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Angelim CC, Martins LD, Andrade ÁAF, Moreira FC, Guerreiro JF, de Assumpção PP, dos Santos SEB, Costa GDLC. Variants of IFNL4 Gene in Amazonian and Northern Brazilian Populations. Genes (Basel) 2023; 14:2075. [PMID: 38003018 PMCID: PMC10671175 DOI: 10.3390/genes14112075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Since the discovery of the polymorphic nature of the IFNL4 gene, its variants have been investigated and associated with several viral diseases, with an emphasis on hepatitis C. However, the impacts of these variants on mixed-race and native populations in the northern region of Brazil are scarce. We investigated three variants of the IFNL4 gene in populations from this location, which were among the 14 most frequent variants in worldwide populations, and compared the frequencies obtained to populational data from the 1000 Genomes Project, gnomAD and ABraOM databases. Our results demonstrate that mixed-race and native populations from the northern region of Brazil present frequencies like those of European and Asian groups for the rs74597329 and rs11322783 variants, and like all populations presented for the rs4803221 variant. These data reinforce the role of world populations in shaping the genetic profile of Brazilian populations, indicate patterns of illness according to the expressed genotype, and infer an individual predisposition to certain diseases.
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Affiliation(s)
- Carolina Cabral Angelim
- Programa de Pós-Graduação em Agentes Infecciosos e Parasitários, Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, PA, Brazil; (C.C.A.); (L.D.M.); (Á.A.F.A.); (S.E.B.d.S.)
| | - Letícia Dias Martins
- Programa de Pós-Graduação em Agentes Infecciosos e Parasitários, Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, PA, Brazil; (C.C.A.); (L.D.M.); (Á.A.F.A.); (S.E.B.d.S.)
- Programa de Pós-Graduação em Virologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
| | - Álesson Adam Fonseca Andrade
- Programa de Pós-Graduação em Agentes Infecciosos e Parasitários, Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, PA, Brazil; (C.C.A.); (L.D.M.); (Á.A.F.A.); (S.E.B.d.S.)
| | - Fabiano Cordeiro Moreira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, PA, Brazil; (F.C.M.); (J.F.G.)
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, PA, Brazil;
| | - João Farias Guerreiro
- Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, PA, Brazil; (F.C.M.); (J.F.G.)
| | | | - Sidney Emanuel Batista dos Santos
- Programa de Pós-Graduação em Agentes Infecciosos e Parasitários, Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, PA, Brazil; (C.C.A.); (L.D.M.); (Á.A.F.A.); (S.E.B.d.S.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, PA, Brazil; (F.C.M.); (J.F.G.)
| | - Greice de Lemos Cardoso Costa
- Programa de Pós-Graduação em Agentes Infecciosos e Parasitários, Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, PA, Brazil; (C.C.A.); (L.D.M.); (Á.A.F.A.); (S.E.B.d.S.)
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Cohen-Paes ADN, de Carvalho DC, Pastana LF, Dobbin EAF, Moreira FC, de Souza TP, Fernandes MR, Leal DFDVB, de Sá RBA, de Alcântara AL, Guerreiro JF, Ribeiro-dos-Santos Â, dos Santos SEB, de Assumpção PP, dos Santos NPC. Characterization of PCLO Gene in Amazonian Native American Populations. Genes (Basel) 2022; 13:genes13030499. [PMID: 35328053 PMCID: PMC8950494 DOI: 10.3390/genes13030499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic variations in PCLO have been associated with different pathologies in global literature, but there are no data regarding this gene in Native American populations. The Amazonian Native American populations have lower genetic diversity and are more different from other continental groups. We investigated 18 genetic variants in the PCLO gene in Amazonian indigenous and compared our results with the ones found in global populations, which were publicly available in the 1000 Genomes Project, gnmAD and ABraOM databases. The results demonstrated that the variants of the PCLO, especially rs17156844, rs550369696, rs61741659 and rs2877, have a significantly higher frequency in Amerindian populations in comparison with other continental populations. These data outline the singular genetic profile of the Native American population from the Brazilian Amazon region.
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Affiliation(s)
- Amanda de Nazaré Cohen-Paes
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Darlen Cardoso de Carvalho
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
| | - Lucas Favacho Pastana
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Elizabeth Ayres Fragoso Dobbin
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Fabiano Cordeiro Moreira
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Tatiane Piedade de Souza
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Marianne Rodrigues Fernandes
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
- Correspondence: ; Tel.: +55-91-99123-4727
| | - Diana Feio da Veiga Borges Leal
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Roberta Borges Andrade de Sá
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Angélica Leite de Alcântara
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Ândrea Ribeiro-dos-Santos
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Sidney Emanuel Batista dos Santos
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Paulo Pimentel de Assumpção
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
| | - Ney Pereira Carneiro dos Santos
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
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A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics. BIOLOGY 2022; 11:biology11010131. [PMID: 35053129 PMCID: PMC8772911 DOI: 10.3390/biology11010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Fernandes MR, Rodrigues JCG, Maroñas O, Latorre-Pellicer A, Cruz R, Guerreiro JF, Burbano RMR, de Assumpção PP, Ribeiro-Dos-Santos A, Dos Santos SEB, Carracedo A, Dos Santos NPC. Genetic Diversity of Drug-Related Genes in Native Americans of the Brazilian Amazon. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:117-133. [PMID: 33519226 PMCID: PMC7837547 DOI: 10.2147/pgpm.s274741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/23/2020] [Indexed: 12/25/2022]
Abstract
Introduction The genetic admixture of the Brazilian population has considerable relevance to the implementation of the principles of pharmacogenomics (PGx), as it may compromise the extrapolation of data obtained in more homogeneous world populations. Purpose This study aims to investigate a panel of 117 polymorphisms in 35 pharmacogenes, which contains label recommendations or clinical evidence by international drug regulatory agencies, in Amazonian Native American populations, and compare the results obtained with continental population data from the 1000 Genomes Project Consortium. Patients and Methods The study population is composed of 109 Native American individuals from three Brazilian Amazon groups. The genotyping of the PGx polymorphisms was performed by allelic discrimination using TaqMan® OpenArray Genotyping with a panel of 120 customized assays on the QuantStudio™ 12K Flex Real-Time PCR System. Results Statistical differences within the Native American populations were observed regarding both genotypes and phenotypes of some genes of the CYP family. The discriminant analysis of principal components (DAPCs) between the NAM group and the continental populations of the 1000 Genomes Project resulted in the clustering of the three Native American populations. Additionally, in general, the NAM group was determined to be closely situated between East Asia, America, and South Asia groups, which enabled us to infer a genetic similarity between these populations. The DAPC analysis further demonstrated that eight polymorphisms and six polymorphisms were more relevant in differentiating the NAM from the continental populations and the NAM populations among themselves, respectively. Conclusion Some investigated polymorphisms show differences among world populations, particularly with populations of European origin, for whom precision medicine protocols are primarily designed. The accumulated knowledge regarding these variations may assist in the design of specific protocols for Native American populations and populations admixed with them.
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Affiliation(s)
- Marianne Rodrigues Fernandes
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil.,Departamento de ensino e pesquisa, Hospital Ophir Loyola, Belém, Pará, Brazil
| | | | - Olalla Maroñas
- Grupo de Medicina Xenómica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, España
| | - Ana Latorre-Pellicer
- Grupo de Medicina Xenómica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, España.,Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología, Escuela de Medicina, Universidad de Zaragoza, IIS-Aragón, E-50009 Zaragoza, España
| | - Raquel Cruz
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Grupo de Medicina Genómica, CIMUS, Universidad de Santiago de Compostela, Santiago de Compostela, España
| | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Rommel Mario Rodriguez Burbano
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil.,Departamento de ensino e pesquisa, Hospital Ophir Loyola, Belém, Pará, Brazil
| | | | - Andrea Ribeiro-Dos-Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil.,Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Sidney Emanuel Batista Dos Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil.,Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Angel Carracedo
- Grupo de Medicina Xenómica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, España.,Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Grupo de Medicina Genómica, CIMUS, Universidad de Santiago de Compostela, Santiago de Compostela, España.,Fundación Pública de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, España
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Bioinformatics in Mexico: A diagnostic from the academic perspective and recommendations for a public policy. PLoS One 2020; 15:e0243531. [PMID: 33320879 PMCID: PMC7737905 DOI: 10.1371/journal.pone.0243531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
In this work, we present a diagnostic analysis of strengths, weaknesses, opportunities and threats (SWOT) of the current state of Bioinformatics in Mexico. We conducted semi-structured interviews among researchers and academics with key expertise in this field, identified by bibliometric analyses and qualitative sampling techniques. Additionally, an online survey was conducted reaching a higher number of respondents. Among the relevant findings of our study, the lack of specialized human resources and technological infrastructure stood out, along with deficiencies in the number and quality of academic programs, scarce public investment and a weak relationship between public and private institutions. However, there are great opportunities for developing a national Bioinformatics to support different economic sectors. In our opinion, this work could be useful to favor a comprehensive network among Mexican researchers, in order to lay the foundations of a national strategy towards a well designed public policy.
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Martínez-Magaña JJ, Genis-Mendoza AD, Villatoro Velázquez JA, Camarena B, Martín Del Campo Sanchez R, Fleiz Bautista C, Bustos Gamiño M, Reséndiz E, Aguilar A, Medina-Mora ME, Nicolini H. The Identification of Admixture Patterns Could Refine Pharmacogenetic Counseling: Analysis of a Population-Based Sample in Mexico. Front Pharmacol 2020; 11:324. [PMID: 32390825 PMCID: PMC7188951 DOI: 10.3389/fphar.2020.00324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
Pharmacogenetic analysis has generated translational data that could be applied to guide treatments according to individual genetic variations. However, pharmacogenetic counseling in some mestizo (admixed) populations may require tailoring to different patterns of admixture. The identification and clustering of individuals with related admixture patterns in such populations could help to refine the practice of pharmacogenetic counseling. This study identifies related groups in a highly admixed population-based sample from Mexico, and analyzes the differential distribution of actionable pharmacogenetic variants. A subsample of 1728 individuals from the Mexican Genomic Database for Addiction Research (MxGDAR/Encodat) was analyzed. Genotyping was performed with the commercial PsychArray BeadChip, genome-wide ancestry was estimated using EIGENSOFT, and model-based clustering was applied to defined admixture groups. Actionable pharmacogenetic variants were identified with a query to the Pharmacogenomics Knowledge Base (PharmGKB) database, and functional prediction using the Variant Effect Predictor (VEP). Allele frequencies were compared with chi-square tests and differentiation was estimated by FST. Seven admixture groups were identified in Mexico. Some, like Group 1, Group 4, and Group 5, were found exclusively in certain geographic areas. More than 90% of the individuals, in some groups (Group 1, Group 4 and Group 5) were found in the Central-East and Southeast region of the country. MTRR p.I49M, ABCG2 p.Q141K, CHRNA5 p.D398N, SLCO2B1 rs2851069 show a low degree of differentiation between admixture groups. ANKK1 p.G318R and p.H90R, had the lowest allele frequency of Group 1. The reduction in these alleles reduces the risk of toxicity from anticancer and antihypercholesterolemic drugs. Our analysis identified different admixture patterns and described how they could be used to refine the practice of pharmacogenetic counseling for this admixed population.
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Affiliation(s)
- José Jaime Martínez-Magaña
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Alma Delia Genis-Mendoza
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.,Hospital Psiquiátrico Infantil "Juan N. Navarro," Servicios de Atención Psiquiátrica, Mexico City, Mexico
| | - Jorge Ameth Villatoro Velázquez
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM).,Global Studies Seminar, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Beatriz Camarena
- Laboratorio de Farmacogenética, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM), Mexico City, Mexico
| | - Raul Martín Del Campo Sanchez
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM).,Global Studies Seminar, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Clara Fleiz Bautista
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM).,Global Studies Seminar, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Marycarmen Bustos Gamiño
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM)
| | - Esbehidy Reséndiz
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM)
| | - Alejandro Aguilar
- Laboratorio de Farmacogenética, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM), Mexico City, Mexico
| | - María Elena Medina-Mora
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM).,Global Studies Seminar, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Humberto Nicolini
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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Gonzalez-Covarrubias V, Morales-Franco M, Cruz-Correa OF, Martínez-Hernández A, García-Ortíz H, Barajas-Olmos F, Genis-Mendoza AD, Martínez-Magaña JJ, Nicolini H, Orozco L, Soberón X. Variation in Actionable Pharmacogenetic Markers in Natives and Mestizos From Mexico. Front Pharmacol 2019; 10:1169. [PMID: 31649539 PMCID: PMC6796793 DOI: 10.3389/fphar.2019.01169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022] Open
Abstract
The identification and characterization of pharmacogenetic variants in Latin American populations is still an ongoing endeavor. Here, we investigated SNVs on genes listed by the Pharmacogenomics Knowledge Base in 1284 Mestizos and 94 Natives from Mexico. Five institutional cohorts with NGS data were retrieved from different research projects at INMEGEN, sequencing files were filtered for 55 pharmacogenes present in all cohorts to identify novel and known variation. Bioinformatic tools VEP, PROVEAN, and FATHMM were used to assess, in silico, the functional impact of this variation. Next, we focused on 17 genes with actionable variants that have been clinically implemented. Allele frequencies were compared with major continental groups and differences discussed in the scope of a pharmacogenomic impact. We observed a wide genetic variability for known and novel SNVs, the largest variation was on UGT1A > ACE > COMT > ABCB1 and the lowest on APOE and NAT2. Although with allele frequencies around 1%, novel variation was observed in 16 of 17 PGKB genes. In Natives we identified 59 variants and 58 in Mestizos. Several genes did not show novel variation, on CYP2B6, CYP2D6, and CYP3A4 in Natives; and APOE, UGT1A, and VKORC1 in Mestizos. Similarities in allele frequency, comparing major continental groups for VIP pharmacogenes, hint towards a comparable PGx for drugs metabolized by UGT1A1, DPYD, ABCB1, CBR3, COMT, and TPMT; in contrast to variants on CYP3A5 and CYP2B6 for which significant MAF differences were identified. Our observations offer some discernment into the extent of pharmacogenetic variation registered up-to-date in Mexicans and contribute to quantitatively dissect actionable pharmacogenetic variants in Natives and Mestizos.
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Affiliation(s)
| | | | | | | | - Humberto García-Ortíz
- Immunogenomics and Metabolic Diseases Laboratory, INMEGEN, CDMX, Mexico City, Mexico
| | | | | | | | - Humberto Nicolini
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, INMEGEN, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, INMEGEN, CDMX, Mexico City, Mexico
| | - Xavier Soberón
- Pharmacogenomics Laboratory, INMEGEN, CDMX, Mexico City, Mexico
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Gonzalez-Covarrubias V, Martínez-Magaña JJ, Coronado-Sosa R, Villegas-Torres B, Genis-Mendoza AD, Canales-Herrerias P, Nicolini H, Soberón X. Exploring Variation in Known Pharmacogenetic Variants and its Association with Drug Response in Different Mexican Populations. Pharm Res 2016; 33:2644-52. [DOI: 10.1007/s11095-016-1990-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/28/2016] [Indexed: 02/06/2023]
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Marsh S, King CR, Van Booven DJ, Revollo JY, Gilman RH, McLeod HL. Pharmacogenomic assessment of Mexican and Peruvian populations. Pharmacogenomics 2016; 16:441-8. [PMID: 25916516 DOI: 10.2217/pgs.15.10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Clinically relevant polymorphisms often demonstrate population-specific allele frequencies. Central and South America remain largely uncategorized in the context of pharmacogenomics. MATERIALS & METHODS We assessed 15 polymorphisms from 12 genes (ABCB1 3435C>T, ABCG2 Q141K, CYP1B1*3, CYP2C19*2, CYP3A4*1B, CYP3A5*3C, ERCC1 N118N, ERCC2 K751Q, GSTP1 I105V, TPMT 238G>C, TPMT 460G>A, TPMT 719A>G, TYMS TSER, UGT1A1*28 and UGT1A1 -3156G>A) in 81 Peruvian and 95 Mexican individuals. RESULTS Six polymorphism frequencies differed significantly between the two populations: ABCB1 3435C>T, CYP1B1*3, GSTP1 I105V, TPMT 460G>A, UGT1A1*28 and UGT1A1 -3156G>A. The pattern of observed allele frequencies for all polymorphisms could not be accurately estimated from any single previously studied population. CONCLUSION This highlights the need to expand the scope of geographic data for use in pharmacogenomics studies.
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Affiliation(s)
- Sharon Marsh
- Faculty of Pharmacy & Pharmaceutical Sciences, 3142F Katz Centre for Pharmacy & Health Research, University of Alberta, Edmonton, AB T6G 2E1, Canada
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