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Jallul M, Alhudiri I, Al-Eitan L, Elzagheid A. Warfarin pharmacogenomics in African populations: the importance of ethnicity-based algorithms. Pharmacogenomics 2022; 23:753-757. [PMID: 36004679 DOI: 10.2217/pgs-2022-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tweetable abstract It is well accepted that pharmacogenomics (PGx) information from Asia and Europe should not be applied to Africa. More work is needed on different ethnic groups to generate population-specific algorithms that can be used effectively and safely.
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Affiliation(s)
- Mwada Jallul
- Genetic Engineering Department, Libyan Biotechnology Research Centre, Tripoli, P.O. Box. 30313, Libya
| | - Inas Alhudiri
- Genetic Engineering Department, Libyan Biotechnology Research Centre, Tripoli, P.O. Box. 30313, Libya
| | - Laith Al-Eitan
- Department of Biotechnology & Genetic Engineering, Jordan University of Science & Technology, Irbid, 22110, Jordan
| | - Adam Elzagheid
- Genetic Engineering Department, Libyan Biotechnology Research Centre, Tripoli, P.O. Box. 30313, Libya
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Shafique H, Ashraf NM, Rashid A, Majeed A, Afsar T, Daly AK, Almajwal A, Alruwaili NW, Khan AU, Razak S. Determination of Pleiotropic Effect of Warfarin in VKORC1 and CYP2C9 Genotypes in Patients With Heart Valve Replacement. Front Cardiovasc Med 2022; 9:895169. [PMID: 35757332 PMCID: PMC9226342 DOI: 10.3389/fcvm.2022.895169] [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: 03/13/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Warfarin has been widely used as an oral anticoagulant agent. In past, efforts have been done to study the contribution of genetic variation on warfarin dose requirements. The possible therapeutic dose determination of warfarin is very challenging, i.e., extremely low dose leading to unusable antithrombotic therapy or high dose causes particularly bleeding complications. Our study aimed to investigate these observations in more detail, we determined the correlation of interleukin-6 (IL-6), cyclooxygenase-2 (COX-2), and tumor necrosis factor-α (TNF-α) among VKORC1 and CYP2C9 genetic variants in patients with heart valve replacement who were treated with a range of warfarin doses and compared with levels in healthy controls. A total of 107 human subjects were recruited with low < 5 mg, medium 5–10 mg/day, and high > 10 mg/day warfarin doses. The genetic study of VKORC1–1639G/A, C1173T, 3730G > A, CYP2C9*2, and CYP2C9*3 was performed using TaqMan genotyping and DNA sequencing. The gene expression of IL-6, TNF-α, and COX-2 mRNA was analyzed. IL-6, TNF-α, and COX-2 protein expressions were determined by ELISA and Western blot analysis to evaluate the pro- and anti-inflammatory effects of warfarin. A statistically significant difference was found among the haplotypes of VKORC1 rs9934438 (C1173T), rs9923231 (−1639G > A), rs7294 (3730G > A) and CYP2C9 *2 p. Arg144 Cys (rs28371674), CYP2C9 *3 p. Ile359Leu (rs1057910) genotypes with warfarin dose requirements (p = 0.001). The increased levels of COX-2, IL-6, and TNF-α proteins were observed when a high dose of warfarin (>10 mg/ml) was administered. However, a lower concentration (1.0 mg/ml) was observed with decreased warfarin dose (<5 mg/day). The present study reported that in addition to its anticoagulant action, the genetic variants of warfarin may have a pleiotropic effect by influencing IL-6 depending on the dosing regimen and inducing the expression of COX-2.
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Affiliation(s)
- Huma Shafique
- Department of Biochemistry, Army Medical College, National University of Medical Sciences, Rawalpindi, Pakistan
- Institute of Cellular Medicine, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Naeem Mahmood Ashraf
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Amir Rashid
- Department of Biochemistry, Army Medical College, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Asifa Majeed
- Department of Biochemistry, Army Medical College, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ann K. Daly
- Institute of Cellular Medicine, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nawaf W. Alruwaili
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Azmat Ullah Khan
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- *Correspondence: Suhail Razak,
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Osman A, Jonasson J. Cross-ethnic analysis of common gene variants in hemostasis show lopsided representation of global populations in genetic databases. BMC Med Genomics 2022; 15:69. [PMID: 35337356 PMCID: PMC8957123 DOI: 10.1186/s12920-022-01220-0] [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: 11/09/2021] [Accepted: 03/21/2022] [Indexed: 11/12/2022] Open
Abstract
A majority of studies reporting human genetic variants were performed in populations of European ancestry whereas other global populations, and particularly many ethnolinguistic groups in other continents, are heavily underrepresented in these studies. To investigate the extent of this disproportionate representation of global populations concerning variants of significance to thrombosis and hemostasis, 845 single nucleotide polymorphisms (SNPs) in and around 34 genes associated with thrombosis and hemostasis and included in the commercial Axiom Precision Medicine Research Array (PMRA) were evaluated, using gene frequencies in 3 African (Somali and Luhya in East Africa, and Yoruba in West Africa) and 14 non-African (admixed American, East Asian, European, South Asian, and sub-groups) populations. Among the populations studied, Europeans were observed to be the best represented population by the hemostatic SNPs included in the PMRA. The European population also presented the largest number of common pharmacogenetic and pathogenic hemostatic variants reported in the ClinVar database. The number of such variants decreased the farther the genetic distance a population was from Europeans, with Yoruba and East Asians presenting the least number of clinically significant hemostatic SNPs in ClinVar while also being the two genetically most distinct populations from Europeans among the populations compared. Current study shows the lopsided representation of global populations as regards to hemostatic genetic variants listed in different commercial SNP arrays, such as the PMRA, and reported in genetic databases while also underlining the importance of inclusion of non-European ethnolinguistic populations in genomics studies designed to discover variants of significance to bleeding and thrombotic disorders.
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Affiliation(s)
- Abdimajid Osman
- Department of Clinical Chemistry, University Hospital in Linköping, Ing. 64, Plan 11, 581 85, Linköping, Sweden. .,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
| | - Jon Jonasson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Clinical Genetics, University Hospital in Linköping, Linköping, Sweden
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Lopes JL, Harris K, Karow MB, Peterson SE, Kluge ML, Kotzer KE, Lopes GS, Larson NB, Bielinski SJ, Scherer SE, Wang L, Weinshilboum RM, Black JL, Moyer AM. Targeted Genotyping in Clinical Pharmacogenomics: What Is Missing? J Mol Diagn 2022; 24:253-261. [PMID: 35041929 PMCID: PMC8961466 DOI: 10.1016/j.jmoldx.2021.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/09/2021] [Accepted: 11/29/2021] [Indexed: 01/01/2023] Open
Abstract
Clinical pharmacogenomic testing typically uses targeted genotyping, which only detects variants included in the test design and may vary among laboratories. To evaluate the potential patient impact of genotyping compared with sequencing, which can detect common and rare variants, an in silico targeted genotyping panel was developed based on the variants most commonly included in clinical tests and applied to a cohort of 10,030 participants who underwent sequencing for CYP1A2, CYP2C19, CYP2C9, CYP2D6, CYP3A4, CYP3A5, DPYD, SLCO1B1, TPMT, UGT1A1, and VKORC1. The results of in silico targeted genotyping were compared with the clinically reported sequencing results. Of the 10,030 participants, 2780 (28%) had at least one potentially clinically relevant variant/allele identified by sequencing that would not have been detected in a standard targeted genotyping panel. The genes with the largest number of participants with variants only detected by sequencing were SLCO1B1, DPYD, and CYP2D6, which affected 13%, 6.3%, and 3.5% of participants, respectively. DPYD (112 variants) and CYP2D6 (103 variants) had the largest number of unique variants detected only by sequencing. Although targeted genotyping detects most clinically significant pharmacogenomic variants, sequencing-based approaches are necessary to detect rare variants that collectively affect many patients. However, efforts to establish pharmacogenomic variant classification systems and nomenclature to accommodate rare variants will be required to adopt sequencing-based pharmacogenomics.
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Affiliation(s)
- Jaime L. Lopes
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kimberley Harris
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mary Beth Karow
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sandra E. Peterson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Michelle L. Kluge
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Katrina E. Kotzer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Guilherme S. Lopes
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Nicholas B. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | | | - Steven E. Scherer
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Richard M. Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - John L. Black
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ann M. Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota,Address correspondence to Ann M. Moyer, M.D., Ph.D., Mayo Clinic, 200 First St SW, Rochester, MN 55905.
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Ndadza A, Muyambo S, Mntla P, Wonkam A, Chimusa E, Kengne AP, Ntsekhe M, Dandara C. Profiling of warfarin pharmacokinetics-associated genetic variants: Black Africans portray unique genetic markers important for an African specific warfarin pharmacogenetics-dosing algorithm. J Thromb Haemost 2021; 19:2957-2973. [PMID: 34382722 PMCID: PMC9543705 DOI: 10.1111/jth.15494] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/28/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Warfarin dose variability observed in patients is attributed to variation in genes involved in the warfarin metabolic pathway. Genetic variation in CYP2C9 and VKORC1 has been the traditional focus in evaluating warfarin dose variability, with little focus on other genes. OBJECTIVE We set out to evaluate 27 single nucleotide polymorphisms (SNPs) in the CYP2C cluster loci and 8 genes (VKORC1, ABCB1, CYP2C9, CYP2C19, CYP2C8, CYP1A2, CYP3A4, and CYP3A5) involved in pharmacokinetics of warfarin. PATIENTS/METHODS 503 participants were recruited among black Africans and Mixed Ancestry population groups, from South Africa and Zimbabwe, and a blood sample taken for DNA. Clinical parameters were obtained from patient medical records, and these were correlated with genetic variation. RESULTS Among black Africans, the SNPs CYP2C rs12777823G>A, CYP2C9 c.449G>A (*8), CYP2C9 c.1003C>T (*11) and CYP2C8 c.805A>T (*2) were significantly associated with warfarin maintenance dose. Conversely, CYP2C9 c.430C>T (*2), CYP2C8 c.792C>G (*4) and VKORC1 g.-1639G>A were significantly associated with maintenance dose among the Mixed Ancestry. The presence of CYP2C8*2 and CYP3A5*6 alleles was associated with increased mean warfarin maintenance dose, whereas CYP2C9*8 allele was associated with reduced warfarin maintenance dose. CONCLUSION African populations present with a diversity of variants that are important in predicting pharmacogenetics-based warfarin dosing in addition to those reported in CYP2C9 and VKORC1. It is therefore important, to include African populations in pharmacogenomics studies to be able to identify all possible biomarkers that are potential predictors for drug response.
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Affiliation(s)
- Arinao Ndadza
- Pharmacogenomics and Drug Metabolism Research GroupDivision of Human GeneticsDepartment of Pathology & Institute of Infectious Disease and Molecular Medicine (IDM)Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Sarudzai Muyambo
- Department of Clinical PharmacologyCollege of Health ScienceUniversity of ZimbabweHarareZimbabwe
- Department of Biological SciencesFaculty of Science and EngineeringBindura University of Science and EducationBinduraZimbabwe
| | - Pindile Mntla
- Department of CardiologySefako Makgatho Health Sciences University and Dr. George Mukhari HospitalPretoriaSouth Africa
| | - Ambroise Wonkam
- Pharmacogenomics and Drug Metabolism Research GroupDivision of Human GeneticsDepartment of Pathology & Institute of Infectious Disease and Molecular Medicine (IDM)Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Emile Chimusa
- Pharmacogenomics and Drug Metabolism Research GroupDivision of Human GeneticsDepartment of Pathology & Institute of Infectious Disease and Molecular Medicine (IDM)Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Andre P. Kengne
- Non‐Communicable Diseases Research UnitSouth African Medical Research Council and University of Cape TownCape TownSouth Africa
| | - Mpiko Ntsekhe
- Division of CardiologyDepartment of MedicineFaculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Collet Dandara
- Pharmacogenomics and Drug Metabolism Research GroupDivision of Human GeneticsDepartment of Pathology & Institute of Infectious Disease and Molecular Medicine (IDM)Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
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Pratt VM, Cavallari LH, Del Tredici AL, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, Whirl-Carrillo M, Weck KE. Recommendations for Clinical Warfarin Genotyping Allele Selection: A Report of the Association for Molecular Pathology and the College of American Pathologists. J Mol Diagn 2020; 22:847-859. [PMID: 32380173 DOI: 10.1016/j.jmoldx.2020.04.204] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/18/2020] [Accepted: 04/01/2020] [Indexed: 11/19/2022] Open
Abstract
The goal of the Association for Molecular Pathology (AMP) Clinical Practice Committee's AMP Pharmacogenomics (PGx) Working Group is to define the key attributes of PGx alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations for a minimum panel of variant alleles (tier 1) and an extended panel of variant alleles (tier 2) that will aid clinical laboratories when designing assays for PGx testing. The AMP PGx Working Group considered functional impact of the variants, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations for PGx testing when developing these recommendations. The ultimate goal is to promote standardization of PGx gene/allele testing across clinical laboratories. These recommendations are not to be interpreted as prescriptive but to provide a reference guide. Of note, a separate article with recommendations for CYP2C9 allele selection was previously developed by the PGx Working Group that can be applied broadly to CYP2C9-related medications. The warfarin allele recommendations in this report incorporate the previous CYP2C9 allele recommendations and additional genes and alleles that are specific to warfarin testing.
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Affiliation(s)
- Victoria M Pratt
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Larisa H Cavallari
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida
| | - Andria L Del Tredici
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Millennium Health, LLC, San Diego, California
| | - Houda Hachad
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Translational Software, Bellevue, Washington
| | - Yuan Ji
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Lisa V Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Reynold C Ly
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stuart A Scott
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Sema4, a Mount Sinai venture, Stamford, Connecticut
| | - Michelle Whirl-Carrillo
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Karen E Weck
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Departments of Pathology and Laboratory Medicine and Genetics, University of North Carolina, Chapel Hill, North Carolina
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Ndadza A, Thomford NE, Mukanganyama S, Wonkam A, Ntsekhe M, Dandara C. The Genetics of Warfarin Dose-Response Variability in Africans: An Expert Perspective on Past, Present, and Future. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:152-166. [PMID: 30883300 DOI: 10.1089/omi.2019.0018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coumarins such as warfarin are prescribed for prevention and treatment of thromboembolic disorders. Warfarin remains the most widely prescribed and an anticoagulant of choice in Africa. Warfarin use is, however, limited by interindividual variability in pharmacokinetics and a narrow therapeutic index. The difference in patients' pharmacodynamic responses to warfarin has been attributed to genetic variation in warfarin metabolism and molecular targets (e.g., CYP2C9 and VKORC1) and host-environment interactions. This expert review offers a synthesis of human genetics studies in Africans with respect to pharmacogenetics-informed warfarin dosing. We identify areas that need future research attention or could benefit from harnessing existing pharmacogenetics knowledge toward rational and optimal therapeutics with warfarin in African patients. A literature search was conducted until January 2019. A total of 343 articles were retrieved from nine African countries: Botswana, Ethiopia, Egypt, Ghana, Kenya, South Africa, Sudan, Tanzania, and Mozambique. We found 19 studies on genetics of warfarin treatment specifically among Africans. Genes examined included CYP2C9, VKORC1, CYP4F2, APOE, CALU, GGCX, and EPHX1. CYP2C9*2 and *3 alleles were highly frequent among Egyptians, while rare in other African populations. CYP2C9*5, *8, *9, and *11, and VKORC1 Asp36Tyr genetic variants explained warfarin variability in Africans better, compared to CYP2C9*2 and *3. In Africa, there is limited pharmacogenetics data on warfarin. Therefore, future research and funding commitments should be prioritized to ensure safe and effective use of warfarin in Africa. Lessons learned in Africa from the science of pharmacogenetics would inform rational therapeutics in hematology, cardiology, and surgical specialties worldwide.
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Affiliation(s)
- Arinao Ndadza
- 1 Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicholas Ekow Thomford
- 1 Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Ambroise Wonkam
- 1 Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mpiko Ntsekhe
- 3 Division of Cardiology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Collet Dandara
- 1 Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population. Sci Rep 2020; 10:5652. [PMID: 32221414 PMCID: PMC7101338 DOI: 10.1038/s41598-020-62645-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/17/2020] [Indexed: 12/16/2022] Open
Abstract
African populations are underrepresented in medical genomics studies. For the Somali population, there is virtually no information on genomic markers with significance to precision medicine. Here, we analyzed nearly 900,000 genomic markers in samples collected from 95 unrelated individuals in the North Eastern Somalia. ADMIXTURE program for estimation of individual ancestries revealed a homogenous Somali population. Principal component analysis with PLINK software showed approximately 60% East African and 40% West Eurasian genes in the Somali population, with a close relation to the Cushitic and Semitic speaking Ethiopian populations. We report the unique features of human leukocyte antigens (HLA) in the Somali population, which seem to differentiate from all other neighboring regions compared. Current study identified high prevalence of the diabetes type 1 (T1D) predisposing HLA DR-DQ haplotypes in Somalia. This finding may explain the increased T1D risk observed among Somali children. In addition, ethnic Somalis were found to host the highest frequencies observed thus far for several pharmacogenetic variants, including UGT1A4*2. In conclusion, we report that the Somali population displays genetic traits of significance to health and disease. The Somali dataset is publicly available and will add more information to the few genomic datasets available for African populations.
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Radouani F, Zass L, Hamdi Y, Rocha JD, Sallam R, Abdelhak S, Ahmed S, Azzouzi M, Benamri I, Benkahla A, Bouhaouala-Zahar B, Chaouch M, Jmel H, Kefi R, Ksouri A, Kumuthini J, Masilela P, Masimirembwa C, Othman H, Panji S, Romdhane L, Samtal C, Sibira R, Ghedira K, Fadlelmola F, Kassim SK, Mulder N. A review of clinical pharmacogenetics Studies in African populations. Per Med 2020; 17:155-170. [PMID: 32125935 PMCID: PMC8093600 DOI: 10.2217/pme-2019-0110] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Effective interventions and treatments for complex diseases have been implemented globally, however, coverage in Africa has been comparatively lower due to lack of capacity, clinical applicability and knowledge on the genetic contribution to disease and treatment. Currently, there is a scarcity of genetic data on African populations, which have enormous genetic diversity. Pharmacogenomics studies have the potential to revolutionise treatment of diseases, therefore, African populations are likely to benefit from these approaches to identify likely responders, reduce adverse side effects and optimise drug dosing. This review discusses clinical pharmacogenetics studies conducted in African populations, focusing on studies that examined drug response in complex diseases relevant to healthcare. Several pharmacogenetics associations have emerged from African studies, as have gaps in knowledge.
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Affiliation(s)
- Fouzia Radouani
- Research Department, Chlamydiae & Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca 20360, Morocco
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Jorge da Rocha
- Sydney Brenner Institute for Molecular Bioscience, University of The Witwatersrand, Johannesburg, South Africa
| | - Reem Sallam
- Medical Biochemistry & Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo 11381, Egypt
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Samah Ahmed
- Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, 321 Khartoum, Sudan.,Faculty of Clinical & Industrial Pharmacy, National University, Khartoum, Sudan
| | - Maryame Azzouzi
- Research Department, Chlamydiae & Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca 20360, Morocco
| | - Ichrak Benamri
- Research Department, Chlamydiae & Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca 20360, Morocco.,Systems & Data Engineering Team, National School of Applied Sciences of Tangier, Morocco
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia
| | - Balkiss Bouhaouala-Zahar
- Laboratory of Venoms & Therapeutic Molecules, Pasteur Institute of Tunis, 13 Place Pasteur, BP74, Tunis Belvedere- University of Tunis El Manar, Tunisia
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia
| | - Haifa Jmel
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Rym Kefi
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Ayoub Ksouri
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia.,Laboratory of Venoms & Therapeutic Molecules, Pasteur Institute of Tunis, 13 Place Pasteur, BP74, Tunis Belvedere- University of Tunis El Manar, Tunisia
| | - Judit Kumuthini
- H3ABioNet, Bioinformatics Department, Centre for Proteomic & Genomic Research, Cape Town, South Africa
| | - Phumlani Masilela
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
| | - Collen Masimirembwa
- Sydney Brenner Institute for Molecular Bioscience, University of The Witwatersrand, Johannesburg, South Africa.,DMPK Department, African Institute of Biomedical Science & Technology, Harare, Zimbabwe
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of The Witwatersrand, Johannesburg, South Africa
| | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie.,Département des Sciences de la Vie, Faculté des Sciences de Bizerte, Université Carthage, 7021 Jarzouna, BP 21, Tunisie
| | - Chaimae Samtal
- Biotechnology Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco.,Department of Biology, University of Mohammed Premier, Oujda, Morocco.,Department of Biology Faculty of Sciences, University of Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - Rania Sibira
- Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, 321 Khartoum, Sudan.,Department of Neurosurgery, National Center For Neurological Sciences, Khartoum, Sudan
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia
| | - Faisal Fadlelmola
- Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, 321 Khartoum, Sudan
| | - Samar Kamal Kassim
- Medical Biochemistry & Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo 11381, Egypt
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
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Bader L, Mahfouz A, Kasem M, Mohammed S, Alsaadi S, Abdelsamad O, Elenani R, Soaly E, Elzouki A, Rizk N, Khalifa S, Shahin MH, Cavallari LH, Mraiche F, Elewa H. The effect of genetic and nongenetic factors on warfarin dose variability in Qatari population. THE PHARMACOGENOMICS JOURNAL 2019; 20:277-284. [PMID: 31653973 DOI: 10.1038/s41397-019-0116-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023]
Abstract
The objective of this study is to estimate the prevalence of VKORC1, CYP2C9, and CYP4F2 genetic variants and their contribution to warfarin dose variability in Qataris. One hundred and fifty warfarin-treated Qatari patients on a stable dose and with a therapeutic INR for at least three consecutive clinic visits were recruited. Saliva samples were collected using Oragene DNA self-collection kit, followed by DNA purification and genotyping via TaqMan Real-Time-PCR assay. The population was stratified into derivation and validation cohorts for the dosing model. The minor allele frequency (MAF) of VKORC1 (-1639G>A) was A (0.47), while the MAF's for the CYP2C9*2 and *3 and CYP4F2*3 were T (0.12), C (0.04) and T (0.43), respectively. Carriers of at least one CYP2C9 decreased function allele (*2 or *3) required lower median (IQR) warfarin doses compared to noncarriers [24.5 (14.5) mg/week vs. 35 (21) mg/week, p < 0.001]. Similarly, carriers of each additional copy of (A) variant in VKORC1 (-1639G>A) led to reduction in warfarin dose requirement compared to noncarriers [21(7.5) vs. 31.5(18.7) vs. 43.7(15), p < 0.0001]. CYP4F2*3 polymorphism on the other hand was not associated with warfarin dose. Multivariate analysis on the derivation cohort (n = 104) showed that a dosing model consisting of hypertension (HTN), heart failure (HF), VKORC1 (-1639G>A), CYP2C9*2 & *3, and smoking could explain 39.2% of warfarin dose variability in Qataris (P < 0.001). In the validation cohort (n = 45), correlation between predicted and actual warfarin doses was moderate (Spearman's rho correlation coefficient = 0.711, p < 0.001). This study concluded that VKORC1 (-1639G>A), CYP2C9*2 & *3 are the most significant predictors of warfarin dose along with HTN, HF and smoking.
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Alsultan A, Al-Suliman AM, Aleem A, AlGahtani FH, Alfadhel M. Utilizing Whole-Exome Sequencing to Characterize the Phenotypic Variability of Sickle Cell Disease. Genet Test Mol Biomarkers 2018; 22:561-567. [PMID: 30183354 DOI: 10.1089/gtmb.2018.0058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Sickle cell disease (SCD) is a monogenic disease that has wide variety of phenotypes with both and environmental factors contributing to its severity. METHODS We performed whole-exome sequencing (WES) in 22 Saudi SCD patients to identify variants that could explain differences in disease phenotypes. All variants, except those that were benign and likely benign, described in the ClinVar database, were considered in our analysis. Gene-based association testing using sequence kernel association optimal unified test (SKAT-O) with small sample adjustment was performed to evaluate the effect of multiple variants in genes on SCD phenotypes. RESULTS The mean age of participants was 28 (range, 10-48 years). All patients were homozygous for the sickle cell mutation. The Benin haplotype was present in 15 patients and the Arab-Indian haplotype in 7 patients. One patient who had both SCD and CHARGE association was heterozygous for pathogenic mutation p.Arg987Ter in the CHD7 gene. One SCD individual who had a stroke was a carrier of the pathogenic variant p.Asp36Tyr in the VKORC1 gene which is, associated with warfarin resistance. Two patients with steady hemoglobin levels of 7.5 and 7.1 g/dL were carriers of the pathogenic mutation p.Gly140Ser in the RPL5 gene that is associated with Diamond-Blackfan anemia. None of the patients were transfusion dependent. A heterozygous pathogenic mutation in the LDLR gene associated with autosomal dominant familial hypercholesterolemia was present in one patient with deep venous thrombosis, although their cholesterol level was normal. One individual with stroke was a carrier for the p.Arg284Ter variant in the NLRP12 gene, which is associated with familial cold autoinflammatory syndrome 2. Another patient with stroke and a pulmonary embolism was heterozygous for the p.Pro106Leu variant of the MPL gene, which has been associated with thrombocytosis. Coding variants in the GOLGB1, ENPP1, and PON1 genes showed no association with stroke in our study. SKAT-O analysis did not explain SCD heterogeneity. CONCLUSION WES provided limited information to explain the severity of SCD. Whole genome sequencing, epigenetic studies, and assessment of environmental factors might expand our knowledge of SCD heterogeneity.
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Affiliation(s)
- Abdulrahman Alsultan
- 1 Department of Pediatrics, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | | | - Aamer Aleem
- 3 Department of Internal Medicine, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Farjah H AlGahtani
- 3 Department of Internal Medicine, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Majid Alfadhel
- 4 Department of Pediatrics, King Abdullah Specialist Children's Hospital , King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia .,5 King Saud bin Abdulaziz University for Health Sciences , Riyadh, Saudi Arabia
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12
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Pharmacogenetic and clinical predictors of response to clopidogrel plus aspirin after acute coronary syndrome in Egyptians. Pharmacogenet Genomics 2018; 28:207-213. [PMID: 30188374 PMCID: PMC9903350 DOI: 10.1097/fpc.0000000000000349] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVES Dual antiplatelet therapy (DAPT) with aspirin and clopidogrel reduces the risk for recurrent cardiovascular events after acute coronary syndrome (ACS). However, there is significant variation in response to DAPT that may be influenced by both genetic and nongenetic factors. This study aimed to assess the effect of genetic polymorphisms in PON-1, PEAR-1, P2Y12, CES1, and CYP2C19, along with clinical, demographic, and social factors, on variation in response to DAPT in Egyptians. PARTICIPANTS AND METHODS This study included 230 Egyptians treated with clopidogrel 75 mg/day and aspirin 81 mg/day for at least 12 months following their first ACS. Simple and multivariable logistic regression analyses were carried out to identify factors associated with major adverse cardiovascular events (MACE), defined as the occurrence of recurrent ACS, ischemic stroke, stent-related revascularization, or death, in clopidogrel-treated participants. RESULTS Using multivariable logistic regression analysis, the CYP2C19*2 polymorphism was the only genetic predictor of MACE [odds ratio (OR): 2.23, 95% confidence interval (CI): 1.15-4.33, P=0.01]. In addition, proton pump inhibitor use (OR: 4.77, 95% CI: 1.47-15.54, P=0.009) and diabetes (OR: 1.83, 95% CI: 1.03-3.26, P=0.03) were associated with higher cardiovascular risk, whereas statin use was associated with lower risk (OR: 0.43, 95% CI: 0.25-0.76, P=0.003). The contribution of these four genetic and nongenetic factors explained 19% of the variability in risk for MACE in Egyptians treated with DAPT. CONCLUSION These results highlight that CYP2C19*2, along with diabetes, and use of proton pump inhibitor and statin are important factors jointly associated with variability in clinical response to DAPT following ACS in Egyptians.
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Jiang J, Ji N, Lan J, Ge X, Du X. Clinical verification of Lou type warfarin pharmacokinetic dosing algorithms equation. Mol Med Rep 2018; 17:6144-6149. [PMID: 29436624 DOI: 10.3892/mmr.2018.8562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 12/22/2017] [Indexed: 01/07/2023] Open
Abstract
Warfarin is the most commonly used oral anti-coagulant in clinic practice. However, it is difficult to recommend the correct dosage due to its narrow therapeutic window. The aim of the present study was to verify the clinical value of the Lou type equation, using pharmacogenetics‑based warfarin dosing algorithms to appropriately predict the actual maintenance dose. A total of 87 Chinese Han patients who required treatment with warfarin were enrolled and randomly divided into the experimental and control groups. In the experimental group, the first 3 doses of warfarin were calculated according to the Lou type equation. While in the control group, these 3 treatments were performed following the doctors' recommendations. Then the dose of warfarin was gradually adjusted to the stable dose according to the changes in the international standardized ratio. At the end of the 50 day experimental period, there were a greater number of patients in the experimental group who exhibited a stable blood concentration of warfarin than those in the control group (83.35 and 64.4%, respectively). In addition, the mean and median times for patients to obtain a stable dose in the experimental group were significantly shorter than those in the control group (mean, 18.2±1.7 and 27.3±2.0 days; and median, 11.7±1.1 and 20.5±1.8 days, respectively). The adverse reaction rate of the experimental group (9.5%) was markedly lower than that of the control group (26.7%). The occurrence of adverse reactions in the experimental group was also significantly later when compared with the control group (43.9±1.6 and 38.6±1.5 days, respectively). Furthermore, there was no significant difference between the average predicted dose (3.4±1.1 mg/day) and the average actual dose (3.5±1.4 mg/day; P=0.313). In conclusion, using the Lou type warfarin pharmacokinetic dosing algorithm equation to administer warfarin markedly shortened the adjustment time of warfarin to reach a stable dose and reduced the adverse reactions rate, thus supporting clinical feasibility.
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Affiliation(s)
- Jiangang Jiang
- Department of Cardiology, Jinhua Hospital of TCM Affiliated to Zhejiang University of Traditional Chinese Medicine, Jinhua, Zhejiang 321000, P.R. China
| | - Ningning Ji
- Department of Cardiology, Yiwu Central Hospital, Yiwu, Zhejiang 322000, P.R. China
| | - Jingliang Lan
- Department of Cardiology, Jinhua Hospital of TCM Affiliated to Zhejiang University of Traditional Chinese Medicine, Jinhua, Zhejiang 321000, P.R. China
| | - Xiaoping Ge
- Department of Geriatrics, Zhejiang Jinhua Guangfu Hospital, Jinhua, Zhejiang 321000, P.R. China
| | - Xiaoma Du
- Department of Cardiology, Jinhua Hospital of TCM Affiliated to Zhejiang University of Traditional Chinese Medicine, Jinhua, Zhejiang 321000, P.R. China
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The Impact of Genetic and Non-Genetic Factors on Warfarin Dose Prediction in MENA Region: A Systematic Review. PLoS One 2016; 11:e0168732. [PMID: 27992547 PMCID: PMC5167425 DOI: 10.1371/journal.pone.0168732] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/05/2016] [Indexed: 01/13/2023] Open
Abstract
Background Warfarin is the most commonly used oral anticoagulant for the treatment and prevention of thromboembolic disorders. Pharmacogenomics studies have shown that variants in CYP2C9 and VKORC1 genes are strongly and consistently associated with warfarin dose variability. Although different populations from the Middle East and North Africa (MENA) region may share the same ancestry, it is still unclear how they compare in the genetic and non-genetic factors affecting their warfarin dosing. Objective To explore the prevalence of CYP2C9 and VKORC1 variants in MENA, and the effect of these variants along with other non-genetic factors in predicting warfarin dose. Methods In this systematic review, we included observational cross sectional and cohort studies that enrolled patients on stable warfarin dose and had the genetics and non-genetics factors associated with mean warfarin dose as the primary outcome. We searched PubMed, Medline, Scopus, PharmGKB, PHGKB, Google scholar and reference lists of relevant reviews. Results We identified 17 studies in eight different populations: Iranian, Israeli, Egyptian, Lebanese, Omani, Kuwaiti, Sudanese and Turkish. Most common genetic variant in all populations was the VKORC1 (-1639G>A), with a minor allele frequency ranging from 30% in Egyptians and up to 52% and 56% in Lebanese and Iranian, respectively. Variants in the CYP2C9 were less common, with the highest MAF for CYP2C9*2 among Iranians (27%). Variants in the VKORC1 and CYP2C9 were the most significant predictors of warfarin dose in all populations. Along with other genetic and non-genetic factors, they explained up to 63% of the dose variability in Omani and Israeli patients. Conclusion Variants of VKORC1 and CYP2C9 are the strongest predictors of warfarin dose variability among the different populations from MENA. Although many of those populations share the same ancestry and are similar in their warfarin dose predictors, a population specific dosing algorithm is needed for the prospective estimation of warfarin dose.
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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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Yang Y, Peter I, Scott SA. Pharmacogenetics in Jewish populations. ACTA ACUST UNITED AC 2015; 29:221-33. [PMID: 24867283 DOI: 10.1515/dmdi-2013-0069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/04/2014] [Indexed: 12/24/2022]
Abstract
Spanning over 2000 years, the Jewish population has a long history of migration, population bottlenecks, expansions, and geographical isolation, which has resulted in a unique genetic architecture among the Jewish people. As such, many Mendelian disease genes and founder mutations for autosomal recessive diseases have been discovered in several Jewish groups, which have prompted recent genomic studies in the Jewish population on common disease susceptibility and other complex traits. Although few studies on the genetic determinants of drug response variability have been reported in the Jewish population, a number of unique pharmacogenetic variants have been discovered that are more common in Jewish populations than in other major racial groups. Notable examples identified in the Ashkenazi Jewish (AJ) population include the vitamin K epoxide reductase complex subunit 1 (VKORC1) c.106G>T (p.D36Y) variant associated with high warfarin dosing requirements and the recently reported cytochrome P450 2C19 (CYP2C19) allele, CYP2C19*4B, that harbors both loss-of-function [*4 (c.1A>G)] and increased-function [*17 (c.-806C>T)] variants on the same haplotype. These data are encouraging in that like other ethnicities and subpopulations, the Jewish population likely harbors numerous pharmacogenetic variants that are uncommon or absent in other larger racial groups and ethnicities. In addition to unique variants, common multi-ethnic variants in key drug metabolism genes (e.g., ABCB1, CYP2C8, CYP2C9, CYP2C19, CYP2D6, NAT2) have also been detected in the AJ and other Jewish groups. This review aims to summarize the currently available pharmacogenetics literature and discuss future directions for related research with this unique population.
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18
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Watzka M, Geisen C, Scheer M, Wieland R, Wiegering V, Dörner T, Laws HJ, Gümrük F, Hanalioglu S, Unal S, Albayrak D, Oldenburg J. Bleeding and non-bleeding phenotypes in patients with GGCX gene mutations. Thromb Res 2014; 134:856-65. [PMID: 25151188 DOI: 10.1016/j.thromres.2014.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/13/2014] [Accepted: 07/07/2014] [Indexed: 11/30/2022]
Abstract
Functional limitations for the vitamin K cycle, caused either by mutations in gamma-glutamyl carboxylase or vitamin K epoxide reductase genes, result in hereditary deficiency of vitamin K-dependent coagulation factors (VKCFD1 and VKCFD2, respectively). Patients suffering from VKCFD often share several other anatomical irregularities which are not related to haemostasis. Here we report on nine patients, eight of them previously unreported, who presented with VKCFD1. All were examined with special attention to vitamin K-dependent coagulation factors as well as to bone and heart development and to other anatomical signs of embryonal vitamin K deficiency. In total, we detected ten mutations in the gamma-glutamyl carboxylase gene of which seven have not been previously reported. Most interestingly, additional non-bleeding phenotypes were observed in all patients including midfacial hypoplasia, premature osteoporosis, cochlear hearing loss, heart valve defects, pulmonary stenosis, or pseudoxanthoma elasticum-like phenotype. Undercarboxylated matrix Gla protein, osteocalcin, and periostin appear to be responsible for these defects which are also observed in cases of fetal warfarin syndrome.
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Affiliation(s)
- Matthias Watzka
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, 53105 Bonn, Germany
| | - Christof Geisen
- Institute of Transfusion Medicine and Immunohaematology, DRK Blood Donor Service Baden-Württemberg-Hessen, 60526 Frankfurt/Main, Germany
| | - Monika Scheer
- Pediatrics 5 (Oncology, Hematology, Immunology), Klinikum Stuttgart, Olgahospital, 70176 Stuttgart, Germany
| | - Regina Wieland
- Department of Paediatric Haematology and Oncology, Children's Hospital, University of Essen, 45122 Essen, Germany
| | - Verena Wiegering
- Department of Paediatric Haematology, Oncology, Paediatric Stem Cell Transplantation Program, University Children's Hospital Würzburg, 97080 Würzburg, Germany
| | - Thomas Dörner
- Department of Medicine/ Rheumatology and Clinical Immunology, Clinical Hemostaseology, Charité University Medicine Berlin, 10098 Berlin, Germany
| | - Hans-Jürgen Laws
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Fatma Gümrük
- Division of Pediatric Hematology, Faculty of Medicine, Hacettepe University, 06100 Sihhiye/Ankara, Turkey
| | - Sahin Hanalioglu
- Division of Pediatric Hematology, Faculty of Medicine, Hacettepe University, 06100 Sihhiye/Ankara, Turkey
| | - Sule Unal
- Division of Pediatric Hematology, Faculty of Medicine, Hacettepe University, 06100 Sihhiye/Ankara, Turkey
| | - Davut Albayrak
- Department of Pediatric Hematology, Ondokuz Mayis University, 55139 Samsun, Turkey
| | - Johannes Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, 53105 Bonn, Germany.
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The VKORC1 Asp36Tyr variant and VKORC1 haplotype diversity in Ashkenazi and Ethiopian populations. J Appl Genet 2014; 55:163-71. [PMID: 24425227 DOI: 10.1007/s13353-013-0189-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/16/2013] [Accepted: 12/26/2013] [Indexed: 12/30/2022]
Abstract
The vitamin K epoxide reductase (VKORC1) is a key enzyme in the vitamin K cycle impacting various biological processes. VKORC1 genetic variability has been extensively studied in the context of warfarin pharmacogenetics revealing different distributions of VKORC1 haplotypes in various populations. We previously identified the VKORC1 Asp36Tyr mutation that was associated with warfarin resistance and with distinctive ethnic distribution. In this study, we performed haplotype analysis using Asp36Tyr and seven other VKORC1 markers in Ashkenazi and Ethiopian-Jewish and non-Jewish individuals. The VKORC1 variability was represented by nine haplotypes (V1-V9) that could be grouped into two distinct clusters (V1-V3 and V4-V9) with intra-cluster difference limited to two nucleotide changes. Phylogeny analysis suggested that these haplotypes could have developed from an ancestral variant, the common V8 haplotype (40 % in all population samples), after ten single mutation events. Asp36Tyr was exclusive to the V5 haplotype of the second cluster. Two haplotypes V5 and V4, distinguished only by Asp36Tyr, were prevalent in both Ethiopian population samples. The V2 haplotype, belonging to the first cluster, was the second most prevalent haplotype in the Ashkenazi population sample (15.8 %) but relatively uncommon in the Ethiopian origin (4.5-4.7 %). We discuss the genetic diversity among studied populations and its potential impact on warfarin-dose management in certain populations of African and European origin.
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Oldenburg J, Müller CR, Rost S, Watzka M, Bevans CG. Comparative genetics of warfarin resistance. Hamostaseologie 2013; 34:143-59. [PMID: 24287886 DOI: 10.5482/hamo-13-09-0047] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 09/25/2013] [Indexed: 11/05/2022] Open
Abstract
Warfarin and other 4-hydroxycoumarin-based oral anticoagulants targeting vitamin K 2,3-epoxide reductase complex subunit 1 (VKORC1) are administered to humans, mice and rats with different purposes in mind - to act as pesticides in high-dosage baits for killing rodents, but also to save lives when administered in low dosages as antithrombotic drugs in humans. However, high-dosage warfarin used to control rodent populations has resulted in numerous mutations causing warfarin resistance. Currently, six single missense mutations in mice, 12 distinct missense mutations in rats, as well as compound heterozygous or homozygous mutations with up to six distinct missense mutations per Vkorc1 allele have been described. Warfarin resistance missense mutations for human VKORC1 have also been found world-wide, but differ characteristically from those in rodents. In humans, 26 distinct mutations have been characterized, but occur only rarely either in heterozygous or, even rarer, in homozygous form. In this review, we summarize the known VKORC1 missense mutations causing warfarin and other 4-hydroxycoumarin drug resistance, identify genomics databases as new sources of data, explore possible underlying genetic mechanisms, and summarize similarities and differences between warfarin resistant VKORC1 variants in humans and rodents.
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Affiliation(s)
- J Oldenburg
- Prof. Dr. Johannes Oldenburg, Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Sigmund Freud Str. 25, 53105 Bonn, Germany, E-mail: , Tel. +49/(0)228/287 51 75, Fax +49/(0)228/287 51 76
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