Ciudad de México, Mexico
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría. Centro Medico Nacional (CMN) ''Siglo XXI'', Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
- Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Patricio Gariglio
- Laboratorio de Oncología Molecular, Departamento de Genética y Biología Molecular. Centro de Investigación y de Estudios Avanzados (Cinvestav), Ciudad de México, Mexico.
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Rodríguez-Rodríguez JE, Ioannidis AG, Medina-Muñoz SG, Barberena-Jonas C, Blanco-Portillo J, Quinto-Cortés CD, Moreno-Estrada A. The genetic legacy of the Manila galleon trade in Mexico. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200419. [PMID: 35430879 PMCID: PMC9014187 DOI: 10.1098/rstb.2020.0419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The population of Mexico has a considerable genetic substructure due to both its pre-Columbian diversity and due to genetic admixture from post-Columbian trans-oceanic migrations. The latter primarily originated in Europe and Africa, but also, to a lesser extent, in Asia. We analyze previously understudied genetic connections between Asia and Mexico to infer the timing and source of this genetic ancestry in Mexico. We identify the predominant origin within Southeast Asia—specifically western Indonesian and non-Negrito Filipino sources—and we date its arrival in Mexico to approximately 13 generations ago (1620 CE). This points to a genetic legacy from the seventeenth century Manila galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco. Indeed, within Mexico we observe the highest level of this trans-Pacific ancestry in Acapulco, located in the state of Guerrero. This colonial Spanish trade route from East Asia to Europe was centred on Mexico and appears in historical records, but its legacy has been largely ignored. Identities and stories were suppressed due to slavery, assimilation of the immigrants as ‘Indios’ and incomplete historical records. Here we characterize this understudied Mexican ancestry. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Santiago G. Medina-Muñoz
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
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32
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Gopalan S, Smith SP, Korunes K, Hamid I, Ramachandran S, Goldberg A. Human genetic admixture through the lens of population genomics. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200410. [PMID: 35430881 PMCID: PMC9014191 DOI: 10.1098/rstb.2020.0410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Over the past 50 years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, ‘The Apportionment of Human Diversity’. One evolutionary process that requires special attention in both population genetics and statistical genetics is admixture: gene flow between two or more previously separated source populations to form a new admixed population. The admixture process introduces ancestry-based structure into patterns of genetic variation within and between populations, which in turn influences the inference of demographic histories, identification of genetic targets of selection and prediction of complex traits. In this review, we outline some challenges for admixture population genetics, including limitations of applying methods designed for populations without recent admixture to the study of admixed populations. We highlight recent studies and methodological advances that aim to overcome such challenges, leveraging genomic signatures of admixture that occurred in the past tens of generations to gain insights into human history, natural selection and complex trait architecture. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Samuel Pattillo Smith
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Katharine Korunes
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Iman Hamid
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
- Data Science Initiative, Brown University, Providence, RI 02912, USA
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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Fernández-Rhodes L, Graff M, Buchanan VL, Justice AE, Highland HM, Guo X, Zhu W, Chen HH, Young KL, Adhikari K, Palmer ND, Below JE, Bradfield J, Pereira AC, Glover L, Kim D, Lilly AG, Shrestha P, Thomas AG, Zhang X, Chen M, Chiang CW, Pulit S, Horimoto A, Krieger JE, Guindo-Martínez M, Preuss M, Schumann C, Smit RA, Torres-Mejía G, Acuña-Alonzo V, Bedoya G, Bortolini MC, Canizales-Quinteros S, Gallo C, González-José R, Poletti G, Rothhammer F, Hakonarson H, Igo R, Adler SG, Iyengar SK, Nicholas SB, Gogarten SM, Isasi CR, Papnicolaou G, Stilp AM, Qi Q, Kho M, Smith JA, Langefeld CD, Wagenknecht L, Mckean-Cowdin R, Gao XR, Nousome D, Conti DV, Feng Y, Allison MA, Arzumanyan Z, Buchanan TA, Ida Chen YD, Genter PM, Goodarzi MO, Hai Y, Hsueh W, Ipp E, Kandeel FR, Lam K, Li X, Nadler JL, Raffel LJ, Roll K, Sandow K, Tan J, Taylor KD, Xiang AH, Yao J, Audirac-Chalifour A, de Jesus Peralta Romero J, Hartwig F, Horta B, Blangero J, Curran JE, Duggirala R, Lehman DE, Puppala S, Fejerman L, John EM, Aguilar-Salinas C, Burtt NP, Florez JC, García-Ortíz H, González-Villalpando C, Mercader J, Orozco L, Tusié-Luna T, Blanco E, Gahagan S, Cox NJ, Hanis C, Butte NF, Cole SA, Comuzzie AG, Voruganti VS, Rohde R, Wang Y, Sofer T, Ziv E, Grant SF, Ruiz-Linares A, Rotter JI, Haiman CA, Parra EJ, Cruz M, Loos RJ, North KE. Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium. HGG Adv 2022; 3:100099. [PMID: 35399580 PMCID: PMC8990175 DOI: 10.1016/j.xhgg.2022.100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/06/2022] [Indexed: 02/05/2023] Open
Abstract
Hispanic/Latinos have been underrepresented in genome-wide association studies (GWAS) for anthropometric traits despite their notable anthropometric variability, ancestry proportions, and high burden of growth stunting and overweight/obesity. To address this knowledge gap, we analyzed densely imputed genetic data in a sample of Hispanic/Latino adults to identify and fine-map genetic variants associated with body mass index (BMI), height, and BMI-adjusted waist-to-hip ratio (WHRadjBMI). We conducted a GWAS of 18 studies/consortia as part of the Hispanic/Latino Anthropometry (HISLA) Consortium (stage 1, n = 59,771) and generalized our findings in 9 additional studies (stage 2, n = 10,538). We conducted a trans-ancestral GWAS with summary statistics from HISLA stage 1 and existing consortia of European and African ancestries. In our HISLA stage 1 + 2 analyses, we discovered one BMI locus, as well as two BMI signals and another height signal each within established anthropometric loci. In our trans-ancestral meta-analysis, we discovered three BMI loci, one height locus, and one WHRadjBMI locus. We also identified 3 secondary signals for BMI, 28 for height, and 2 for WHRadjBMI in established loci. We show that 336 known BMI, 1,177 known height, and 143 known WHRadjBMI (combined) SNPs demonstrated suggestive transferability (nominal significance and effect estimate directional consistency) in Hispanic/Latino adults. Of these, 36 BMI, 124 height, and 11 WHRadjBMI SNPs were significant after trait-specific Bonferroni correction. Trans-ancestral meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our findings demonstrate that future studies may also benefit from leveraging diverse ancestries and differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification.
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Affiliation(s)
- Lindsay Fernández-Rhodes
- Department of Biobehavioral Health, Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA 16802, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Victoria L. Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anne E. Justice
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, PA 17822, USA
| | - Heather M. Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Wanying Zhu
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Hung-Hsin Chen
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kristin L. Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, MK7 6AA Milton Keynes, UK
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Jennifer E. Below
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan Bradfield
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandre C. Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, São Paulo 05508-220, Brazil
| | - LáShauntá Glover
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daeeun Kim
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adam G. Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Poojan Shrestha
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alvin G. Thomas
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xinruo Zhang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Charleston W.K. Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Sara Pulit
- Vertex Pharmaceuticals, W2 6BD Oxford, UK
| | - Andrea Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, São Paulo 05508-220, Brazil
| | - Jose E. Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, São Paulo 05508-220, Brazil
| | - Marta Guindo-Martínez
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Novo Nordisk Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Michael Preuss
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claudia Schumann
- Hasso Plattner Institute, University of Potsdam, Digital Health Center, 14482 Potsdam, Germany
| | - Roelof A.J. Smit
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriela Torres-Mejía
- Department of Research in Cardiovascular Diseases, Diabetes Mellitus, and Cancer, Population Health Research Center, National Institute of Public Health, Cuernavaca, Morelos 62100, Mexico
| | | | - Gabriel Bedoya
- Molecular Genetics Investigation Group, University of Antioquia, Medellín 1226, Colombia
| | - Maria-Cátira Bortolini
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Samuel Canizales-Quinteros
- Population Genomics Applied to Health Unit, The National Institute of Genomic Medicine and the Faculty of Chemistry at the National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Rolando González-José
- Patagonian Institute of the Social and Human Sciences, Patagonian National Center, Puerto Madryn U9120, Argentina
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | | | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sharon G. Adler
- Division of Nephrology and Hypertension, Harbor-University of California Los Angeles Medical Center, Torrance, CA 90502, USA
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Susanne B. Nicholas
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA
| | | | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Lynne Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Roberta Mckean-Cowdin
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Xiaoyi Raymond Gao
- Department of Ophthalmology and Visual Sciences, Department of Biomedical Informatics, Division of Human Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Darryl Nousome
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - David V. Conti
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ye Feng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Matthew A. Allison
- Department of Family Medicine, University of California, San Diego, CA 92161, USA
| | - Zorayr Arzumanyan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Thomas A. Buchanan
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Pauline M. Genter
- Department of Medicine, Division of Endocrinology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yang Hai
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Willa Hsueh
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Eli Ipp
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA
- Department of Medicine, Division of Endocrinology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Fouad R. Kandeel
- Department of Translational Research & Cellular Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Kelvin Lam
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Jerry L. Nadler
- Department of Pharmacology at New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Leslie J. Raffel
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
| | - Kathryn Roll
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Kevin Sandow
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Anny H. Xiang
- Research and Evaluation Branch, Kaiser Permanente of Southern California, Pasadena, CA 91101, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Astride Audirac-Chalifour
- Medical Research Unit in Biochemistry, Specialty Hospital, National Medical Center of the Twenty-First Century, Mexican Institute of Social Security, Mexico City 06725, Mexico
| | - Jose de Jesus Peralta Romero
- Medical Research Unit in Biochemistry, Specialty Hospital, National Medical Center of the Twenty-First Century, Mexican Institute of Social Security, Mexico City 06725, Mexico
| | - Fernando Hartwig
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas 96010-610, Brazil
| | - Bernando Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas 96010-610, Brazil
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520 and 78539, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520 and 78539, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520 and 78539, USA
| | - Donna E. Lehman
- Department of Medicine, School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Sobha Puppala
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27109, USA
| | - Laura Fejerman
- Department of Public Health Sciences, School of Medicine, and the Comprehensive Cancer Center, University of California Davis, Davis, CA 95616, USA
| | - Esther M. John
- Departments of Epidemiology & Population Health and Medicine-Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carlos Aguilar-Salinas
- Division of Nutrition, Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | - Noël P. Burtt
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Jose C. Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Humberto García-Ortíz
- Laboratory of Immunogenomics and Metabolic Diseases, National Institute of Genomic Medicine, Mexico City 14610, Mexico
| | - Clicerio González-Villalpando
- Center for Diabetes Studies, Research Unit for Diabetes and Cardiovascular Risk, Center for Population Health Studies, National Institute of Public Health, Mexico City 14080, Mexico
| | - Josep Mercader
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lorena Orozco
- Laboratory of Immunogenomics and Metabolic Diseases, National Institute of Genomic Medicine, Mexico City 14610, Mexico
| | - Teresa Tusié-Luna
- Molecular Biology and Medical Genomics Unity, Institute of Biomedical Research, The National Autonomous University of Mexico and the Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | - Estela Blanco
- Center for Community Health, Division of Academic General Pediatrics, University of California at San Diego, San Diego, CA 92093, USA
| | - Sheila Gahagan
- Center for Community Health, Division of Academic General Pediatrics, University of California at San Diego, San Diego, CA 92093, USA
| | - Nancy J. Cox
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Craig Hanis
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nancy F. Butte
- United States Department of Agriculture, Agricultural Research Service, The Children’s Nutrition Research Center, and the Department Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shelley A. Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | | | - V. Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Rebecca Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yujie Wang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tamar Sofer
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Struan F.A. Grant
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Andres Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
- Department of Genetics, Evolution and Environment, and Genetics Institute of the University College London, London WC1E 6BT, UK
- Laboratory of Biocultural Anthropology, Law, Ethics, and Health, Aix-Marseille University, Marseille 13385, France
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto- Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Miguel Cruz
- Medical Research Unit in Biochemistry, Specialty Hospital, National Medical Center of the Twenty-First Century, Mexican Institute of Social Security, Mexico City 06725, Mexico
| | - Ruth J.F. Loos
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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34
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Mendoza-Revilla J, Chacón-Duque JC, Fuentes-Guajardo M, Ormond L, Wang K, Hurtado M, Villegas V, Granja V, Acuña-Alonzo V, Jaramillo C, Arias W, Barquera R, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Badillo Rivera KM, Nieves-Colón MA, Gignoux CR, Wojcik GL, Moreno-Estrada A, Hünemeier T, Ramallo V, Schuler-Faccini L, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Fumagalli M, Adhikari K, Ruiz-Linares A, Hellenthal G. Disentangling Signatures of Selection Before and After European Colonization in Latin Americans. Mol Biol Evol 2022; 39:6565306. [PMID: 35460423 PMCID: PMC9034689 DOI: 10.1093/molbev/msac076] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.
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Affiliation(s)
- Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Louise Ormond
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
| | - Ke Wang
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,National School of Anthropology and History, Mexico City, Mexico
| | | | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | | | - Maria A Nieves-Colón
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Christopher R Gignoux
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Genevieve L Wojcik
- Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Tábita Hünemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | | | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | | | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, Australia
| | - Matteo Fumagalli
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China.,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
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35
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Alexa VQ, Carlos PL, Mirsha QS, Alejandra CA, Ana María SR, Jorge A GV, Margarita O, Jesús-Bonilla Vladimir D, Roxana EF, Luis Jiro SH. Teaching Forensic Entomology, Forensic Anthropology, and Haematology & Serology during the COVID-19 pandemic: Practical activities for distance learning. Sci Justice 2022; 62:721-734. [PMCID: PMC9040468 DOI: 10.1016/j.scijus.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/28/2022] [Accepted: 04/22/2022] [Indexed: 10/25/2022]
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36
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Azcorra H, Dickinson F, Mendez-Dominguez N, Mumm R, Valentín G. Development of birthweight and length for gestational age and sex references in Yucatan, Mexico. Am J Hum Biol 2022; 34:e23732. [PMID: 35179265 PMCID: PMC9285606 DOI: 10.1002/ajhb.23732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVE To develop sex- and gestational age specific reference percentiles and curves for birth weight and length for Yucatec neonates using data from birth registers of infants born during 2015-2019. MATERIAL AND METHODS Observational, descriptive, epidemiologic study in a 5-year period including every registered birth in the state of Yucatan, Mexico using birth registries. A total of 158 432 live, physically healthy singletons (76 442 females and 81 990 males) between 25 and 42 weeks of gestation were included in the analysis. We used the LMS method to construct smoothed reference centiles (3rd, 10th, 25th, 50th, 75th, 95th, and 97th) and curves for males and females separately. RESULTS Mean maternal age was 26 (SD = 6.22) years. Fifty-two percent of births occurred by vaginal delivery, 37% were firstborn and similar proportions were second (33%) and third or more (30%) born. 5.5% of newborns included in the references corresponds to neonates born before 37 weeks of gestation (5.9% boys and 5.1% girls). In both sexes, the percentage of infants with a birthweight less than 2500 g was 6.7%. The birthweight at the 50th percentile for males and females at 40 weeks of gestation in this cohort was 3256 and 3167 g, respectively, and the corresponding values for birth length were 50.23 and 49.84 cm (mean differences between sexes: 89 g and 0.40 cm, respectively). CONCLUSION The reference percentile and curves developed in this study are useful for research purposes and can help health practitioners to assess the biological status of infants born in Yucatán.
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Affiliation(s)
- Hugo Azcorra
- Centro de Investigaciones Silvio Zavala, Universidad Modelo, Mérida, Yucatán, Mexico
| | | | - Nina Mendez-Dominguez
- Hospital Regional de Alta Especialidad de la Península de Yucatán, Mérida, Yucatán, Mexico
| | - Rebekka Mumm
- Department of Human Biology, University of Potsdam, Germany
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37
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Jiménez-Kaufmann A, Chong AY, Cortés A, Quinto-Cortés CD, Fernandez-Valverde SL, Ferreyra-Reyes L, Cruz-Hervert LP, Medina-Muñoz SG, Sohail M, Palma-Martinez MJ, Delgado-Sánchez G, Mongua-Rodríguez N, Mentzer AJ, Hill AVS, Moreno-Macías H, Huerta-Chagoya A, Aguilar-Salinas CA, Torres M, Kim HL, Kalsi N, Schuster SC, Tusié-Luna T, Del-Vecchyo DO, García-García L, Moreno-Estrada A. Imputation Performance in Latin American Populations: Improving Rare Variants Representation With the Inclusion of Native American Genomes. Front Genet 2022; 12:719791. [PMID: 35046991 PMCID: PMC8762266 DOI: 10.3389/fgene.2021.719791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Current Genome-Wide Association Studies (GWAS) rely on genotype imputation to increase statistical power, improve fine-mapping of association signals, and facilitate meta-analyses. Due to the complex demographic history of Latin America and the lack of balanced representation of Native American genomes in current imputation panels, the discovery of locally relevant disease variants is likely to be missed, limiting the scope and impact of biomedical research in these populations. Therefore, the necessity of better diversity representation in genomic databases is a scientific imperative. Here, we expand the 1,000 Genomes reference panel (1KGP) with 134 Native American genomes (1KGP + NAT) to assess imputation performance in Latin American individuals of mixed ancestry. Our panel increased the number of SNPs above the GWAS quality threshold, thus improving statistical power for association studies in the region. It also increased imputation accuracy, particularly in low-frequency variants segregating in Native American ancestry tracts. The improvement is subtle but consistent across countries and proportional to the number of genomes added from local source populations. To project the potential improvement with a higher number of reference genomes, we performed simulations and found that at least 3,000 Native American genomes are needed to equal the imputation performance of variants in European ancestry tracts. This reflects the concerning imbalance of diversity in current references and highlights the contribution of our work to reducing it while complementing efforts to improve global equity in genomic research.
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Affiliation(s)
- Andrés Jiménez-Kaufmann
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | - Amanda Y Chong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Adrián Cortés
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Consuelo D Quinto-Cortés
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | - Selene L Fernandez-Valverde
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | | | | | - Santiago G Medina-Muñoz
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | - Mashaal Sohail
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico.,Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - María J Palma-Martinez
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | | | | | - Alexander J Mentzer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.,Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Hortensia Moreno-Macías
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Mexico City, Mexico.,Departamento de Economía, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Alicia Huerta-Chagoya
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Mexico City, Mexico
| | - Carlos A Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Unidad de Investigación de Enfermedades Metabólicas, Mexico City, Mexico.,Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Michael Torres
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | - Hie Lim Kim
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.,GenomeAsia 100K (GA100K) Consortium, Singapore.,School of Biological Science, Nanyang Technological University, Singapore
| | - Namrata Kalsi
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.,GenomeAsia 100K (GA100K) Consortium, Singapore
| | - Stephan C Schuster
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.,GenomeAsia 100K (GA100K) Consortium, Singapore.,School of Biological Science, Nanyang Technological University, Singapore
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas de la UNAM, Mexico City, Mexico
| | - Diego Ortega Del-Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), UNAM, Juriquilla, Mexico
| | | | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
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Gómez R, Tapia-Guerrero YS, Cisneros B, Orozco L, Cerecedo-Zapata C, Mendoza-Caamal E, Leyva-Gómez G, Leyva-García N, Velázquez-Pérez L, Magaña JJ. Genetic Distribution of Five Spinocerebellar Ataxia Microsatellite Loci in Mexican Native American Populations and Its Impact on Contemporary Mestizo Populations. Genes (Basel) 2022; 13:genes13010157. [PMID: 35052497 PMCID: PMC8775409 DOI: 10.3390/genes13010157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/04/2022] [Accepted: 01/13/2022] [Indexed: 12/17/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) conform a heterogeneous group of neurodegenerative disorders with autosomal dominant inheritance. Five of the most frequent SCAs are caused by a CAG repeat expansion in the exons of specific genes. The SCAs incidence and the distribution of polymorphic CAG alleles vary among populations and ethnicities. Thus, characterization of the genetic architecture of ethnically diverse populations, which have undergone recent admixture and demographic events, could facilitate the identification of genetic risk factors. Owing to the great ethnic diversity of the Mexican population, this study aimed to analyze the allele frequencies of five SCA microsatellite loci (SCA1, SCA2, SCA3, SCA6, and SCA7) in eleven Mexican Native American (MNA) populations. Data from the literature were used to compare the allelic distribution of SCA loci with worldwide populations. The SCA loci allelic frequencies evidenced a certain genetic homogeneity in the MNA populations, except for Mayans, who exhibited distinctive genetic profiles. Neither pathological nor large normal alleles were found in MNA populations, except for the SCA2 pre-mutated allele in the Zapotec population. Collectively, our findings demonstrated the contribution of the MNA ancestry in shaping the genetic structure of contemporary Mexican Mestizo populations. Our results also suggest that Native American ancestry has no impact on the origin of SCAs in the Mexican population. Instead, the acquisition of pathological SCA alleles could be associated with European migration.
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Affiliation(s)
- Rocío Gómez
- Department of Toxicology, CINVESTAV-IPN, Mexico City 07360, Mexico;
| | - Yessica S. Tapia-Guerrero
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
| | - Bulmaro Cisneros
- Department of Genetics and Molecular Biology, CINVESTAV-IPN, Mexico City 07360, Mexico;
| | - Lorena Orozco
- Laboratory of Immunogenomics and Metabolic Diseases, National Genomic Medicine Institute (INMEGEN), Mexico City 14610, Mexico; (L.O.); (E.M.-C.)
| | - César Cerecedo-Zapata
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
- Rehabilitation and Social Inclusion Center of Veracruz (CRIS-DIF), Xalapa, Veracruz 91097, Mexico
| | - Elvia Mendoza-Caamal
- Laboratory of Immunogenomics and Metabolic Diseases, National Genomic Medicine Institute (INMEGEN), Mexico City 14610, Mexico; (L.O.); (E.M.-C.)
| | - Gerardo Leyva-Gómez
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México (UNAM); Mexico City 04510, Mexico;
| | - Norberto Leyva-García
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
| | | | - Jonathan J. Magaña
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
- Department of Bioengineering, School of Engineering and Sciences, Tecnologico de Monterrey, Campus Ciudad de México (ITESM-CCM), Mexico City 14380, Mexico
- Correspondence: ; Tel.: +52-(55)-5999-1000 (ext. 14708)
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Armenta-medina D, Díaz de León Castañeda C, Armenta-medina A, Perez-rueda E. A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics. Biology 2022; 11:131. [PMID: 35053129 PMCID: PMC8772911 DOI: 10.3390/biology11010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 11/17/2022]
Abstract
Bioinformatics is a very important informatics tool for health and biological sciences, focusing on biological data management. The objective of this work was to perform a bibliometric analysis regarding the development of Mexican bioinformatics. An exhaustive revision of the literature associated with Mexican bioinformatics in a period of 25-years was performed. Bibliometric tools, such as performance analysis and science mapping were included in the analysis. We identified the main actors as well as the structure and dynamics of Mexican bioinformatics. Some of the main findings were as follows: the thematic structure in the field is defined by the research lines of outstanding authors; the outstanding collaborations of Mexican institutions with foreign countries and institutions are influenced by the geographic proximity and binational agreements, as well as philanthropic and academic programs that promote collaborations, and there is an inclination for health issues promoted by public health financing and philanthropic organizations. It is identified that publications had an explosion since 2012, we consider that this growth may be influenced by the democratization of data, derived from the mass sequencing of biological molecules stored in public databases.
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Hinojosa CA, Ibanez-rodriguez JF, Serrato-auld RC, Lozano-corona R, Olivares-cruz S, Lecuona-huet NE, Garza-herrera R, Ochoa-armendariz L, Perez-damian V, Gonzalez-fregoso R, Anaya-ayala JE. “Prevalence of Abdominal Aortic Aneurysms in four different metropolitan areas in Mexico”. Ann Vasc Surg 2022. [DOI: 10.1016/j.avsg.2021.12.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/07/2021] [Accepted: 12/29/2021] [Indexed: 11/20/2022]
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41
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Kun Á. Is there still evolution in the human population? Biol Futur 2022; 73:359-374. [PMID: 36592324 PMCID: PMC9806833 DOI: 10.1007/s42977-022-00146-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/08/2022] [Indexed: 01/03/2023]
Abstract
It is often claimed that humanity has stopped evolving because modern medicine erased all selection on survival. Even if that would be true, and it is not, there would be other mechanisms of evolution which could still led to changes in allelic frequencies. Here I show, by applying basic evolutionary genetics knowledge, that we expect humanity to evolve. The results from genome sequencing projects have repeatedly affirmed that there are still recent signs of selection in our genomes. I give some examples of such adaptation. Then I briefly discuss what our evolutionary future has in store for us.
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Affiliation(s)
- Ádám Kun
- grid.5591.80000 0001 2294 6276Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary ,Parmenides Center for the Conceptual Foundations of Science, Pöcking, Germany ,grid.481817.3Institute of Evolution, Centre for Ecological Research, Budapest, Hungary ,grid.5018.c0000 0001 2149 4407MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary ,grid.5018.c0000 0001 2149 4407MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary
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Costa-Urrutia P, Colistro V, Franco-Trecu V, Granados J, Álvarez Fariña R, Rodríguez-Arellano ME. Dyslipidemia, Obesity, and Ethnicity in Mexican Children. Int J Environ Res Public Health 2021; 18:ijerph182312659. [PMID: 34886385 PMCID: PMC8656470 DOI: 10.3390/ijerph182312659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022]
Abstract
The aim of this study was to assess lipid disorders in children from five ethnic groups, both urban and indigenous, from northern and central Mexico. We measured the lipid profile to determine the ability of the body mass index (BMI) to discriminate an abnormally high lipid level using receiving operating characteristics (ROC). We analyzed the association and interaction of obesity and ethnicity with lipid disorders using generalized linear models in 977 children. The highest prevalence of lipid disorders (high TG, high TC, high LDL, high APOB, and dyslipidemia) was found in central Mexico-Mexico City and urban northern Mexico. The BMI performed better at predicting low HDL in Seris, a northern indigenous group (0.95, CI: 0.69–0.85), and Mexico City (0.75, CI: 0.69–0.82), and high LDL in Puebla (central Mexico, 0.80, CI: 0.69–0.85). Obesity significantly (p < 0.05) increases lipid disorders by around two times (OR~2) for almost all lipid markers. Obesity and ethnic interaction increase the lipid disorders by more than five times for different lipid markers and ethnic groups (high total cholesterol OR = 5.31; low HDL OR = 5.11, and dyslipidemia OR = 5.68). Lipid disorders are not restricted to children with high BMIs, but obesity exacerbates these. The emerging lipid disorder risk depends on the ethnic group.
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Affiliation(s)
- Paula Costa-Urrutia
- Laboratorio de Medicina Genómica del Hospital Regional Lic. Adolfo López Mateos, ISSSTE, Ciudad de México 01030, Mexico
- Correspondence: (P.C.-U.); (M.E.R.-A.)
| | - Valentina Colistro
- Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Avda, General Flores 2125, Montevideo 11800, Uruguay;
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay;
| | - Julio Granados
- Departamento de Trasplantes, División de Inmunogenética, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avda, Vasco de Quiroga, Ciudad de México 14080, Mexico;
| | - Rafael Álvarez Fariña
- Ciencias del Deporte, Universidad Anáhuac, Av. Universidad Anáhuac 46, Col. Lomas Anáhuac, Huixquilucan, Naucalpan de Juárez 52786, Mexico;
| | - Martha Eunice Rodríguez-Arellano
- Laboratorio de Medicina Genómica del Hospital Regional Lic. Adolfo López Mateos, ISSSTE, Ciudad de México 01030, Mexico
- Correspondence: (P.C.-U.); (M.E.R.-A.)
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Camarena B, Atkinson EG, Baker M, Becerra-Palars C, Chibnik LB, Escamilla-Orozco R, Jiménez-Pavón J, Koenig Z, Márquez-Luna C, Martin AR, Morales-Cedillo IP, Olivares AM, Ortega-Ortiz H, Rodriguez-Ramírez AM, Saracco-Alvarez R, Basaldua RE, Sena BF, Koenen KC. Neuropsychiatric Genetics of Psychosis in the Mexican Population: A Genome-Wide Association Study Protocol for Schizophrenia, Schizoaffective, and Bipolar Disorder Patients and Controls. Complex Psychiatry 2021; 7:60-70. [PMID: 36017067 PMCID: PMC8740081 DOI: 10.1159/000518926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/03/2021] [Indexed: 11/12/2023] Open
Abstract
No large-scale genome-wide association studies (GWASs) of psychosis have been conducted in Mexico or Latin America to date. Schizophrenia and bipolar disorder in particular have been found to be highly heritable and genetically influenced. However, understanding of the biological basis of psychosis in Latin American populations is limited as previous genomic studies have almost exclusively relied on participants of Northern European ancestry. With the goal of expanding knowledge on the genomic basis of psychotic disorders within the Mexican population, the National Institute of Psychiatry Ramón de la Fuente Muñiz (INPRFM), the Harvard T.H. Chan School of Public Health, and the Broad Institute's Stanley Center for Psychiatric Research launched the Neuropsychiatric Genetics Research of Psychosis in Mexican Populations (NeuroMex) project to collect and analyze case-control psychosis samples from 5 states across Mexico. This article describes the planned sample collection and GWAS protocol for the NeuroMex study. The 4-year study will span from April 2018 to 2022 and aims to recruit 9,208 participants: 4,604 cases and 4,604 controls. Study sites across Mexico were selected to ensure collected samples capture the genomic diversity within the Mexican population. Blood samples and phenotypic data will be collected during the participant interview process and will contribute to the development of a local biobank in Mexico. DNA extraction will be done locally and genetic analysis will take place at the Broad Institute in Cambridge, MA. We will collect extensive phenotypic information using several clinical scales. All study materials including phenotypic instruments utilized are openly available in Spanish and English. The described study represents a long-term collaboration of a number of institutions from across Mexico and the Boston area, including clinical psychiatrists, clinical researchers, computational biologists, and managers at the 3 collaborating institutions. The development of relevant data management, quality assurance, and analysis plans are the primary considerations in this protocol article. Extensive management and analysis processes were developed for both the phenotypic and genetic data collected. Capacity building, partnerships, and training between and among the collaborating institutions are intrinsic components to this study and its long-term success.
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Affiliation(s)
- Beatriz Camarena
- Pharmacogenetics Department, National Institute of Psychiatry Ramón de la Fuente Muñiz, Mexico City, Mexico
| | - Elizabeth G. Atkinson
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Analytical and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Mark Baker
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
| | - Claudia Becerra-Palars
- National Institute of Psychiatry Ramón de la Fuente Muñiz, Clinical Services Direction, Mexico City, Mexico
| | - Lori B. Chibnik
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Analytical and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Raúl Escamilla-Orozco
- National Institute of Psychiatry Ramón de la Fuente Muñiz, Clinical Services Direction, Mexico City, Mexico
| | - Joanna Jiménez-Pavón
- National Institute of Psychiatry Ramón de la Fuente Muñiz, Clinical Services Direction, Mexico City, Mexico
| | - Zan Koenig
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Carla Márquez-Luna
- Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alicia R. Martin
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Analytical and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Ana Maria Olivares
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
| | - Hiram Ortega-Ortiz
- National Institute of Psychiatry Ramón de la Fuente Muñiz, Clinical Services Direction, Mexico City, Mexico
| | | | - Ricardo Saracco-Alvarez
- National Institute of Psychiatry Ramon de la Fuente Muñiz, Clinical Research Sub-direction, Mexico City, Mexico
| | - Rebecca E. Basaldua
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Brena F. Sena
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Karestan C. Koenen
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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Favela-Mendoza AF, Rodríguez-Rodríguez BG, Rojas-Prado E, Chávez-Arreguin M, Aguilar-Velázquez JA, Martínez-Cortés G, Rangel-Villalobos H. Prevalence of protective haplotypes of the SLCO1B1 gene for statin transport in Mexican populations. Per Med 2021; 18:533-540. [PMID: 34674552 DOI: 10.2217/pme-2020-0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To evaluate the genetic distribution of the rs4149056 and rs2306283 variants in the SLCO1B1 gene in Mexican Mestizo (admixed) and Native American groups. Materials & methods: We recruited 360 volunteers who were qPCR-genotyped with TaqMan probes. Results: Allele and genotype frequencies are reported. Among the expected rs4149056-rs2306283 haplotypes, T-A (42.35-58.47%) was the most prevalent which relates to the normal activity of the OATP1B1 transporter. This was followed by the T-G haplotype associated with further statin transport and cholesterol reduction (32.49-43.76%). Conclusion: Based on these SLCO1B1 gene variants, we confirmed that a minimum fraction of the Mexican study populations would be at risk from decreasing simvastatin transport and the development of statin-induced myopathy.
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Affiliation(s)
- Alma Faviola Favela-Mendoza
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Brenda Guadalupe Rodríguez-Rodríguez
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Eduardo Rojas-Prado
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Mariana Chávez-Arreguin
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - José Alonso Aguilar-Velázquez
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Gabriela Martínez-Cortés
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
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Pakstis AJ, Gandotra N, Speed WC, Murtha M, Scharfe C, Kidd KK. The population genetics characteristics of a 90 locus panel of microhaplotypes. Hum Genet 2021; 140:1753-1773. [PMID: 34643790 PMCID: PMC8553733 DOI: 10.1007/s00439-021-02382-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) and small genomic regions with multiple SNPs (microhaplotypes, MHs) are rapidly emerging as novel forensic investigative tools to assist in individual identification, kinship analyses, ancestry inference, and deconvolution of DNA mixtures. Here, we analyzed information for 90 microhaplotype loci in 4009 individuals from 79 world populations in 6 major biogeographic regions. The study included multiplex microhaplotype sequencing (mMHseq) data analyzed for 524 individuals from 16 populations and genotype data for 3485 individuals from 63 populations curated from public repositories. Analyses of the 79 populations revealed excellent characteristics for this 90-plex MH panel for various forensic applications achieving an overall average effective number of allele values (Ae) of 4.55 (range 1.04–19.27) for individualization and mixture deconvolution. Population-specific random match probabilities ranged from a low of 10–115 to a maximum of 10–66. Mean informativeness (In) for ancestry inference was 0.355 (range 0.117–0.883). 65 novel SNPs were detected in 39 of the MHs using mMHseq. Of the 3018 different microhaplotype alleles identified, 1337 occurred at frequencies > 5% in at least one of the populations studied. The 90-plex MH panel enables effective differentiation of population groupings for major biogeographic regions as well as delineation of distinct subgroupings within regions. Open-source, web-based software is available to support validation of this technology for forensic case work analysis and to tailor MH analysis for specific geographical regions.
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Affiliation(s)
- Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Neeru Gandotra
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Michael Murtha
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Curt Scharfe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA.
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Nagar SD, Conley AB, Chande AT, Rishishwar L, Sharma S, Mariño-Ramírez L, Aguinaga-Romero G, González-Andrade F, Jordan IK. Genetic ancestry and ethnic identity in Ecuador. HGG Adv 2021; 2:100050. [PMID: 35047841 PMCID: PMC8756502 DOI: 10.1016/j.xhgg.2021.100050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 08/09/2021] [Indexed: 02/05/2023] Open
Abstract
We investigated the ancestral origins of four Ecuadorian ethnic groups-Afro-Ecuadorian, Mestizo, Montubio, and the Indigenous Tsáchila-in an effort to gain insight on the relationship between ancestry, culture, and the formation of ethnic identities in Latin America. The observed patterns of genetic ancestry are largely concordant with ethnic identities and historical records of conquest and colonization in Ecuador. Nevertheless, a number of exceptional findings highlight the complex relationship between genetic ancestry and ethnicity in Ecuador. Afro-Ecuadorians show far less African ancestry, and the highest levels of Native American ancestry, seen for any Afro-descendant population in the Americas. Mestizos in Ecuador show high levels of Native American ancestry, with substantially less European ancestry, despite the relatively low Indigenous population in the country. The recently recognized Montubio ethnic group is highly admixed, with substantial contributions from all three continental ancestries. The Tsáchila show two distinct ancestry subgroups, with most individuals showing almost exclusively Native American ancestry and a smaller group showing a Mestizo characteristic pattern. Considered together with historical data and sociological studies, our results indicate the extent to which ancestry and culture interact, often in unexpected ways, to shape ethnic identity in Ecuador.
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Affiliation(s)
- Shashwat Deepali Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Andrew B Conley
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA.,National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lavanya Rishishwar
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA.,National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Shivam Sharma
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Leonardo Mariño-Ramírez
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | | | | | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, USA
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García-Ortiz H, Barajas-Olmos F, Contreras-Cubas C, Cid-Soto MÁ, Córdova EJ, Centeno-Cruz F, Mendoza-Caamal E, Cicerón-Arellano I, Flores-Huacuja M, Baca P, Bolnick DA, Snow M, Flores-Martínez SE, Ortiz-Lopez R, Reynolds AW, Blanchet A, Morales-Marín M, Velázquez-Cruz R, Kostic AD, Galaviz-Hernández C, García-Zapién AG, Jiménez-López JC, León-Reyes G, Salas-Bautista EG, Lazalde-Ramos BP, Jiménez-Ruíz JL, Salas-Martínez G, Ramos-Madrigal J, Mirzaeicheshmeh E, Saldaña-Alvarez Y, Del Carmen Abrahantes-Pérez M, Loeza-Becerra F, Mojica-Espinosa R, Sánchez-Quinto F, Rangel-Villalobos H, Sosa-Macías M, Sánchez-Corona J, Rojas-Martinez A, Martínez-Hernández A, Orozco L. The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas. Nat Commun 2021; 12:5942. [PMID: 34642312 DOI: 10.1038/s41467-021-26188-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/22/2021] [Indexed: 12/30/2022] Open
Abstract
The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15-30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4-9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.
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Fricke-Galindo I, Jung-Cook H, Martínez-Juárez IE, Monroy-Jaramillo N, Ortega-Vázquez A, Rojas-Tomé IS, Dorado P, Peñas-Lledó E, Llerena A, López-López M. Relevance of NR1I2 variants on carbamazepine therapy in Mexican Mestizos with epilepsy at a tertiary-care hospital. Pharmacogenomics 2021; 22:983-996. [PMID: 34612084 DOI: 10.2217/pgs-2021-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We evaluated the potential influence of genetic (CYP3A5, EPHX1, NR1I2, HNF4A, ABCC2, RALBP1, SCN1A, SCN2A and GABRA1) and nongenetic factors on carbamazepine (CBZ) response, adverse drug reactions and CBZ plasma concentrations in 126 Mexican Mestizos (MM) with epilepsy. Subjects & methods: Patients were genotyped for 27 variants using TaqMan® assays. Results: CBZ response was associated with NR1I2 variants and lamotrigine cotreatment. CBZ-induced adverse drug reactions were related to antiepileptic polytherapy and SCN1A rs2298771/rs3812718 haplotype. CBZ plasma concentrations were influenced by NR1I2-rs2276707 and -rs3814058, and by phenytoin cotreatment. CBZ daily dose was also influenced by NR1I2-rs3814055 and EPHX1-rs1051740. Conclusion: Interindividual variability in CBZ treatment was partly explained by NR1I2, EPHX1 and SCN1A variants, as well as antiepileptic cotreatment in MM with epilepsy.
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Affiliation(s)
- Ingrid Fricke-Galindo
- Metropolitan Autonomous University, Campus Xochimilco, Calzada del Hueso 1100, Villa Quietud, 04960, Coyoacán, Mexico City, Mexico
| | - Helgi Jung-Cook
- National Institute of Neurology & Neurosurgery, Manuel Velasco Suárez, Insurgentes Sur 3877, La Fama, 14269, Tlalpan, Mexico City, Mexico.,National Autonomous University of Mexico, Mexico City, Mexico, Av. Universidad 3000, C.U., 04510, Coyoacán, Mexico City, Mexico
| | - Iris E Martínez-Juárez
- National Institute of Neurology & Neurosurgery, Manuel Velasco Suárez, Insurgentes Sur 3877, La Fama, 14269, Tlalpan, Mexico City, Mexico
| | - Nancy Monroy-Jaramillo
- National Institute of Neurology & Neurosurgery, Manuel Velasco Suárez, Insurgentes Sur 3877, La Fama, 14269, Tlalpan, Mexico City, Mexico
| | - Alberto Ortega-Vázquez
- Metropolitan Autonomous University, Campus Xochimilco, Calzada del Hueso 1100, Villa Quietud, 04960, Coyoacán, Mexico City, Mexico
| | - Irma S Rojas-Tomé
- National Institute of Neurology & Neurosurgery, Manuel Velasco Suárez, Insurgentes Sur 3877, La Fama, 14269, Tlalpan, Mexico City, Mexico
| | - Pedro Dorado
- Biosanitary Research Institute, INUBE Extremadura University, Avda. de Elvas, Badajoz, 06006, Spain.,Department of Medical-Surgery Therapeutics, University of Extremadura, Avda. Virgen del Puerto, Plasencia, 10600, Spain
| | - Eva Peñas-Lledó
- Biosanitary Research Institute, INUBE Extremadura University, Avda. de Elvas, Badajoz, 06006, Spain.,Faculty of Medicine, University of Extremadura, Av. de Elvas, s/n, Badajoz, 06006, Spain
| | - Adrián Llerena
- Biosanitary Research Institute, INUBE Extremadura University, Avda. de Elvas, Badajoz, 06006, Spain.,Faculty of Medicine, University of Extremadura, Av. de Elvas, s/n, Badajoz, 06006, Spain.,CICAB Clinical Research Center, Extremadura University Hospital, Campus Universitario, Av. de Elvas, s/n, Badajoz, 06080, Spain
| | - Marisol López-López
- Metropolitan Autonomous University, Campus Xochimilco, Calzada del Hueso 1100, Villa Quietud, 04960, Coyoacán, Mexico City, Mexico
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Silva-Ramirez B, Macías-González EJ, Frausto-Valdes OS, Calao-Pérez MB, Ibarra-Pérez DI, Torres-García JE, Aragón-Tovar AR, Peñuelas-Urquides K, González-Escalante LA, Bermúdez de León M. Association between genetic variations at 8q24 and prostate cancer risk in Mexican Men. Prostate Cancer Prostatic Dis 2021. [PMID: 34599275 DOI: 10.1038/s41391-021-00461-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/10/2021] [Accepted: 09/20/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND Variants of 8q24 locus have been associated with prostate cancer (PCa) susceptibility. This study aims to analyze the genetic basis of PCa susceptibility in Mexican men by analyzing SNPs in the 8q24 locus for the first time. METHODS A case-control study was performed in 875 men recruited from the Mexican Social Security Institute, 326 patients with PCa, and 549 non-PCa patients (88 with benign prostatic hyperplasia BPH and 461 healthy controls). The 8q24 locus SNPs: rs16901979, rs16983267, rs1447295, and rs7837328 were genotyped by allelic discrimination assays using TaqMan probes. Statistical analysis was performed using Epi Info statistical 7.0 and SNPstats softwares. RESULTS All genotype frequencies were in Hardy-Weinberg Equilibrium. No differences were observed in genotype distribution between PCa and non-PCa patients for rs6983267. Under different inheritance models, the rs16901979, rs1447295, and rs7837328 SNPs were associated with PCa (OR = 2.8, 1.8, and 1.72, respectively; Pc < 0.001) when comparing PCa patients against controls. This association remains between PCa and BPH patients under different models (OR = 8.5, 2.2, and 1.9, respectively; Pc < 0.001). There were no significant differences in allele and genotype distribution among BPH patients and controls. The combined effect of the alleles CGAA for the SNPs rs16901979, rs6983267, rs1447295, and rs7837328 showed significant differences between PCa patients and controls (OR = 2.9, 95% CI = 1.48-5.83, Pc = 0.008). Four 8q24 variants were not associated with D'Amico score, age at diagnosis, and bone metastases. CONCLUSIONS Our study provides the first confirmation that variants rs16901979, rs1447295, and 7837328 at 8q24 locus are associated with PCa susceptibility in Mexican men.
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