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Olvany JM, Williams SM, Zimmerman PA. Global perspectives on CYP2D6 associations with primaquine metabolism and Plasmodium vivax radical cure. Front Pharmacol 2022; 13:752314. [PMID: 36457706 PMCID: PMC9705595 DOI: 10.3389/fphar.2022.752314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/27/2022] [Indexed: 07/30/2023] Open
Abstract
Clinical trial and individual patient treatment outcomes have produced accumulating evidence that effective primaquine (PQ) treatment of Plasmodium vivax and P. ovale liver stage hypnozoites is associated with genetic variation in the human cytochrome P450 gene, CYP2D6. Successful PQ treatment of individual and population-wide infections by the Plasmodium species that generate these dormant liver stage forms is likely to be necessary to reach elimination of malaria caused by these parasites globally. Optimizing safe and effective PQ treatment will require coordination of efforts between the malaria and pharmacogenomics research communities.
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Affiliation(s)
- Jasmine M. Olvany
- The Center for Global Health and Diseases, Pathology Department, Case Western Reserve University, Cleveland, OH, United States
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Scott M. Williams
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Peter A. Zimmerman
- The Center for Global Health and Diseases, Pathology Department, Case Western Reserve University, Cleveland, OH, United States
- Master of Public Health Program, Case Western Reserve University, Cleveland, OH, United States
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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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Rossi LMG, Escobar-Gutierrez A, Rahal P. Advanced molecular surveillance of hepatitis C virus. Viruses 2015; 7:1153-88. [PMID: 25781918 PMCID: PMC4379565 DOI: 10.3390/v7031153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/05/2015] [Accepted: 02/20/2015] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infection is an important public health problem worldwide. HCV exploits complex molecular mechanisms, which result in a high degree of intrahost genetic heterogeneity. This high degree of variability represents a challenge for the accurate establishment of genetic relatedness between cases and complicates the identification of sources of infection. Tracking HCV infections is crucial for the elucidation of routes of transmission in a variety of settings. Therefore, implementation of HCV advanced molecular surveillance (AMS) is essential for disease control. Accounting for virulence is also important for HCV AMS and both viral and host factors contribute to the disease outcome. Therefore, HCV AMS requires the incorporation of host factors as an integral component of the algorithms used to monitor disease occurrence. Importantly, implementation of comprehensive global databases and data mining are also needed for the proper study of the mechanisms responsible for HCV transmission. Here, we review molecular aspects associated with HCV transmission, as well as the most recent technological advances used for virus and host characterization. Additionally, the cornerstone discoveries that have defined the pathway for viral characterization are presented and the importance of implementing advanced HCV molecular surveillance is highlighted.
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Affiliation(s)
- Livia Maria Gonçalves Rossi
- Department of Biology, Institute of Bioscience, Language and Exact Science, Sao Paulo State University, Sao Jose do Rio Preto, SP 15054-000, Brazil.
| | | | - Paula Rahal
- Department of Biology, Institute of Bioscience, Language and Exact Science, Sao Paulo State University, Sao Jose do Rio Preto, SP 15054-000, Brazil.
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Rooij TV, Roederer M, Wareham T, Rooij IV, McLeod HL, Marsh S. Fast and frugal trees: translating population-based pharmacogenomics to medication prioritization. Per Med 2015; 12:117-128. [DOI: 10.2217/pme.14.66] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aim: Fast and frugal decision trees (FFTs) can simplify clinical decision making by providing a heuristic approach to contextual guidance. We wanted to use FFTs for pharmacogenomic knowledge translation at point-of-care. Materials & Methods: The Pharmacogenomics for Every Nation Initiative (PGENI), an international nonprofit organization, collects data on regional polymorphisms as a predictor of metabolism for individual drugs and dosages. We advanced FFTs to work with PGENI pharmacogenomic data to produce medication recommendations that are accurate, transparent and straightforward to automate. Results: By streamlining medication selection processes in the PGENI workflow, information technology applications can now be deployed. Conclusion: We developed a decision tree approach that can translate pharmacogenomic data to provide up-to-date recommended care for populations based on their medication-specific markers.
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Affiliation(s)
- Tibor van Rooij
- Faculty of Pharmacy & Pharmaceutical Sciences, Katz Group Centre for Pharmacy & Health Research, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Mary Roederer
- Eshelman School of Pharmacy, Department of Pharmacy Practice, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Todd Wareham
- Department of Computer Science, Memorial University of Newfoundland, St. John's, Newfoundland & Labrador, Canada
| | - Iris van Rooij
- Donders Institute for Brain, Cognition & Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Sharon Marsh
- Faculty of Pharmacy & Pharmaceutical Sciences, Katz Group Centre for Pharmacy & Health Research, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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Kudzi W, Adjei GO, Ofori-Adjei D, Dodoo ANO. Pharmacogenetics in Ghana: reviewing the evidence. Ghana Med J 2013; 45:73-80. [PMID: 21857725 DOI: 10.4314/gmj.v45i2.68932] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Different clinical response of different patients to the same medicine has been recognised and documented since the 1950's. Variability in response of individuals to standard doses of drug therapy is important in clinical practice and can lead to therapeutic failures or adverse drug reactions. Pharmacogenetics seeks to identify individual genetic differences (polymorphisms) in drug absorption, metabolism, distribution and excretion that can affect the activity of a particular drug with the view of improving efficacy and reducing toxicity. Although knowledge of pharmacogenetics is being translated into clinical practice in the developed world, its applicability in the developing countries is low. Several factors account for this including the fact that there is very little pharmacogenetic information available in many indigenous African populations including Ghanaians. A number of genes including Cytochrome P450 (CYP) 2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, MDR1 and TPMT have been genotyped in the Ghanaian population since the completion of the Human genome project. There is however, an urgent need to increase pharmacogenetic research in Ghana to increase availability of data. Introducing Pharmacogenetics into the curriculum of Medical and Pharmacy training institutions will influence translating knowledge of pharmacogenetics into clinical practice. This will also equip health professionals with the skill to integrate genetic information into public health decision making.
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Affiliation(s)
- W Kudzi
- Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School. P.O. GP 4236, Accra, Ghana.
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Roederer MW, Sanchez-Giron F, Kalideen K, Kudzi W, McLeod HL, Zhang W. Pharmacogenetics and rational drug use around the world. Pharmacogenomics 2011; 12:897-905. [PMID: 21692619 DOI: 10.2217/pgs.11.17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The WHO embraces evidence-based medicine to formulate an essential medicines list (EML) considering disease prevalence, drug efficacy, drug safety and cost-effectiveness. The EML is used by developing countries to build a national formulary. As pharmacogenetics in developed countries evolves, the Pharmacogenetics for Every Nation Initiative (PGENI) convened with representatives from China, Mexico, Ghana and South Africa in August 2009 to evaluate the use of human pharmacogenetics to enhance global drug use policy. The diseases causing mortality, the lack of integration of pharmacovigilance at the national formulary level, the pharmacogenetics research agenda and pharmacogenetics clinician education did not differ greatly among the countries. While there are many unanswered questions, systematically incorporating pharmacogenetics at the national formulary level promises to improve global drug use.
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Affiliation(s)
- Mary W Roederer
- Institute of Pharmacogenomics & Individualized Therapy, UNC Eshelman School of Pharmacy, CB #7361, 120 Mason Farm Road, 1092 Genetic Medicine Building, Chapel Hill, NC 27599-7361, USA.
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Roederer MW, McLeod H, Juliano JJ. Can pharmacogenomics improve malaria drug policy? Bull World Health Organ 2011; 89:838-45. [PMID: 22084530 DOI: 10.2471/blt.11.087320] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 07/05/2011] [Accepted: 07/08/2011] [Indexed: 01/27/2023] Open
Abstract
Coordinated global efforts to prevent and control malaria have been a tour-de-force for public health, but success appears to have reached a plateau in many parts of the world. While this is a multifaceted problem, policy strategies have largely ignored genetic variations in humans as a factor that influences both selection and dosing of antimalarial drugs. This includes attempts to decrease toxicity, increase effectiveness and reduce the development of drug resistance, thereby lowering health care costs. We review the potential hurdles to developing and implementing pharmacogenetic-guided policies at a national or regional scale for the treatment of uncomplicated falciparum malaria. We also consider current knowledge on some component drugs of artemisinin combination therapies and ways to increase our understanding of host genetics, with the goal of guiding policy decisions for drug selection.
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Affiliation(s)
- Mary W Roederer
- Institute of Pharmacogenomics and Individualized Therapy, Eshelman School of Pharmacy, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC 27599-7361, United States of America.
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Ayuso C, Abad-Santos F, Dal-Ré R, Gracia D. Ética en investigación genética (1). Estudios farmacogenéticos. Med Clin (Barc) 2011; 136:678-82. [DOI: 10.1016/j.medcli.2009.10.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/19/2009] [Accepted: 10/22/2009] [Indexed: 12/24/2022]
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Mitropoulos K, Johnson L, Vozikis A, Patrinos GP. Relevance of pharmacogenomics for developing countries in Europe. ACTA ACUST UNITED AC 2011; 26:143-6. [DOI: 10.1515/dmdi.2011.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Roederer MW, McLeod HL. Applying the genome to national drug formulary policy in the developing world. Pharmacogenomics 2010; 11:633-6. [DOI: 10.2217/pgs.10.55] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
With pharmacogenetics comes the promise of individualized therapy selection for many common diseases where multiple treatment options are available. Recent advances including the Human Genome Project, the International HapMap project, advances in throughput technology and reduction in cost of genetic testing, and the inclusion of genotype-related dosing recommendations into package inserts all point to the integration of pharmacogenetics into clinical practice. However, many countries will not have access to pharmacogenetics resources to individualize patient therapy for decades to come. The PharmacoGenetics for Every Nation Initiative (PGENI) is a first step to making pharmacogenetics applicable on a global level. Generation of genotype profiles for ‘common’ population groups within a country will provide a useful, but not perfect resource for incorporating pharmacogenetics into national drug formularies in the form of prioritization or tailored surveillance recommendations for a country’s population. Targeted educational efforts will also prepare the Ministry of Health staff from participating countries to better integrate genetic information into many areas of healthcare, including disease management and therapeutic development. The goal should always be optimizing therapy for each individual patient, but pharmacogenetics can be useful now and essential in the future for the developing world.
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Affiliation(s)
- Mary W Roederer
- Institute of Pharmacogenomics & Individualized Therapy, UNC Eshelman School of Pharmacy, CB #7361, Genomic Medicine Building, Room 1094, Chapel Hill, NC 27599-7361, USA
| | - Howard L McLeod
- Institute of Pharmacogenomics & Individualized Therapy, UNC Eshelman School of Pharmacy, CB #7361, Genomic Medicine Building, Room 1094, Chapel Hill, NC 27599-7361, USA
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Warfarin pharmacogenetics: a single VKORC1 polymorphism is predictive of dose across 3 racial groups. Blood 2010; 115:3827-34. [PMID: 20203262 DOI: 10.1182/blood-2009-12-255992] [Citation(s) in RCA: 272] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Warfarin-dosing algorithms incorporating CYP2C9 and VKORC1 -1639G>A improve dose prediction compared with algorithms based solely on clinical and demographic factors. However, these algorithms better capture dose variability among whites than Asians or blacks. Herein, we evaluate whether other VKORC1 polymorphisms and haplotypes explain additional variation in warfarin dose beyond that explained by VKORC1 -1639G>A among Asians (n = 1103), blacks (n = 670), and whites (n = 3113). Participants were recruited from 11 countries as part of the International Warfarin Pharmacogenetics Consortium effort. Evaluation of the effects of individual VKORC1 single nucleotide polymorphisms (SNPs) and haplotypes on warfarin dose used both univariate and multi variable linear regression. VKORC1 -1639G>A and 1173C>T individually explained the greatest variance in dose in all 3 racial groups. Incorporation of additional VKORC1 SNPs or haplotypes did not further improve dose prediction. VKORC1 explained greater variability in dose among whites than blacks and Asians. Differences in the percentage of variance in dose explained by VKORC1 across race were largely accounted for by the frequency of the -1639A (or 1173T) allele. Thus, clinicians should recognize that, although at a population level, the contribution of VKORC1 toward dose requirements is higher in whites than in nonwhites; genotype predicts similar dose requirements across racial groups.
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Influence of ethnicity on pharmacogenetic variation in the Ghanaian population. THE PHARMACOGENOMICS JOURNAL 2009; 9:373-9. [PMID: 19546880 DOI: 10.1038/tpj.2009.28] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It has been well established that the frequencies of genomic variants can vary greatly between the populations of different countries. We sought to quantify the intra-population variability in Ghana to determine the value of genotyping studies done at a nationwide level. Further, we investigated the differences between the Ghanaian and other African populations to determine the quality of genomic representation provided by a small subgroup within the continent with regard to the general population. We genotyped 934 unrelated Ghanaian individuals for 15 single nucleotide polymorphisms (SNPs) from genes defined as clinically relevant based on their reported roles in the transport of, metabolism of, or as targets of the medicines listed in the World Health Organization Essential Medicines list. Populations within Ghana and between nations in Western Africa were genetically cohesive. In contrast, populations in other areas of Africa were genetically divergent. Gene allele frequency also differed significantly between the populations in African nations and the United States for several of the SNPs. These results demonstrate that national populations in similar geographic regions, like Africa, may have widely varying genetic allele frequencies for clinically relevant SNPs. Further genotyping studies of specific populations are necessary to provide the best medical care to all individuals.
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Marini F, Brandi ML. Pharmacogenetics of osteoporosis: future perspectives. Calcif Tissue Int 2009; 84:337-47. [PMID: 19271099 DOI: 10.1007/s00223-009-9226-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 02/04/2009] [Indexed: 10/21/2022]
Abstract
Drug response is known to be highly variable among treated patients and affected by many factors, such as age, sex, ethnicity, concomitant diseases, and pharmacological therapy. However, sequence variants in the human genome are now considered an important cause of differences in drug responses. Pharmacogenetics, which is the utilization of individual genetic data to predict the outcome of drug treatment with respect to both beneficial and adverse effects, represents an emerging field of genetics with the potential to become useful for the identification of the most effective drug and the most beneficial dose for a given individual. On the basis of these considerations and thanks to recent advances in genetics and molecular biology, pharmacogenetics is becoming a flowering field in both basic and clinical research. Nevertheless, to date the opportunity to apply pharmacogenetic approaches to drug response and the possibility to use genetic screenings to tailor decisions about pharmacological treatments have limited applications. And this is even truer in the field of osteoporosis, in which pharmacogenetic studies are in their infancy. In this paper we review the most recent data on pharmacogenetics of osteoporosis, highlighting the presentations at the Second International Meeting on Pharmacogenetics of Osteoarticular Disorders held in Florence in April 2008.
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Affiliation(s)
- Francesca Marini
- Mineral and Bone Metabolism Unit, Department of Internal Medicine, University of Florence, Florence, Italy.
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Evans CP. Identification of molecular targets in urologic oncology. World J Urol 2008; 27:3-8. [PMID: 19002690 DOI: 10.1007/s00345-008-0339-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 09/27/2008] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVES Molecular targets in cancer diagnosis and therapy have come to the fore of the oncology field in the last decade. Their identification is rooted in basic science investigation and enhanced knowledge in the fields of genetics, biochemistry, molecular and tumor biology, and pathology among others. METHODS A medical literature search in English using MEDLINE/PUBMed was performed on the topics of molecular targets, targeted therapy, and biomarkers in the areas of bladder, prostate, and renal cancers. This information was analyzed and combined with the author's personal knowledge in the identification and development of molecular targets. Data is included from the author's laboratory regarding examples of target development and clinical translation. RESULTS Molecular targets are often biomarkers; either prognostic ones that reflect the natural history of the cancer or predictive ones that reflect the impact of a therapy. Molecular targets in urologic cancer may arise from four sources: the host, the tumor, as a result of a treatment, or associated with a specific disease stage. Understanding the continuum of targets through the progression of a urologic cancer is central to the translational applications of diagnostics, individualized medicine and targeted therapeutics. Urologists are most familiar with targeted therapy in renal cancer with the introduction of tyrosine kinase inhibitors. Yet, herein are examples of biomarkers and targets across the spectrum of urologic tumors, stages and treatments. CONCLUSIONS Identification of events, signals, and pathways in urologic cancer are opportunities to develop biomarkers and targets for diagnosis and treatment.
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Affiliation(s)
- Christopher P Evans
- Department of Urology, Davis School of Medicine, University of California, 4860 Y St., Suite 3500, Sacramento, CA, 95817, USA.
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Séguin B, Hardy BJ, Singer PA, Daar AS. Universal health care, genomic medicine and Thailand: investing in today and tomorrow. Nat Rev Genet 2008; 9 Suppl 1:S14-9. [PMID: 18802416 DOI: 10.1038/nrg2443] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
One potential outcome of investing in genomic medicine is the provision of tools for creating a more cost-effective health-care system. Partly with this aim in mind, Thailand has launched two genotyping initiatives: the Thai SNP Discovery Project and the Thai Centre for Excellence in Life Sciences Pharmacogenomics Project. Together, these projects will help Thailand understand the genomic diversity of its population and explore the role that this diversity has in drug response and disease susceptibility in its population. A major future challenge will be for Thailand to integrate genomic medicine in its relatively young universal health-care system.
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Affiliation(s)
- Béatrice Séguin
- McLaughlin-Rotman Centre for Global Health, Program on Life Sciences, Ethics and Policy, University Health Network and University of Toronto, MaRS Centre, South Tower, Suite 406, 101 College Street, Toronto, Ontario M5G 1L7, Canada
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Makeeva O, Stepanov V, Puzyrev V, Goldstein DB, Grossman I. Global pharmacogenetics: genetic substructure of Eurasian populations and its effect on variants of drug-metabolizing enzymes. Pharmacogenomics 2008; 9:847-68. [PMID: 18597650 DOI: 10.2217/14622416.9.7.847] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIMS To study the frequency distribution of cytochrome P450 (CYP) functional genetic variants in five Eurasian populations from the territory of Siberia in Russia. MATERIALS & METHODS Unrelated healthy Tuvinians, Buryats, Altaians, Yakuts and Russians (n = 87-88) were genotyped for CYP2C9*2, CYP2C9*3, CYP2C19*2, CYP2C19*3, CYP3A5*3 and CYP3A5*6. Standard pairwise genetic distances, locus-specific and global Fst statistics were calculated. RESULTS CYP allele and genotype frequencies demonstrated significant variability. Overall, the degree of between-population variance displayed by CYP SNPs was lower than that recorded from neutral short tandem repeats and Alu-insertion polymorphism, indicating evolutionary conservation of CYP polymorphisms. CYP-based genetic distances were well correlated with the geographic distances across populations (r = 0.822, p = 0.008). CONCLUSIONS Although the tested variants were present in the neighboring, yet secluded, populations at the expected range of frequencies, the observed frequencies were significantly variable across Eurasian populations, indicating potential relevance to clinical decision making.
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Affiliation(s)
- Oksana Makeeva
- Tomsk Research Institute of Medical Genetics, The Russian Academy of Medical Sciences, 10 Nab. Ushaiky, Tomsk, 634050 Russia.
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Oliveira E, Marsh S, van Booven DJ, Amorim A, Prata MJ, McLeod HL. Pharmacogenetically relevant polymorphisms in Portugal. Pharmacogenomics 2008; 8:703-12. [PMID: 18240903 DOI: 10.2217/14622416.8.7.703] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
OBJECTIVE Most drugs are developed based on data from European-derived 'reference' populations; however, clinically relevant DNA polymorphisms often demonstrate population-specific patterns of allele frequencies. Given that the knowledge of the frequency distribution of functional polymorphisms in a population may guide national planning for selection of therapeutic options, in the present study we examined the allele frequencies of enzymes responsible for drug disposition in Portugal. PATIENTS & METHODS Using PCR- and Pyrosequencing-based methods, the current study assessed the frequencies of 15 key polymorphisms from genes encoding enzymes involved in Phases I, II and III of drug metabolism, DNA repair and intracellular metabolism in 135 healthy individuals from Portugal. RESULTS Allele frequencies were derived for cytochrome P450 (CYP)2C9*2 (13.2%), CYP2C9*3 (8%), CYP2C19*2 (14%), CYP3A4*1B (7%), CYP3A5*3C (87.5%), glutathione S-transferase (GST)M1*0 (77.9%), GSTP1 313A>G (33%), inosine triphosphatase 94C>A (7%), UDP-glucuronosyltransferase (UGT)1A1*28 (28%), UGT1A1 -3156G>A (23%), ATP-binding cassette (ABC)B1 1236C>T (46%), ABCB1 2677G>A/T (2 and 42%), ABCG2 421C>A (8%), excision repair cross-complementing rodent repair deficiency 2 2251A>C (3%) and thymidylate synthetase 1494del (31%). CONCLUSION Although, on the whole, the frequency distributions among the Portuguese fitted the patterns commonly found in other Europeans well, evidence for some degree of African influence was observed. This is the most comprehensive study on pharmacogenetically relevant variations in Portugal to date, and the baseline of pharmacogenetic data might be important for determining policy guidelines for cancer prevention and drug treatments in the Portuguese population.
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Affiliation(s)
- E Oliveira
- University of Porto, Institute of Pathology and Molecular Immunology, 4200-465 Porto, Portugal.
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Marsh S, Paul J, McLeod HL, Brown R. In Reply. J Clin Oncol 2008. [DOI: 10.1200/jco.2007.15.8212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sharon Marsh
- Division of Oncology, Washington University School of Medicine, St Louis, MO
| | - Jim Paul
- Cancer Research UK Clinical Trials Unit, Division of Cancer Sciences, Faculty of Medicine, University of Glasgow, The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Howard L. McLeod
- UNC Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC
| | - Robert Brown
- Department of Oncology, Imperial College London, Hammersmith Hospital, London, United Kingdom
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Aksimentiev A, Brunner R, Cohen J, Comer J, Cruz-Chu E, Hardy D, Rajan A, Shih A, Sigalov G, Yin Y, Schulten K. Computer modeling in biotechnology: a partner in development. Methods Mol Biol 2008; 474:181-234. [PMID: 19031067 DOI: 10.1007/978-1-59745-480-3_11] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Computational modeling can be a useful partner in biotechnology, in particular, in nanodevice engineering. Such modeling guides development through nanoscale views of biomolecules and devices not available through experimental imaging methods. We illustrate the role of computational modeling, mainly of molecular dynamics, through four case studies: development of silicon bionanodevices for single molecule electrical recording, development of carbon nano-tube-biomolecular systems as in vivo sensors, development of lipoprotein nanodiscs for assays of single membrane proteins, and engineering of oxygen tolerance into the enzyme hydrogenase for photosynthetic hydrogen gas production. The four case studies show how molecular dynamics approaches were adapted to the specific technical uses through (i) multi-scale extensions, (ii) fast quantum chemical force field evaluation, (iii) coarse graining, and (iv) novel sampling methods. The adapted molecular dynamics simulations provided key information on device behavior and revealed development opportunities, arguing that the "computational microscope" is an indispensable nanoengineering tool.
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Affiliation(s)
- Aleksei Aksimentiev
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Affiliation(s)
- S Marsh
- Washington University, Division of Molecular Oncology, St Louis, USA
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