1
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Shaaban S, Ji Y. Pharmacogenomics and health disparities, are we helping? Front Genet 2023; 14:1099541. [PMID: 36755573 PMCID: PMC9900000 DOI: 10.3389/fgene.2023.1099541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Pharmacogenomics has been at the forefront of precision medicine during the last few decades. Precision medicine carries the potential of improving health outcomes at both the individual as well as population levels. To harness the benefits of its initiatives, careful dissection of existing health disparities as they relate to precision medicine is of paramount importance. Attempting to address the existing disparities at the early stages of design and implementation of these efforts is the only guarantee of a successful just outcome. In this review, we glance at a few determinants of existing health disparities as they intersect with pharmacogenomics research and implementation. In our opinion, highlighting these disparities is imperative for the purpose of researching meaningful solutions. Failing to identify, and hence address, these disparities in the context of the current and future precision medicine initiatives would leave an already strained health system, even more inundated with inequality.
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Affiliation(s)
- Sherin Shaaban
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States,ARUP Laboratories, Salt Lake City, Utah, United States,*Correspondence: Sherin Shaaban,
| | - Yuan Ji
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States,ARUP Laboratories, Salt Lake City, Utah, United States
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2
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Zhou Y, Lauschke VM. Population pharmacogenomics: an update on ethnogeographic differences and opportunities for precision public health. Hum Genet 2022; 141:1113-1136. [PMID: 34652573 PMCID: PMC9177500 DOI: 10.1007/s00439-021-02385-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Both safety and efficacy of medical treatment can vary depending on the ethnogeographic background of the patient. One of the reasons underlying this variability is differences in pharmacogenetic polymorphisms in genes involved in drug disposition, as well as in drug targets. Knowledge and appreciation of these differences is thus essential to optimize population-stratified care. Here, we provide an extensive updated analysis of population pharmacogenomics in ten pharmacokinetic genes (CYP2D6, CYP2C19, DPYD, TPMT, NUDT15 and SLC22A1), drug targets (CFTR) and genes involved in drug hypersensitivity (HLA-A, HLA-B) or drug-induced acute hemolytic anemia (G6PD). Combined, polymorphisms in the analyzed genes affect the pharmacology, efficacy or safety of 141 different drugs and therapeutic regimens. The data reveal pronounced differences in the genetic landscape, complexity and variant frequencies between ethnogeographic groups. Reduced function alleles of CYP2D6, SLC22A1 and CFTR were most prevalent in individuals of European descent, whereas DPYD and TPMT deficiencies were most common in Sub-Saharan Africa. Oceanian populations showed the highest frequencies of CYP2C19 loss-of-function alleles while their inferred CYP2D6 activity was among the highest worldwide. Frequencies of HLA-B*15:02 and HLA-B*58:01 were highest across Asia, which has important implications for the risk of severe cutaneous adverse reactions upon treatment with carbamazepine and allopurinol. G6PD deficiencies were most frequent in Africa, the Middle East and Southeast Asia with pronounced differences in variant composition. These variability data provide an important resource to inform cost-effectiveness modeling and guide population-specific genotyping strategies with the goal of optimizing the implementation of precision public health.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
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3
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Patrinos GP, Shuldiner AR. Pharmacogenomics: the low-hanging fruit in the personalized medicine tree. Hum Genet 2022; 141:1109-1111. [PMID: 35482087 DOI: 10.1007/s00439-022-02456-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- George P Patrinos
- Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras School of Health Sciences, University Campus, Rion, 265 04, Patras, Greece. .,College of Medicine and Health Sciences, Department of Genetics and Genomics, United Arab Emirates University, Al-Ain, United Arab Emirates. .,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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4
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Jithesh PV, Abuhaliqa M, Syed N, Ahmed I, El Anbari M, Bastaki K, Sherif S, Umlai UK, Jan Z, Gandhi G, Manickam C, Selvaraj S, George C, Bangarusamy D, Abdel-Latif R, Al-Shafai M, Tatari-Calderone Z, Estivill X, Pirmohamed M. A population study of clinically actionable genetic variation affecting drug response from the Middle East. NPJ Genom Med 2022; 7:10. [PMID: 35169154 PMCID: PMC8847489 DOI: 10.1038/s41525-022-00281-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/22/2021] [Indexed: 02/08/2023] Open
Abstract
Clinical implementation of pharmacogenomics will help in personalizing drug prescriptions and alleviate the personal and financial burden due to inefficacy and adverse reactions to drugs. However, such implementation is lagging in many parts of the world, including the Middle East, mainly due to the lack of data on the distribution of actionable pharmacogenomic variation in these ethnicities. We analyzed 6,045 whole genomes from the Qatari population for the distribution of allele frequencies of 2,629 variants in 1,026 genes known to affect 559 drugs or classes of drugs. We also performed a focused analysis of genotypes or diplotypes of 15 genes affecting 46 drugs, which have guidelines for clinical implementation and predicted their phenotypic impact. The allele frequencies of 1,320 variants in 703 genes affecting 299 drugs or class of drugs were significantly different between the Qatari population and other world populations. On average, Qataris carry 3.6 actionable genotypes/diplotypes, affecting 13 drugs with guidelines for clinical implementation, and 99.5% of the individuals had at least one clinically actionable genotype/diplotype. Increased risk of simvastatin-induced myopathy could be predicted in ~32% of Qataris from the diplotypes of SLCO1B1, which is higher compared to many other populations, while fewer Qataris may need tacrolimus dosage adjustments for achieving immunosuppression based on the CYP3A5 diplotypes compared to other world populations. Distinct distribution of actionable pharmacogenomic variation was also observed among the Qatari subpopulations. Our comprehensive study of the distribution of actionable genetic variation affecting drugs in a Middle Eastern population has potential implications for preemptive pharmacogenomic implementation in the region and beyond.
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Affiliation(s)
| | | | - Najeeb Syed
- Research Branch, Sidra Medicine, Doha, Qatar
| | | | | | - Kholoud Bastaki
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.,Hamad Medical Corporation, Doha, Qatar
| | - Shimaa Sherif
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Umm-Kulthum Umlai
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Zainab Jan
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Geethanjali Gandhi
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.,Research Branch, Sidra Medicine, Doha, Qatar
| | | | | | | | - Dhinoth Bangarusamy
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Rania Abdel-Latif
- Qatar Genome Program, Qatar Foundation Research Development and Innovation, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | | | - Xavier Estivill
- Quantitative Genomics Laboratories, Barcelona, Catalonia, Spain
| | - Munir Pirmohamed
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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5
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Stanković B, Kotur N, Gašić V, Klaassen K, Ristivojević B, Stojiljković M, Pavlović S, Zukić B. Pharmacogenomics landscape of COVID-19 therapy response in Serbian population and comparison with worldwide populations. J Med Biochem 2020; 39:488-499. [PMID: 33312066 DOI: 10.5937/jomb0-26725] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
Background Since there are no certified therapeutics to treat COVID-19 patients, drug repurposing became important. With lack of time to test individual pharmacogenomics markers, population pharmacogenomics could be helpful in predicting a higher risk of developing adverse reactions and treatment failure in COVID-19 patients. Aim of our study was to identify pharmacogenes and pharmacogenomics markers associated with drugs recommended for COVID-19 treatment, chloroquine/hydroxychloroquine, azithromycin, lopinavir and ritonavir, in population of Serbia and other world populations. Methods Genotype information of 143 individuals of Serbian origin was extracted from database previously obtained using TruSight One Gene Panel (Illumina). Genotype data of individuals from different world populations were extracted from the 1000 Genome Project. Fisher's exact test was used for comparison of allele frequencies. Results We have identified 11 potential pharmacogenomics markers in 7 pharmacogenes relevant for COVID-19 treatment. Based on high alternative allele frequencies in population and the functional effect of the variants, ABCB1 rs1045642 and rs2032582 could be relevant for reduced clearance of azithromycin, lopinavir and ritonavir drugs and UGT1A7 rs17868323 for hyperbilirubinemia in ritonavir treated COVID-19 patients in Serbian population. SLCO1B1 rs4149056 is a potential marker of lopinavir response, especially in Italian population. Our results confirmed that pharmacogenomics profile of African population is different from the rest of the world. Conclusions Considering population specific pharmacogenomics landscape, preemptive testing for pharmacogenes relevant for drugs used in COVID-19 treatment could contribute to better understanding of the inconsistency in therapy response and could be applied to improve the outcome of the COVID-19 patients.
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Affiliation(s)
- Biljana Stanković
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Nikola Kotur
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Vladimir Gašić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Kristel Klaassen
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Bojan Ristivojević
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Maja Stojiljković
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Sonja Pavlović
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Branka Zukić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
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6
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Sketching the prevalence of pharmacogenomic biomarkers among populations for clinical pharmacogenomics. Eur J Hum Genet 2019; 28:1-3. [PMID: 31485027 DOI: 10.1038/s41431-019-0499-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 08/06/2019] [Indexed: 02/08/2023] Open
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7
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Patrinos GP. Population pharmacogenomics: impact on public health and drug development. Pharmacogenomics 2018; 19:3-6. [DOI: 10.2217/pgs-2017-0166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- George P Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
- Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
- Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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8
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Schärfe CPI, Tremmel R, Schwab M, Kohlbacher O, Marks DS. Genetic variation in human drug-related genes. Genome Med 2017; 9:117. [PMID: 29273096 PMCID: PMC5740940 DOI: 10.1186/s13073-017-0502-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/24/2017] [Indexed: 12/17/2022] Open
Abstract
Background Variability in drug efficacy and adverse effects are observed in clinical practice. While the extent of genetic variability in classic pharmacokinetic genes is rather well understood, the role of genetic variation in drug targets is typically less studied. Methods Based on 60,706 human exomes from the ExAC dataset, we performed an in-depth computational analysis of the prevalence of functional variants in 806 drug-related genes, including 628 known drug targets. We further computed the likelihood of 1236 FDA-approved drugs to be affected by functional variants in their targets in the whole ExAC population as well as different geographic sub-populations. Results We find that most genetic variants in drug-related genes are very rare (f < 0.1%) and thus will likely not be observed in clinical trials. Furthermore, we show that patient risk varies for many drugs and with respect to geographic ancestry. A focused analysis of oncological drug targets indicates that the probability of a patient carrying germline variants in oncological drug targets is, at 44%, high enough to suggest that not only somatic alterations but also germline variants carried over into the tumor genome could affect the response to antineoplastic agents. Conclusions This study indicates that even though many variants are very rare and thus likely not observed in clinical trials, four in five patients are likely to carry a variant with possibly functional effects in a target for commonly prescribed drugs. Such variants could potentially alter drug efficacy. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0502-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charlotta Pauline Irmgard Schärfe
- Department of Systems Biology, Harvard Medical School, Boston, 02115, Massachusetts, USA.,Center for Bioinformatics, University of Tübingen, 72076, Tübingen, Germany.,pplied Bioinformatics, Department of Computer Science, 72076, Tübingen, Germany
| | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital Tübingen, 72076, Tübingen, Germany.,Department of Pharmacy and Biochemistry, University of Tübingen, 72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, 72076, Tübingen, Germany. .,pplied Bioinformatics, Department of Computer Science, 72076, Tübingen, Germany. .,Quantitative Biology Center, 72076, Tübingen, Germany. .,Faculty of Medicine, University of Tübingen, 72076, Tübingen, Germany. .,Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
| | - Debora Susan Marks
- Department of Systems Biology, Harvard Medical School, Boston, 02115, Massachusetts, USA.
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9
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Patrinos GP, Katsila T. Pharmacogenomics education and research at the Department of Pharmacy, University of Patras, Greece. Pharmacogenomics 2016; 17:1865-1872. [DOI: 10.2217/pgs-2016-0142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Pharmacogenomics and Personalized Medicine group belongs to the Laboratory of Molecular Biology and Immunology, Department of Pharmacy and is active since 2009 mainly in the field of pharmacogenomics and personalized medicine. Herein, we describe the research interests, collaborations and accomplishments of the Pharmacogenomics and Personalized Medicine group together with the teaching activities of the group that greatly enhance the pharmacogenomics knowledge of graduate/postgraduate students and healthcare professionals.
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
- Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
- Department of Bioinformatics, Faculty of Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
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10
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Vozikis A, Cooper DN, Mitropoulou C, Kambouris ME, Brand A, Dolzan V, Fortina P, Innocenti F, Lee MTM, Leyens L, Macek Jr M, Al-Mulla F, Prainsack B, Squassina A, Taruscio D, van Schaik RH, Vayena E, Williams MS, Patrinos GP. Test Pricing and Reimbursement in Genomic Medicine: Towards a General Strategy. Public Health Genomics 2016; 19:352-363. [DOI: 10.1159/000449152] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/16/2016] [Indexed: 11/19/2022] Open
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11
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ePGA: A Web-Based Information System for Translational Pharmacogenomics. PLoS One 2016; 11:e0162801. [PMID: 27631363 PMCID: PMC5025168 DOI: 10.1371/journal.pone.0162801] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/29/2016] [Indexed: 11/19/2022] Open
Abstract
One of the challenges that arise from the advent of personal genomics services is to efficiently couple individual data with state of the art Pharmacogenomics (PGx) knowledge. Existing services are limited to either providing static views of PGx variants or applying a simplistic match between individual genotypes and existing PGx variants. Moreover, there is a considerable amount of haplotype variation associated with drug metabolism that is currently insufficiently addressed. Here, we present a web-based electronic Pharmacogenomics Assistant (ePGA; http://www.epga.gr/) that provides personalized genotype-to-phenotype translation, linked to state of the art clinical guidelines. ePGA's translation service matches individual genotype-profiles with PGx gene haplotypes and infers the corresponding diplotype and phenotype profiles, accompanied with summary statistics. Additional features include i) the ability to customize translation based on subsets of variants of clinical interest, and ii) to update the knowledge base with novel PGx findings. We demonstrate ePGA's functionality on genetic variation data from the 1000 Genomes Project.
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12
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Douzgou S, Pollalis YA, Vozikis A, Patrinos GP, Clayton-Smith J. Collaborative Crowdsourcing for the Diagnosis of Rare Genetic Syndromes: The DYSCERNE Experience. Public Health Genomics 2015; 19:19-24. [PMID: 26447648 DOI: 10.1159/000440710] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/31/2015] [Indexed: 11/19/2022] Open
Abstract
The big-data revolution is creating a challenge for the provision of services in the health sector to keep pace with the expectations of the general population. Utilization of crowdsourcing can impact positively on the quality, cost and speed of healthcare by involving large sections of professionals and the public and creating novel science within an ethical framework. In 2007, the DYSCERNE project was funded by the European Commission Public Health Executive Agency (EU DG Sanco) aimed at setting up a network of expertise for rare dysmorphic disorders. As part of DYSCERNE, a Dysmorphology Diagnostic System was set up to enable clinicians throughout the EU to submit cases electronically for diagnosis using a secure, web-based interface, hosted at specified access points (submitting nodes), in 26 different European countries. DYSCERNE utilized the process of crowdsourcing international expertise for the clinical diagnosis of very rare genetic syndromes of multiple congenital anomalies. This is the first reported account of collaborative crowd sourcing in dysmorphology, as part of a clinical genetics service.
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Affiliation(s)
- Sofia Douzgou
- Department of Economics, University of Piraeus, Piraeus, Greece
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13
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Mizzi C, Peters B, Mitropoulou C, Mitropoulos K, Katsila T, Agarwal MR, van Schaik RHN, Drmanac R, Borg J, Patrinos GP. Personalized pharmacogenomics profiling using whole-genome sequencing. Pharmacogenomics 2015; 15:1223-34. [PMID: 25141897 DOI: 10.2217/pgs.14.102] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIM Pharmacogenomics holds promise to rationalize drug use by minimizing drug toxicity and at the same time increase drug efficacy. There are currently several assays to screen for known pharmacogenomic biomarkers for the most commonly prescribed drugs. However, these genetic screening assays cannot account for other known or novel pharmacogenomic markers. MATERIALS & METHODS We analyzed whole-genome sequences of 482 unrelated individuals of various ethnic backgrounds to obtain their personalized pharmacogenomics profiles. RESULTS Bioinformatics analysis revealed 408,964 variants in 231 pharmacogenes, from which 26,807 were residing on exons and proximal regulatory sequences, whereas 16,487 were novel. In silico analyses indicated that 1012 novel pharmacogene-related variants possibly abolish protein function. We have also performed whole-genome sequencing analysis in a seven-member family of Greek origin in an effort to explain the variable response rate to acenocoumarol treatment in two family members. CONCLUSION Overall, our data demonstrate that whole-genome sequencing, unlike conventional genetic screening methods, is necessary to determine an individual's pharmacogenomics profile in a more comprehensive manner, which, combined with the gradually decreasing whole-genome sequencing costs, would expedite bringing personalized medicine closer to reality.
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Affiliation(s)
- Clint Mizzi
- Laboratory of Molecular Genetics, Department of Physiology & Biochemistry, University of Malta, Msida, Malta
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14
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Pisanu C, Tsermpini EE, Mavroidi E, Katsila T, Patrinos GP, Squassina A. Assessment of the Pharmacogenomics Educational Environment in Southeast Europe. Public Health Genomics 2014; 17:272-9. [DOI: 10.1159/000366461] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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López Aspiroz E, Santos Buelga D, Cabrera Figueroa SE, Valverde Merino MDLP, Cordero Sánchez M, Domínguez-Gil Hurlé A, Carracedo Á, García Sánchez MJ. Population pharmacokinetic/pharmacogenetic model of lopinavir/ritonavir in HIV-infected patients. Per Med 2014; 11:693-704. [PMID: 29764054 DOI: 10.2217/pme.14.58] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
AIM This study aims to develop a population pharmacokinetic/pharmacogenetic model for lopinavir/ritonavir (LPV/r) in European HIV-infected patients. MATERIALS & METHODS A total of 693 LPV/r plasma concentrations were assessed and 15 single-nucleotide polymorphisms were genotyped. The population pharmacokinetic/pharmacogenetic model was created using a nonlinear mixed-effect approach (NONMEM® v.7.2.0., ICON Development Solutions, Dublin, Ireland). RESULTS Covariates significantly related to LPV/r apparent clearance (CL/F) were ritonavir trough concentration (RTC), BMI, high-density lipoprotein cholesterol (HDL-C) and certain single-nucleotide polymorphisms in genes encoding for metabolizing enzymes, which are representable as follows: CL/F = (0.216BMI + 0.0125HDL-C) × 0.713RTC × 1.26rs28371764[C/T] × 0.528rs6945984[C/C] × 0.302 CYP3A4[1461insA/del] Conclusion: The LPV/r standard dose appears to be appropriate for the rs28371764[C/T] genotype. However, lower doses should be recommended for the rs6945984[C/C] and CYP3A4[1461insA/del] genotypes and even for those patients without any of these variants, as the standard dose seems to be higher than that which is required in order to achieve therapeutic levels.
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Affiliation(s)
- Elena López Aspiroz
- Pharmacy Service, University Hospital of Salamanca, Paseo de San Vicente 58, 37007 Salamanca, Spain
| | - Dolores Santos Buelga
- Department of Pharmacy & Pharmaceutical Technology, Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Salvador Enrique Cabrera Figueroa
- Pharmacy Service, University Hospital of Salamanca, Paseo de San Vicente 58, 37007 Salamanca, Spain.,Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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- Tormes Team: Carmen Bustos Bernal, Aurelio Fuertes Martín, María Jesús Hernández Arroyo, Alicia Iglesias Gómez and Guillermo Luna Rodrigo
| | | | - Alfonso Domínguez-Gil Hurlé
- Pharmacy Service, University Hospital of Salamanca, Paseo de San Vicente 58, 37007 Salamanca, Spain.,Department of Pharmacy & Pharmaceutical Technology, Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica. Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidad de Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), SERGAS (Servicio Galega de Saude), Santiago de Compostela, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - María José García Sánchez
- Department of Pharmacy & Pharmaceutical Technology, Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
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16
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Cooper DN, Brand A, Dolzan V, Fortina P, Innocenti F, Michael Lee MT, Macek M, Al-Mulla F, Prainsack B, Squassina A, Vayena E, Vozikis A, Williams MS, Patrinos GP. Bridging genomics research between developed and developing countries: the Genomic Medicine Alliance. Per Med 2014; 11:615-623. [PMID: 29764053 DOI: 10.2217/pme.14.59] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Genomic Medicine Alliance is a global academic research network that aims to establish and strengthen collaborative ties between the various genomic medicine stakeholders. Its focus lies on the translation of scientific research findings into clinical practice. It brings together experts from disciplines including genome informatics, pharmacogenomics, public health genomics, ethics in genomics and health economics, and it is supervised by a 14-member International Scientific Advisory Committee comprising internationally renowned scientists. The Alliance's official journal, Public Health Genomics, offers members a highly respected publication forum for their original research findings. In the short-to-medium term, the Genomic Medicine Alliance hopes to harmonize research activities between developed and developing countries and to organize educational activities in the field of genomic medicine.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Angela Brand
- University of Maastricht, Institute of Public Health Genomics, Maastricht, The Netherlands
| | - Vita Dolzan
- University of Ljubljana, School of Medicine, Ljubljana, Slovenia
| | - Paolo Fortina
- Thomas Jefferson University, Kimmel Cancer Center, Philadelphia, PA, USA
| | - Federico Innocenti
- Institute of Pharmacogenomics & Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - Ming Ta Michael Lee
- Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Milan Macek
- Charles University Prague & Faculty Hospital Motol, Institute of Biology & Medical Genetics, Prague, Czech Republic
| | - Fahd Al-Mulla
- University of Kuwait, Molecular Pathology Unit, Safat, Kuwait
| | - Barbara Prainsack
- King's College London, Department of Social Science, Health & Medicine, London, UK
| | - Alessio Squassina
- University of Cagliari, School of Medicine, Department of Biomedical Sciences, Cagliari, Italy
| | - Effy Vayena
- University of Zurich, Institute of Biomedical Ethics, Zurich, Switzerland
| | | | - Marc S Williams
- Geisinger Health System, Genomic Medicine Institute, Danville, PA, USA
| | - George P Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, GR-26504, Patras, Greece
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17
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Fortina P, Al Khaja N, Al Ali MT, Hamzeh AR, Nair P, Innocenti F, Patrinos GP, Kricka LJ. Genomics into Healthcare: the 5th Pan Arab Human Genetics Conference and 2013 Golden Helix Symposium. Hum Mutat 2014; 35:637-40. [PMID: 24526565 DOI: 10.1002/humu.22530] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 02/09/2014] [Indexed: 11/07/2022]
Abstract
The joint 5th Pan Arab Human Genetics conference and 2013 Golden Helix Symposium, "Genomics into Healthcare" was coorganized by the Center for Arab Genomic Studies (http://www.cags.org.ae) in collaboration with the Golden Helix Foundation (http://www.goldenhelix.org) in Dubai, United Arab Emirates from 17 to 19 November, 2013. The meeting was attended by over 900 participants, doctors and biomedical students from over 50 countries and was organized into a series of nine themed sessions that covered cancer genomics and epigenetics, genomic and epigenetic studies, genomics of blood and metabolic disorders, cytogenetic diagnosis and molecular profiling, next-generation sequencing, consanguinity and hereditary diseases, clinical genomics, clinical applications of pharmacogenomics, and genomics in public health.
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Affiliation(s)
- Paolo Fortina
- Cancer Genomics Laboratory, Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University Jefferson Medical College, Philadelphia, Pennsylvania; Department of Molecular Medicine, Universita' La Sapienza, Rome, Italy
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18
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Zhao Q, Sun J, Tao Y, Wang S, Jiang C, Zhu Y, Yu F, Zhu J. A logistic equation to determine the validity of tramadol from related gene polymorphisms and psychological factors. Pharmacogenomics 2014; 15:487-95. [PMID: 24624916 DOI: 10.2217/pgs.14.22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Aim: This study was performed to develop an algorithm using polymorphisms of CYP2D6, p-gp, OPRM1, COMT and psychological variables to predict tramadol response in Chinese patients recovering from upper limb fracture internal fixation surgery. Methods: A total of 250 Han Chinese patients recovering from fracture in the upper limb were enrolled. CYP2D6*10, p-gp G2677T, p-gp C3435T, OPRM1 A118G and COMT Val158Met were detected by the ligase detection reaction (LDR) method. The algorithm was developed with binary logistic regression in cohort 1 (200 patients) and assessed with Wilcoxon signed-rank test in cohort 2 (50 patients). Results: According to cohort 1, the predictive equation was calculated with the following logistic regression parameters: Logit (1) = 2.304–4.841 × (anxiety I) – 23.709 × (anxiety II) + 2.823 × (p-gp 3435CT) + 5.737 × (p-gp 3435 TT) – 1.586 × (CYP2D6*10 CT) – 4.542 × (CYP2D6*10 TT). The cutoff point for the prediction was defined as a probability value ≥0.5. The equation’s positive predictive value is 90%. When applied to a new sample, the equation’s positive predictive value is 86%. The Nagelkerke R2 of the model is 0.819, the results of the Hosmer and Leme test show a value of 0.981. The nonparametric correlations between predicted and observed response showed significant correlation (coefficient = 0.879; p < 0.001). Conclusion: The algorithm we have developed might predict tramadol response in Chinese upper limb fracture patients. Original submitted 24 April 2013; Revision submitted 24 January 2014
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Affiliation(s)
- Qin Zhao
- Department of Clinical Pharmacology, Nanjing First Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jianguo Sun
- Center of Pharmacokinetics, Key Laboratory of Drug Metabolism & Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Yifu Tao
- Department of Clinical Pharmacology, Nanjing First Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shukui Wang
- Examination Centres, Nanjing First Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chunzhi Jiang
- Department of Orthopedics, Nanjing First Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yubing Zhu
- Department of Clinical Pharmacology, Nanjing First Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
| | - Feng Yu
- Department of Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Junrong Zhu
- Department of Clinical Pharmacology, Nanjing First Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
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19
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The undiscovered country: the future of integrating genomic information into the EHR. Genet Med 2013; 15:842-5. [PMID: 24071799 PMCID: PMC4259267 DOI: 10.1038/gim.2013.130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 07/18/2013] [Indexed: 12/12/2022] Open
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