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Wroblewski TH, Witt KE, Lee SB, Malhi RS, Peede D, Huerta-Sánchez E, Villanea FA, Claw KG. Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications. Genome Biol Evol 2023; 15:evad222. [PMID: 38051947 PMCID: PMC10727477 DOI: 10.1093/gbe/evad222] [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: 04/03/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023] Open
Abstract
Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.
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Affiliation(s)
- Tadeusz H Wroblewski
- Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kelsey E Witt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, South Carolina, USA
| | - Seung-been Lee
- Precision Medicine Institute, Macrogen Inc., Seoul, Republic of Korea
| | - Ripan S Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Illinois, USA
| | - David Peede
- Department of Ecology, Evolution, and Organismal Biology and Center for Computational and Molecular Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Emilia Huerta-Sánchez
- Department of Ecology, Evolution, and Organismal Biology and Center for Computational and Molecular Biology, Brown University, Providence, Rhode Island, USA
| | | | - Katrina G Claw
- Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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2
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Atiq MA, Peterson SE, Langman LJ, Baudhuin LM, Black JL, Moyer AM. Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach. J Pers Med 2023; 13:883. [PMID: 37373874 DOI: 10.3390/jpm13060883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/29/2023] Open
Abstract
CYP2D6 duplication has important pharmacogenomic implications. Reflex testing with long-range PCR (LR-PCR) can resolve the genotype when a duplication and alleles with differing activity scores are detected. We evaluated whether visual inspection of plots from real-time-PCR-based targeted genotyping with copy number variation (CNV) detection could reliably determine the duplicated CYP2D6 allele. Six reviewers evaluated QuantStudio OpenArray CYP2D6 genotyping results and the TaqMan Genotyper plots for seventy-three well-characterized cases with three copies of CYP2D6 and two different alleles. Reviewers blinded to the final genotype visually assessed the plots to determine the duplicated allele or opt for reflex sequencing. Reviewers achieved 100% accuracy for cases with three CYP2D6 copies that they opted to report. Reviewers did not request reflex sequencing in 49-67 (67-92%) cases (and correctly identified the duplicated allele in each case); all remaining cases (6-24) were marked by at least one reviewer for reflex sequencing. In most cases with three copies of CYP2D6, the duplicated allele can be determined using a combination of targeted genotyping using real-time PCR with CNV detection without need for reflex sequencing. In ambiguous cases and those with >3 copies, LR-PCR and Sanger sequencing may still be necessary for determination of the duplicated allele.
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Affiliation(s)
- Mazen A Atiq
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - Sandra E Peterson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - Loralie J Langman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - Linnea M Baudhuin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - John L Black
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
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3
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Mouterde M, Daali Y, Rollason V, Čížková M, Mulugeta A, Al Balushi KA, Fakis G, Constantinidis TC, Al-Thihli K, Černá M, Makonnen E, Boukouvala S, Al-Yahyaee S, Yimer G, Černý V, Desmeules J, Poloni ES. Joint Analysis of Phenotypic and Genomic Diversity Sheds Light on the Evolution of Xenobiotic Metabolism in Humans. Genome Biol Evol 2022; 14:6852765. [PMID: 36445690 PMCID: PMC9750130 DOI: 10.1093/gbe/evac167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 11/03/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Variation in genes involved in the absorption, distribution, metabolism, and excretion of drugs (ADME) can influence individual response to a therapeutic treatment. The study of ADME genetic diversity in human populations has led to evolutionary hypotheses of adaptation to distinct chemical environments. Population differentiation in measured drug metabolism phenotypes is, however, scarcely documented, often indirectly estimated via genotype-predicted phenotypes. We administered seven probe compounds devised to target six cytochrome P450 enzymes and the P-glycoprotein (P-gp) activity to assess phenotypic variation in four populations along a latitudinal transect spanning over Africa, the Middle East, and Europe (349 healthy Ethiopian, Omani, Greek, and Czech volunteers). We demonstrate significant population differentiation for all phenotypes except the one measuring CYP2D6 activity. Genome-wide association studies (GWAS) evidenced that the variability of phenotypes measuring CYP2B6, CYP2C9, CYP2C19, and CYP2D6 activity was associated with genetic variants linked to the corresponding encoding genes, and additional genes for the latter three. Instead, GWAS did not indicate any association between genetic diversity and the phenotypes measuring CYP1A2, CYP3A4, and P-gp activity. Genome scans of selection highlighted multiple candidate regions, a few of which included ADME genes, but none overlapped with the GWAS candidates. Our results suggest that different mechanisms have been shaping the evolution of these phenotypes, including phenotypic plasticity, and possibly some form of balancing selection. We discuss how these contrasting results highlight the diverse evolutionary trajectories of ADME genes and proteins, consistent with the wide spectrum of both endogenous and exogenous molecules that are their substrates.
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Affiliation(s)
| | - Youssef Daali
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Victoria Rollason
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Martina Čížková
- Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anwar Mulugeta
- Department of Pharmacology and Clinical Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Khalid A Al Balushi
- College of Pharmacy, National University of Science and Technology, Muscat, Sultanate of Oman
| | - Giannoulis Fakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Khalid Al-Thihli
- Department of Genetics, Sultan Qaboos University Hospital, Muscat, Sultanate of Oman
| | - Marie Černá
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Eyasu Makonnen
- Department of Pharmacology and Clinical Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia,Center for Innovative Drug Development and Therapeutic Trials for Africa, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sotiria Boukouvala
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Said Al-Yahyaee
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Getnet Yimer
- Center for Global Genomics & Health Equity, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Viktor Černý
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jules Desmeules
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
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4
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Relevance of CYP2D6 Gene Variants in Population Genetic Differentiation. Pharmaceutics 2022; 14:pharmaceutics14112481. [PMID: 36432672 PMCID: PMC9694252 DOI: 10.3390/pharmaceutics14112481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
A significant portion of the variability in complex features, such as drug response, is likely caused by human genetic diversity. One of the highly polymorphic pharmacogenes is CYP2D6, encoding an enzyme involved in the metabolism of about 25% of commonly prescribed drugs. In a directed search of the 1000 Genomes Phase III variation data, 86 single nucleotide polymorphisms (SNPs) in the CYP2D6 gene were extracted from the genotypes of 2504 individuals from 26 populations, and then used to reconstruct haplotypes. Analyses were performed using Haploview, Phase, and Arlequin softwares. Haplotype and nucleotide diversity were high in all populations, but highest in populations of African ancestry. Pairwise FST showed significant results for eleven SNPs, six of which were characteristic of African populations, while four SNPs were most common in East Asian populations. A principal component analysis of CYP2D6 haplotypes showed that African populations form one cluster, Asian populations form another cluster with East and South Asian populations separated, while European populations form the third cluster. Linkage disequilibrium showed that all African populations have three or more haplotype blocks within the CYP2D6 gene, while other world populations have one, except for Chinese Dai and Punjabi in Pakistan populations, which have two.
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Nthontho KC, Ndlovu AK, Sharma K, Kasvosve I, Hertz DL, Paganotti GM. Pharmacogenetics of Breast Cancer Treatments: A Sub-Saharan Africa Perspective. Pharmgenomics Pers Med 2022; 15:613-652. [PMID: 35761855 PMCID: PMC9233488 DOI: 10.2147/pgpm.s308531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Breast cancer is the most frequent cause of cancer death in low- and middle-income countries, in particular among sub-Saharan African women, where response to available anticancer treatment therapy is often limited by the recurrent breast tumours and metastasis, ultimately resulting in decreased overall survival rate. This can also be attributed to African genomes that contain more variation than those from other parts of the world. The purpose of this review is to summarize published evidence on pharmacogenetic and pharmacokinetic aspects related to specific available treatments and the known genetic variabilities associated with metabolism and/or transport of breast cancer drugs, and treatment outcomes when possible. The emphasis is on the African genetic variation and focuses on the genes with the highest strength of evidence, with a close look on CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4/5, CYP19A1, UGT1A4, UGT2B7, UGT2B15, SLC22A16, SLC38A7, FcγR, DPYD, ABCB1, and SULT1A1, which are the genes known to play major roles in the metabolism and/or elimination of the respective anti-breast cancer drugs given to the patients. The genetic variability of their metabolism could be associated with different metabolic phenotypes that may cause reduced patients' adherence because of toxicity or sub-therapeutic doses. Finally, this knowledge enhances possible personalized treatment approaches, with the possibility of improving survival outcomes in patients with breast cancer.
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Affiliation(s)
- Keneuoe Cecilia Nthontho
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Andrew Khulekani Ndlovu
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Daniel Louis Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
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6
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Stojanović Marković A, Zajc Petranović M, Tomas Ž, Puljko B, Šetinc M, Škarić-Jurić T, Peričić Salihović M. Untangling SNP Variations within CYP2D6 Gene in Croatian Roma. J Pers Med 2022; 12:jpm12030374. [PMID: 35330374 PMCID: PMC8951754 DOI: 10.3390/jpm12030374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
CYP2D6 is a highly polymorphic gene whose variations affect its enzyme activity. To assess whether the specific population history of Roma, characterized by constant migrations and endogamy, influenced the distribution of alleles and thus phenotypes, the CYP2D6 gene was sequenced using NGS (Next Generation Sequencing) method-targeted sequencing in three groups of Croatian Roma (N = 323) and results were compared to European and Asian populations. Identified single nucleotide polymorphisms (SNPs) were used to reconstruct haplotypes, which were translated into the star-allele nomenclature and later into phenotypes. A total of 43 polymorphic SNPs were identified. The three Roma groups differed significantly in the frequency of alleles of polymorphisms 6769 A > G, 6089 G > A, and 5264 A > G (p < 0.01), as well as in the prevalence of the five most represented star alleles: *1, *2, *4, *10, and *41 (p < 0.0001). Croatian Roma differ from the European and Asian populations in the accumulation of globally rare SNPs (6089 G > A, 4589 C > T, 4622 G > C, 7490 T > C). Our results also show that demographic history influences SNP variations in the Roma population. The three socio-culturally different Roma groups studied differ significantly in the distribution of star alleles, which confirms the importance of a separate study of different Roma groups.
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Affiliation(s)
- Anita Stojanović Marković
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
| | - Matea Zajc Petranović
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
| | - Željka Tomas
- Department for Translational Medicine, Srebrnjak Children’s Hospital, 10000 Zagreb, Croatia;
| | - Borna Puljko
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department for Chemistry and Biochemistry, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Maja Šetinc
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
| | - Tatjana Škarić-Jurić
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
| | - Marijana Peričić Salihović
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
- Correspondence:
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7
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Nakanishi G, Bertagnolli LS, Pita-Oliveira M, Scudeler MM, Torres-Loureiro S, Almeida-Dantas T, Alves MLC, Cirino HS, Rodrigues-Soares F. GSTM1 and GSTT1 polymorphisms in healthy volunteers - a worldwide systematic review. Drug Metab Rev 2022; 54:37-45. [PMID: 35103568 DOI: 10.1080/03602532.2022.2036996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/29/2022] [Indexed: 02/06/2023]
Abstract
The GSTM1 and GSTT1 genes encode homonymous enzymes, which are responsible for the detoxification of several substances potentially harmful to the human body, such as air pollution, drugs, pesticides, and tobacco. However, some individuals may present a complete deletion of these genes and, consequently, an enzyme deficiency leading to an inadequate metabolism and, therefore, a higher susceptibility to some clinical conditions. Interethnic variations have also been described for both genes, making necessary the study of the deletion frequencies of GSTM1 and GSTT1 in different populations around the world. So, the aim of this study was to enable the synthesis and discussion of the main population differences of GSTM1 and GSTT1 polymorphisms in healthy volunteers. Searches were performed in the PubMed database, including 533 articles and 178,566 individuals in the analyses. We found an overrepresentation of European individuals and studies, and an underrepresentation of non-European ethnicities. Moreover, there are significant frequency differences among distinct ethnic groups: East Asians present the highest frequencies worldwide for GSTM1 and GSTT1 deletions, which could suggest higher disorders risk for this population; in contrast, Sub-Saharan Africans presented the lowest frequency of GSTM1 worldwide, corroborating evolution inferences performed previously for other genes codifying metabolism enzymes. Also, admixture is a relevant component when analyzing frequency values for both genes, but further studies focusing on this subject are warranted.
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Affiliation(s)
- Giovana Nakanishi
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Laísa S Bertagnolli
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Murilo Pita-Oliveira
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Mariana M Scudeler
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Sabrina Torres-Loureiro
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Thaís Almeida-Dantas
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Maria Laura C Alves
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Heithor S Cirino
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
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Simple and Robust Detection of CYP2D6 Gene Deletions and Duplications Using CYP2D8P as Reference. Pharmaceuticals (Basel) 2022; 15:ph15020166. [PMID: 35215279 PMCID: PMC8880347 DOI: 10.3390/ph15020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/23/2022] [Accepted: 01/27/2022] [Indexed: 12/04/2022] Open
Abstract
Genotyping of the CYP2D6 gene is the most commonly applied pharmacogenetic test globally. Significant economic interests have led to the development of a plurality of assays, available for almost any genotyping platform or DNA detection chemistry. Of all the genetic variants, copy number variations are particular difficult to detect by polymerase chain reaction. Here, we present two simple novel approaches for the identification of samples carrying either deletions or duplications of the CYP2D6 gene; by relative quantification using a singleplex 5′nuclease real-time PCR assay, and by high-resolution melting of PCR products. These methods make use of universal primers, targeting both the CYP2D6 and the reference gene CYP2D8P, which is necessary for the analysis. The assays were validated against a reference method using a large set of samples. The singleplex nature of the 5′nuclease real-time PCR ensures that the primers anneal with equal affinity to both the sequence of the CYP2D6 and the reference gene. This facilitates robust identification of gene deletions and duplications based on the cycle threshold value. In contrast, the high-resolution melting assay is an end-point PCR, where the identification relies on variations between the amount of product generated from each of the two genes.
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9
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Fuselli S. Beyond drugs: the evolution of genes involved in human response to medications. Proc Biol Sci 2019; 286:20191716. [PMID: 31640517 DOI: 10.1098/rspb.2019.1716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genetic variation of our species reflects human demographic history and adaptation to diverse local environments. Part of this genetic variation affects individual responses to exogenous substances, such as food, pollutants and drugs, and plays an important role in drug efficacy and safety. This review provides a synthesis of the evolution of loci implicated in human pharmacological response and metabolism, interpreted within the theoretical framework of population genetics and molecular evolution. In particular, I review and discuss key evolutionary aspects of different pharmacogenes in humans and other species, such as the relationship between the type of substrates and rate of evolution; the selective pressure exerted by landscape variables or dietary habits; expected and observed patterns of rare genetic variation. Finally, I discuss how this knowledge can be translated directly or after the implementation of specific studies, into practical guidelines.
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Affiliation(s)
- Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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10
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Paradkar MU, Shah SAV, Dherai AJ, Shetty D, Ashavaid TF. Distribution of CYP2D6 genotypes in the Indian population - preliminary report. Drug Metab Pers Ther 2018; 33:141-151. [PMID: 30098281 DOI: 10.1515/dmpt-2018-0011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/16/2018] [Indexed: 11/15/2022]
Abstract
Abstract
Background
Cytochrome P450 2D6 (CYP2D6) allelic distribution exhibits differences amongst worldwide populations. There is lack of data from Mumbai, Western India, on the major CYP2D6 alleles *2, *3, *4, *5, *10 and *41, and gene multiplication alleles. Hence, the present study was undertaken to determine the distribution of these clinically relevant CYP2D6 alleles.
Methods
Fifty-two healthy individuals were screened using TaqMan SNP genotyping and copy number variation (CNV) assays by real-time polymerase chain reaction.
Results
The allele frequencies of CYP2D6*2, *3, *4, *5, *10 and *41 alleles were observed to be 30.8%, 0%, 11.5%, 3.9%, 19.2% and 17.3%, respectively. The frequency of CYP2D6 gene one copy, two copies, three copies and four copies were observed to be 7.7%, 76.9%, 13.5% and 1.9%, respectively. The predicted phenotype frequency was observed to be 78.9%, 3.9% and 9.6% for extensive, intermediate, and ultrarapid metabolizers, respectively, whereas poor metabolizers were not detected.
Conclusions
CYP2D6 allele frequencies showed heterogeneous distribution in the present study as compared to worldwide populations. High frequency of CYP2D6*41 allele, gene duplication alleles and UMs was observed. The scarcity and/or lack of data from the Indian population on these alleles further substantiates the need for screening of CYP2D6 genotyping.
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Affiliation(s)
- Minal U Paradkar
- Research Laboratories, P. D. Hinduja National Hospital and Medical Research Centre, Mahim, Mumbai, India
| | - Swarup A V Shah
- Research Laboratories, P. D. Hinduja National Hospital and Medical Research Centre, Mahim, Mumbai, India
| | - Alpa J Dherai
- Department of Biochemistry, P. D. Hinduja National Hospital and Medical Research Centre, Mahim, Mumbai, India
| | - Dhanashri Shetty
- Department of Biochemistry, P. D. Hinduja National Hospital and Medical Research Centre, Mahim, Mumbai, India
| | - Tester F Ashavaid
- Head - Department of Laboratory Medicine, Director - Lab Research, Department of Biochemistry, P. D. Hinduja National Hospital and Medical Research Centre, Veer Savarkar Marg, Mahim, Mumbai 400 016, India
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11
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Tawe L, Motshoge T, Ramatlho P, Mutukwa N, Muthoga CW, Dongho GBD, Martinelli A, Peloewetse E, Russo G, Quaye IK, Paganotti GM. Human cytochrome P450 2B6 genetic variability in Botswana: a case of haplotype diversity and convergent phenotypes. Sci Rep 2018; 8:4912. [PMID: 29559695 PMCID: PMC5861095 DOI: 10.1038/s41598-018-23350-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 03/09/2018] [Indexed: 01/11/2023] Open
Abstract
Identification of inter-individual variability for drug metabolism through cytochrome P450 2B6 (CYP2B6) enzyme is important for understanding the differences in clinical responses to malaria and HIV. This study evaluates the distribution of CYP2B6 alleles, haplotypes and inferred metabolic phenotypes among subjects with different ethnicity in Botswana. A total of 570 subjects were analyzed for CYP2B6 polymorphisms at position 516 G > T (rs3745274), 785 A > G (rs2279343) and 983 T > C (rs28399499). Samples were collected in three districts of Botswana where the population belongs to Bantu (Serowe/Palapye and Chobe) and San-related (Ghanzi) ethnicity. The three districts showed different haplotype composition according to the ethnic background but similar metabolic inferred phenotypes, with 59.12%, 34.56%, 2.10% and 4.21% of the subjects having, respectively, an extensive, intermediate, slow and rapid metabolic profile. The results hint at the possibility of a convergent adaptation of detoxifying metabolic phenotypes despite a different haplotype structure due to the different genetic background. The main implication is that, while there is substantial homogeneity of metabolic inferred phenotypes among the country, the response to drugs metabolized via CYP2B6 could be individually associated to an increased risk of treatment failure and toxicity. These are important facts since Botswana is facing malaria elimination and a very high HIV prevalence.
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Affiliation(s)
- Leabaneng Tawe
- University of Botswana, Department of Medical Laboratory Sciences, Gaborone, Botswana.,Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Sub-Saharan African Network for TB/HIV Research Excellence at Botswana-Harvard Partnership, Gaborone, Botswana
| | - Thato Motshoge
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Pleasure Ramatlho
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Naledi Mutukwa
- University of Botswana, Department of Pathology, Gaborone, Botswana
| | | | - Ghyslaine Bruna Djeunang Dongho
- Sapienza University of Rome, Department of Infectious Diseases and Public Health, Rome, Italy.,Evangelical University of Cameroon, Department of Biomedical Sciences, Bandjoun, Cameroon
| | - Axel Martinelli
- Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.,King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Thuwal, Saudi Arabia
| | - Elias Peloewetse
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Gianluca Russo
- Sapienza University of Rome, Department of Infectious Diseases and Public Health, Rome, Italy
| | - Isaac Kweku Quaye
- University of Namibia, Department of Biochemistry, Windhoek, Namibia
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana. .,University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA. .,University of Botswana, Department of Biomedical Sciences, Gaborone, Botswana.
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12
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Wendt FR, Sajantila A, Budowle B. Predicted activity of UGT2B7, ABCB1, OPRM1, and COMT using full-gene haplotypes and their association with the CYP2D6-inferred metabolizer phenotype. Forensic Sci Int Genet 2018; 33:48-58. [DOI: 10.1016/j.fsigen.2017.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/01/2017] [Accepted: 11/22/2017] [Indexed: 12/20/2022]
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13
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Mitra S, Kshatriya GK. Genetic variation at Q192R and L55M polymorphisms in PON1. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2016; 45:251-256. [PMID: 27341351 DOI: 10.1016/j.etap.2016.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/26/2016] [Accepted: 06/05/2016] [Indexed: 06/06/2023]
Abstract
Earlier we have reported Q192R allele frequencies among four Indian populations as a part of an investigation of the distribution of Paraoxonase 1 polymorphisms. Here we present the results obtained after screening eleven populations representing different regions of India for Q192R and L55M. Population genetic analysis examining the effect of micro-evolutionary forces at these loci confirmed genetic differentiation at Q192R earlier suggested. The study groups showed high frequencies of L55 and differential distribution of Q192 and R192. Tests for deviation from neutrality indicated heterozygote excess at rs662 which has Q192R polymorphism. Higher levels of heterozygosity at Q192R than L55M might be because of its role in wide substrate specificity of the enzyme. A small but highly significant correlation between genetic and geographic distances was observed in a spatial autocorrelation analysis indicating non-random distribution of Q192 allele. Our findings are pertinent to toxicogenetic studies evaluating risk assessment towards organophosphate compounds among different continental groups.
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Affiliation(s)
- Siuli Mitra
- Department of Anthropology, University of Delhi, Delhi 110007, India
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Jin T, Shi X, Wang L, Wang H, Feng T, Kang L. Genetic polymorphisms of pharmacogenomic VIP variants in the Mongol of Northwestern China. BMC Genet 2016; 17:70. [PMID: 27233804 PMCID: PMC4884435 DOI: 10.1186/s12863-016-0379-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 05/22/2016] [Indexed: 11/23/2022] Open
Abstract
Background Within a population, the differences of pharmacogenomic variant frequencies may produce diversities in drug efficacy, safety, and the risk associated with adverse drug reactions. With the development of pharmacogenomics, widespread genetic research on drug metabolism has been conducted on major populations, but less is known about minorities. Results In this study, we recruited 100 unrelated, healthy Mongol adults from Xinjiang and genotyped 85 VIP variants from the PharmGKB database. We compared our data with eleven populations listed in 1000 genomes project and HapMap database. We used χ2 tests to identify significantly different loci between these populations. We downloaded SNP allele frequencies from the ALlele FREquency Database to observe the global genetic variation distribution for these specific loci. And then we used Structure software to perform the genetic structure analysis of 12 populations. Conclusions Our results demonstrated that different polymorphic allele frequencies exist between different nationalities,and indicated Mongol is most similar to Chinese populations, followed by JPT. This information on the Mongol population complements the existing pharmacogenomic data and provides a theoretical basis for screening and therapy in the different ethnic groups within Xinjiang.
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Affiliation(s)
- Tianbo Jin
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, 712082, China. .,Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, #6 East Wenhui Road, Xianyang, 712082, Shaanxi, China. .,National Engineering Research Center for Miniaturized Detection Systems, Xi'an, 710069, China. .,School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Xugang Shi
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, 712082, China.,Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, #6 East Wenhui Road, Xianyang, 712082, Shaanxi, China
| | - Li Wang
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, 712082, China.,Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, #6 East Wenhui Road, Xianyang, 712082, Shaanxi, China
| | - Huijuan Wang
- National Engineering Research Center for Miniaturized Detection Systems, Xi'an, 710069, China.,School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Tian Feng
- National Engineering Research Center for Miniaturized Detection Systems, Xi'an, 710069, China
| | - Longli Kang
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, 712082, China. .,Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, #6 East Wenhui Road, Xianyang, 712082, Shaanxi, China.
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Shi X, Wang L, Du S, Wang H, Feng T, Jin T, Kang L. Genetic polymorphism of pharmacogenomic VIP variants in the Deng people from the Himalayas in Southeast Tibet. Biomarkers 2015; 20:275-86. [PMID: 26329523 DOI: 10.3109/1354750x.2015.1068859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Little is known about polymorphic distribution of pharmacogenes among ethnicities, including the Deng people. In this study, we recruited 100 unrelated, healthy Deng people and genotyped them with respect to 76 different single-nucleotide polymorphisms by the PharmGKB database. Our results first indicated that the polymorphic distribution of pharmacogenes of the Deng people is most similar to CHD, suggesting that Deng people have a closest genetic relationship with CHD. Our data will enrich the database of pharmacogenomics and provide a theoretical basis for safer drug administration and individualized treatment plans, promoting the development of personalized medicine.
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Affiliation(s)
- Xugang Shi
- a Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University , Xianyang , Shaanxi , China
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Yasukochi Y, Satta Y. Molecular evolution of the CYP2D subfamily in primates: purifying selection on substrate recognition sites without the frequent or long-tract gene conversion. Genome Biol Evol 2015; 7:1053-67. [PMID: 25808902 PMCID: PMC4419802 DOI: 10.1093/gbe/evv056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2015] [Indexed: 01/21/2023] Open
Abstract
The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawa, 240-0193 Japan
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LLerena A, Naranjo MEG, Rodrigues-Soares F, Penas-LLedó EM, Fariñas H, Tarazona-Santos E. Interethnic variability ofCYP2D6alleles and of predicted and measured metabolic phenotypes across world populations. Expert Opin Drug Metab Toxicol 2014; 10:1569-83. [DOI: 10.1517/17425255.2014.964204] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Dandara C, Swart M, Mpeta B, Wonkam A, Masimirembwa C. Cytochrome P450 pharmacogenetics in African populations: implications for public health. Expert Opin Drug Metab Toxicol 2014; 10:769-85. [PMID: 24588448 DOI: 10.1517/17425255.2014.894020] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Africa harbors a disproportionate burden of disease when taking into account the triple challenge caused by HIV/AIDS, tuberculosis (TB) and malaria, against a backdrop of an increasing burden of noncommunicable diseases. More than 80% of therapeutic drugs used in the management of these diseases/conditions are metabolized by CYP enzymes that exhibit genetic polymorphisms. AREAS COVERED There is variability in the expression and activities of CYPs resulting in interindividual differences in the response to standard doses of therapeutic drugs, due to genetic polymorphisms, which exhibit both quantitative and qualitative differences between racial and between ethnic groups. The review aims to evaluate the implications of the genetic variation in CYPs on the public health of Africans. The CYPs reviewed here metabolize most of the commonly used therapeutic drugs and include CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D6, 3A4 and 3A5. Allele frequencies are compared between African ethnic groups and among populations of African, Asian and European origin. Data are obtained from our own studies and literature. EXPERT OPINION The variability in the pattern of genetic variation between populations translates into differences in drug response. Understanding CYP variability improves rational drug use and has public health significance.
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Affiliation(s)
- Collet Dandara
- University of Cape Town, Faculty of Health Sciences, Pharmacogenetics and Cancer Research Group, Division of Human Genetics, Department of Clinical Laboratory Sciences , Anzio Road Observatory, 7925, Cape Town , South Africa +27 21 406 6506 ;
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Chiurillo MA, Griman P, Santiago L, Torres K, Moran Y, Borjas L. Distribution of GSTM1, GSTT1, GSTP1 and TP53 disease-associated gene variants in native and urban Venezuelan populations. Gene 2013; 531:106-11. [PMID: 23994684 DOI: 10.1016/j.gene.2013.08.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/14/2013] [Accepted: 08/14/2013] [Indexed: 02/06/2023]
Abstract
The contemporary Venezuelan population is the product of major admixture process across various historical events, which has provided it a particular genetic background. The aim of this study concerns the analysis of glutathione S-transferase (GST) GSTM1, GSTP1 and GSTT1 genetic variants and five polymorphisms at the TP53 gene, which are related to cancer susceptibility, in an urban/admixed population and five Amerindian tribes (Bari, Panare, Pemon, Warao and Wayuu) from Venezuela. Genotyping was carried out in 120 individuals from an urban sample and 188 Amerindians. The analysis performed on TP53 haplotype and GST allele distribution showed a close correlation for Pemon and Warao populations, while Bari group appears isolated from the other populations. GSTT1 null variant frequency in our admixed (11%) and native samples (0.0-11.4%) was lower when compared with Caucasians, Africans and Asians. Frequency of the GSTP1*Val cancer-associated allele found in Bari (88.6%) and Panare (63.0%) is of the highest so far reported. Fourteen TP53 haplotypes were observed in the admixed populations, whereas only 3 to 5 in Amerindians. To our knowledge this is the first report of GST polymorphisms and TP53 haplotype distribution in Venezuelans. The distribution of most of analyzed polymorphisms in the urban sample is consistent with the admixed origin of the present-day population of Venezuela. While, the inter-ethnic variations in genetic polymorphisms found in Native American tribes seem to be the result of the influence of demographic factors. These results provide additional data for undertaking ethnographic and disease association studies in Venezuela.
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Affiliation(s)
- Miguel Angel Chiurillo
- Laboratorio de Genetica Molecular, Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado, Barquisimeto, Venezuela.
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Polimanti R, Fuciarelli M, Destro-Bisol G, Battaggia C. Functional diversity of the glutathione peroxidase gene family among human populations: implications for genetic predisposition to disease and drug response. Pharmacogenomics 2013; 14:1037-45. [DOI: 10.2217/pgs.13.99] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: To analyze the human genetic variation of glutathione peroxidases (GPX), estimating the functional differences among human populations and suggesting interethnic differences in predisposition to disease and drug response. Materials & methods: Using 1000 Genomes Project data, we analyzed 723 GPX variants in 1092 individuals belonging to 14 populations. Combining functional prediction analyses of coding and noncoding variants, we developed a method to estimate haplotype functionality. Results: GPX rare variants have a higher functional impact than common variants. The frequency among Asian patients of haplotypes associated with normal functionality is significantly higher for GPX1 and lower for GPX3 than for non-Asian patients; no adaptation signals in GPX1 and GPX3 were found in Asian patients. Conclusion: GPX1 and GPX3 differences may be associated with alterations in antioxidant capacity and redox regulation, which suggests diverse susceptibility to complex disease and diverse response to relevant drugs in Asians compared with individuals with other ethnic origins. Original submitted 7 February 2013; Revision submitted 16 May 2013
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Affiliation(s)
- Renato Polimanti
- Department of Biology, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, Rome, Italy.
| | - Maria Fuciarelli
- Department of Biology, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, Rome, Italy
| | | | - Cinzia Battaggia
- Dipartimento di Biologia Ambientale, Università di Roma “La Sapienza”, Rome, Italy
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Polimanti R, Piacentini S, Manfellotto D, Fuciarelli M. Human genetic variation of CYP450 superfamily: analysis of functional diversity in worldwide populations. Pharmacogenomics 2013; 13:1951-60. [PMID: 23215887 DOI: 10.2217/pgs.12.163] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AIM The present study aimed to investigate the human genetic diversity of the CYP450 superfamily in order to identify functional interethnic differences and analyze the role of CYP450 enzymes in human adaptation. MATERIALS & METHODS A computational analysis of genetic and functional differences of the 57 CYP450 genes was performed using the Human Genome Diversity Project and HapMap data; comprising approximately 1694 individuals belonging to 62 human populations. RESULTS Twenty-six CYP450 SNPs with F-statistics significantly different than the general distribution were identified. Some showed high differentiation among human populations, suggesting that functional interethnic differences may be present. Indeed, some of these are significantly associated with drug response or disease risk. Furthermore, our data highlighted that TBXAS1 and genes in CYP3A cluster may have a role in some processes of human adaptation. CONCLUSION Our study provided an analysis of genetic diversity of CYP450 superfamily, identifying functional differences among ethnic groups and their related clinical phenotypes.
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Affiliation(s)
- Renato Polimanti
- Department of Biology, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy.
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22
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Maisano Delser P, Fuselli S. Human loci involved in drug biotransformation: worldwide genetic variation, population structure, and pharmacogenetic implications. Hum Genet 2013; 132:563-77. [PMID: 23354977 DOI: 10.1007/s00439-013-1268-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/08/2013] [Indexed: 12/20/2022]
Abstract
Understanding the role of inheritance in individual variation in drug response is the focus of pharmacogenetics (PGx). A key part of this understanding is quantifying the role of genetic ancestry in this phenotypic outcome. To provide insight into the relationship between ethnicity and drug response, this study first infers the global distribution of PGx variation and defines its structure. Second, the study evaluates if geographic population structure stems from all PGx loci in general, or if structure is caused by specific genes. Lastly, we identify the genetic variants contributing the greatest proportion of such structure. Our study describes the global genetic structure of PGx loci across the 52 populations of the Human Genome Diversity Cell-Line Panel, the most inclusive set of human populations freely available for studies on human genetic variation. By analysing genetic variation at 1,001 single nucleotide polymorphisms (SNPs) involved in biotransformation of exogenous substances, we describe the between-populations PGx variation, as well geographical groupings of diversity. In addition, with discriminant analysis of principal component (DAPC), we infer how many and which groups of populations are supported by PGx variation, and identify which SNPs actually contribute to the PGx structure between such groups. Our results show that intergenic, synonymous and non-synonymous SNPs show similar levels of genetic variation across the globe. Conversely, loci coding for Cytochrome P450s (mainly metabolizing exogenous substances) show significantly higher levels of genetic diversity between populations than the other gene categories. Overall, genetic variation at PGx loci correlates with geographic distances between populations, and the apportionment of genetic variation is similar to that observed for the rest of the genome. In other words, the pattern of PGx variation has been mainly shaped by the demographic history of our species, as in the case of most of our genes. The population structure defined by PGx loci supports the presence of six genetic clusters reflecting geographic location of samples. In particular, the results of the DAPC analyses show that 27 SNPs substantially contribute to the first three discriminant functions. Among these SNPs, some, such as the intronic rs1403527 of NR1I2 and the non-synonymous rs699 of AGT, are known to be associated with specific drug responses. Their substantial variation between different groups of populations may have important implications for PGx practical applications.
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Yang Z, Yang Z, Arheart KL, Morris R, Zhang Y, Rodriguez Y, Song C, Gitlin MC, Candiotti KA. CYP2D6 poor metabolizer genotype and smoking predict severe postoperative pain in female patients on arrival to the recovery room. PAIN MEDICINE 2013; 13:604-9. [PMID: 22497725 DOI: 10.1111/j.1526-4637.2012.01296.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
UNLABELLED Recent studies have shown that CYP2D6 acts at critical steps for endogenous morphine biosynthesis. The present study assessed the contribution of CYP2D6 genetic polymorphisms, smoking, and other factors on acute severe postoperative pain (linear analog pain scores ≥8). METHODS Two hundred thirty-six female patients were found to have adequate information in a previously developed female surgical patient database to be included in this current analysis. Multiple logistic regression analysis was used to assess the predictors for acute severe postoperative pain. DNA had been previously extracted from blood samples in all patients and was genotyped by the Amplichip to determine the specific CYP2D6 genotypes. RESULTS It was noted that the incidence of acute severe postoperative pain (linear analog pain scores ≥8) was more frequent in patients with the CYP2D6 poor metabolizer (PM) genotype, 71%, compared with 28% in intermediate metabolizers (IMs), 26% in extensive metabolizers (EMs), and 27% in ultrarapid metabolizers (UMs). The overall association between metabolizer groups and severe postoperative pain was significant (P=0.023). PMs were significantly more likely to suffer from severe postoperative pain than IMs, EMs, and UMs (P=0.007, 0.002, and 0.050, respectively). There were no significant differences among IMs, EMs, and UMs. Additionally, it was noted that there was an increased frequency of acute severe postoperative pain in smokers vs nonsmokers (P=0.014). CONCLUSION This study demonstrated that female patients possessing the PM genotype of CYP2D6 and patients who smoke had a higher incidence of acute severe postoperative pain.
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Affiliation(s)
- Zongqi Yang
- Department of Anesthesiology, Perioperative Medicine and Pain Management, University of Miami, Miller School of Medicine, Miami, Florida 33101, USA
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Griman P, Moran Y, Valero G, Loreto M, Borjas L, Chiurillo MA. CYP2D6 gene variants in urban/admixed and Amerindian populations of Venezuela: pharmacogenetics and anthropological implications. Ann Hum Biol 2012; 39:137-42. [PMID: 22324840 DOI: 10.3109/03014460.2012.656703] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Differences in genes encoding enzymes involved in the biotransformation of a large number of compounds, such as CYP2D6, are related to inter-individual and inter-ethnic variability in the metabolism of many drugs, which have also been linked to susceptibility to cancer and other health outcomes. Therefore, populations are likely to benefit from inclusion in pharmacogenetic research studies. AIM To determine the frequency of functionally important allele variants of CYP2D6 gene in a sample of an Urban/admixed and five Amerindian Venezuelan populations. SUBJECTS AND METHODS DNA of 328 unrelated volunteers was analysed for the presence of CYP2D6 *2, *3, *4, *5, *6 and *10 variants. RESULTS The frequency in the Urban/admixed population for *2, *3, *4, *5, *6 and *10 alleles was 37.9%, 0%, 13.4%, 2.0%, 1.2% and 4.0%, respectively. In the Bari population, the prevalence of *4 allele associated with decreased enzyme activity was observed in 42.5%, whereas the poor metabolizer genotype *4/*4 was found in 25%. In the Panare, Pemon, Warao and Wayuu populations the *4 allele was found in 5.4%, 2.5%, 1.7% and 4.2%, respectively. The *10 allele frequency found in Amerindians (0.0-6.3%) was lower than reported for Asians. CONCLUSION The results are consistent with the known genetic admixture origin of most Venezuela populations. Nevertheless, the observed significant differences among Amerindians highlight the need for pharmacogenetic studies taking into account biogeographical and anthropological considerations.
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Affiliation(s)
- Pedro Griman
- Laboratorio de Genética Molecular Dr Jorge Yunis-Turbay, Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado, Barquisimeto 3001, Venezuela
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Abstract
Genetic variation influences the absorption and efflux of drugs in the intestine, the metabolism of drugs in the liver and the effects of these drugs on their target proteins. Indeed, variations in genes whose products have a role in the pathophysiology of nonmalignant gastrointestinal diseases, such as IBD, have been shown to affect the response of patients to therapy. This Review provides an overview of pharmacogenetics in the management of nonmalignant gastrointestinal diseases on the basis of data from clinical trials. Genetic variants that have the greatest effect on the management of patients with IBD involve the metabolism of thiopurines. Variation in drug metabolism by cytochrome P450 enzymes also requires attention so as to avoid drug interactions in patients receiving tricyclic antidepressants and PPIs. Few genotyping tests are currently used in the clinical management of patients with nonmalignant gastrointestinal diseases, owing to a lack of data from clinical trials showing their effectiveness in predicting nonresponse or adverse outcomes. However, pharmacogenetics could have a beneficial role in enabling pharmacotherapy for nonmalignant gastrointestinal diseases to be targeted to the individual patient.
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Affiliation(s)
- Michael Camilleri
- College of Medicine, Mayo Clinic, Charlton, 8–110, 200 First Street, South West, Rochester, MN 55905, USA
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Bouchard C, Ordovas JM. Fundamentals of Nutrigenetics and Nutrigenomics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 108:1-15. [DOI: 10.1016/b978-0-12-398397-8.00001-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Sabbagh A, Darlu P, Crouau-Roy B, Poloni ES. Arylamine N-acetyltransferase 2 (NAT2) genetic diversity and traditional subsistence: a worldwide population survey. PLoS One 2011; 6:e18507. [PMID: 21494681 PMCID: PMC3071824 DOI: 10.1371/journal.pone.0018507] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 03/09/2011] [Indexed: 11/19/2022] Open
Abstract
Arylamine N-acetyltransferase 2 (NAT2) is involved in human physiological responses to a variety of xenobiotic compounds, including common therapeutic drugs and exogenous chemicals present in the diet and the environment. Many questions remain about the evolutionary mechanisms that have led to the high prevalence of slow acetylators in the human species. Evidence from recent surveys of NAT2 gene variation suggests that NAT2 slow-causing variants might have become targets of positive selection as a consequence of the shift in modes of subsistence and lifestyle in human populations in the last 10,000 years. We aimed to test more extensively the hypothesis that slow acetylation prevalence in humans is related to the subsistence strategy adopted by the past populations. To this end, published frequency data on the most relevant genetic variants of NAT2 were collected from 128 population samples (14,679 individuals) representing different subsistence modes and dietary habits, allowing a thorough analysis at both a worldwide and continent scale. A significantly higher prevalence of the slow acetylation phenotype was observed in populations practicing farming (45.4%) and herding (48.2%) as compared to populations mostly relying on hunting and gathering (22.4%) (P = 0.0007). This was closely mirrored by the frequency of the slow 590A variant that was found to occur at a three-fold higher frequency in food producers (25%) as compared to hunter-gatherers (8%). These findings are consistent with the hypothesis that the Neolithic transition to subsistence economies based on agricultural and pastoral resources modified the selective regime affecting the NAT2 acetylation pathway. Furthermore, the vast amount of data collected enabled us to provide a comprehensive and up-to-date description of NAT2 worldwide genetic diversity, thus building up a useful resource of frequency data for further studies interested in epidemiological or anthropological research questions involving NAT2.
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Affiliation(s)
- Audrey Sabbagh
- Institut de Recherche pour le Développement, UMR 216, Paris, France.
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Copy number variants in pharmacogenetic genes. Trends Mol Med 2011; 17:244-51. [PMID: 21388883 DOI: 10.1016/j.molmed.2011.01.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 01/14/2011] [Accepted: 01/14/2011] [Indexed: 01/07/2023]
Abstract
Variation in drug efficacy and toxicity remains an important clinical concern. Presently, single nucleotide polymorphisms (SNPs) only explain a portion of this problem, even in situations where the pharmacological trait is clearly heritable. The Human CNV Project identified copy number variations (CNVs) across approximately 12% of the human genome, and these CNVs were considered causes of diseases. Although the contribution of CNVs to the pathogenesis of many common diseases is questionable, CNVs play a clear role in drug-related genes by altering drug metabolizing and drug response. In this review, we provide a comprehensive evaluation of the clinical relevance of CNVs to drug efficacy, toxicity, and disease prevalence in world populations, and discuss the implication of using CNVs as a diagnostic tool in clinical intervention.
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Machado M, Magalhães WC, Sene A, Araújo B, Faria-Campos AC, Chanock SJ, Scott L, Oliveira G, Tarazona-Santos E, Rodrigues MR. Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies. INVESTIGATIVE GENETICS 2011; 2:3. [PMID: 21284835 PMCID: PMC3041995 DOI: 10.1186/2041-2223-2-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 02/01/2011] [Indexed: 11/10/2022]
Abstract
Background Targeted re-sequencing is one of the most powerful and widely used strategies for population genetics studies because it allows an unbiased screening for variation that is suitable for a wide variety of organisms. Examples of studies that require re-sequencing data are evolutionary inferences, epidemiological studies designed to capture rare polymorphisms responsible for complex traits and screenings for mutations in families and small populations with high incidences of specific genetic diseases. Despite the advent of next-generation sequencing technologies, Sanger sequencing is still the most popular approach in population genetics studies because of the widespread availability of automatic sequencers based on capillary electrophoresis and because it is still less prone to sequencing errors, which is critical in population genetics studies. Two popular software applications for re-sequencing studies are Phred-Phrap-Consed-Polyphred, which performs base calling, alignment, graphical edition and genotype calling and DNAsp, which performs a set of population genetics analyses. These independent tools are the start and end points of basic analyses. In between the use of these tools, there is a set of basic but error-prone tasks to be performed with re-sequencing data. Results In order to assist with these intermediate tasks, we developed a pipeline that facilitates data handling typical of re-sequencing studies. Our pipeline: (1) consolidates different outputs produced by distinct Phred-Phrap-Consed contigs sharing a reference sequence; (2) checks for genotyping inconsistencies; (3) reformats genotyping data produced by Polyphred into a matrix of genotypes with individuals as rows and segregating sites as columns; (4) prepares input files for haplotype inferences using the popular software PHASE; and (5) handles PHASE output files that contain only polymorphic sites to reconstruct the inferred haplotypes including polymorphic and monomorphic sites as required by population genetics software for re-sequencing data such as DNAsp. Conclusion We tested the pipeline in re-sequencing studies of haploid and diploid data in humans, plants, animals and microorganisms and observed that it allowed a substantial decrease in the time required for sequencing analyses, as well as being a more controlled process that eliminates several classes of error that may occur when handling datasets. The pipeline is also useful for investigators using other tools for sequencing and population genetics analyses.
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Affiliation(s)
- Moara Machado
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Wagner Cs Magalhães
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Allan Sene
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Bruno Araújo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Alessandra C Faria-Campos
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Stephen J Chanock
- Laboratory of Translational Genomics of the Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, MD, USA.,8717 Grovemont Circle Advanced Technology Center, Room 127, Gaithersburg, MD, 20877, USA
| | - Leandro Scott
- Genomics and Computational Biology Group and Center for Excellence in Bioinformatics, René Rachou Institute, Fundação Oswaldo Cruz, Av Augusto de Lima 1715, Belo Horizonte, MG, 30190-002, Brazil
| | - Guilherme Oliveira
- Genomics and Computational Biology Group and Center for Excellence in Bioinformatics, René Rachou Institute, Fundação Oswaldo Cruz, Av Augusto de Lima 1715, Belo Horizonte, MG, 30190-002, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Maira R Rodrigues
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
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