1
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Hu J, Szymczak S. A review on longitudinal data analysis with random forest. Brief Bioinform 2023; 24:6991123. [PMID: 36653905 PMCID: PMC10025446 DOI: 10.1093/bib/bbad002] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/12/2022] [Accepted: 12/31/2012] [Indexed: 01/20/2023] Open
Abstract
In longitudinal studies variables are measured repeatedly over time, leading to clustered and correlated observations. If the goal of the study is to develop prediction models, machine learning approaches such as the powerful random forest (RF) are often promising alternatives to standard statistical methods, especially in the context of high-dimensional data. In this paper, we review extensions of the standard RF method for the purpose of longitudinal data analysis. Extension methods are categorized according to the data structures for which they are designed. We consider both univariate and multivariate response longitudinal data and further categorize the repeated measurements according to whether the time effect is relevant. Even though most extensions are proposed for low-dimensional data, some can be applied to high-dimensional data. Information of available software implementations of the reviewed extensions is also given. We conclude with discussions on the limitations of our review and some future research directions.
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Affiliation(s)
- Jianchang Hu
- Institute of Medical Biometry and Statistics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Silke Szymczak
- Institute of Medical Biometry and Statistics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
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2
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Tsermpini EE, Serretti A, Dolžan V. Precision Medicine in Antidepressants Treatment. Handb Exp Pharmacol 2023; 280:131-186. [PMID: 37195310 DOI: 10.1007/164_2023_654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Precision medicine uses innovative approaches to improve disease prevention and treatment outcomes by taking into account people's genetic backgrounds, environments, and lifestyles. Treatment of depression is particularly challenging, given that 30-50% of patients do not respond adequately to antidepressants, while those who respond may experience unpleasant adverse drug reactions (ADRs) that decrease their quality of life and compliance. This chapter aims to present the available scientific data that focus on the impact of genetic variants on the efficacy and toxicity of antidepressants. We compiled data from candidate gene and genome-wide association studies that investigated associations between pharmacodynamic and pharmacokinetic genes and response to antidepressants regarding symptom improvement and ADRs. We also summarized the existing pharmacogenetic-based treatment guidelines for antidepressants, used to guide the selection of the right antidepressant and its dose based on the patient's genetic profile, aiming to achieve maximum efficacy and minimum toxicity. Finally, we reviewed the clinical implementation of pharmacogenomics studies focusing on patients on antidepressants. The available data demonstrate that precision medicine can increase the efficacy of antidepressants and reduce the occurrence of ADRs and ultimately improve patients' quality of life.
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Affiliation(s)
- Evangelia Eirini Tsermpini
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Vita Dolžan
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
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3
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Pharmacogenomics: A Step forward Precision Medicine in Childhood Asthma. Genes (Basel) 2022; 13:genes13040599. [PMID: 35456405 PMCID: PMC9031013 DOI: 10.3390/genes13040599] [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: 02/27/2022] [Revised: 03/23/2022] [Accepted: 03/27/2022] [Indexed: 02/05/2023] Open
Abstract
Personalized medicine, an approach to care in which individual characteristics are used for targeting interventions and maximizing health outcomes, is rapidly becoming a reality for many diseases. Childhood asthma is a heterogeneous disease and many children have uncontrolled symptoms. Therefore, an individualized approach is needed for improving asthma outcomes in children. The rapidly evolving fields of genomics and pharmacogenomics may provide a way to achieve asthma control and reduce future risks in children with asthma. In particular, pharmacogenomics can provide tools for identifying novel molecular mechanisms and biomarkers to guide treatment. Emergent high-throughput technologies, along with patient pheno-endotypization, will increase our knowledge of several molecular mechanisms involved in asthma pathophysiology and contribute to selecting and stratifying appropriate treatment for each patient.
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4
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Clinical implementation of drug metabolizing gene-based therapeutic interventions worldwide. Hum Genet 2021; 141:1137-1157. [PMID: 34599365 DOI: 10.1007/s00439-021-02369-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/09/2021] [Indexed: 02/05/2023]
Abstract
Over the last few years, the field of pharmacogenomics has gained considerable momentum. The advances of new genomics and bioinformatics technologies propelled pharmacogenomics towards its implementation in the clinical setting. Since 2007, and especially the last-5 years, many studies have focused on the clinical implementation of pharmacogenomics while identifying obstacles and proposed strategies and approaches for overcoming them in the real world of primary care as well as outpatients and inpatients clinics. Here, we outline the recent pharmacogenomics clinical implementation projects and provide details of the study designs, including the most predominant and innovative, as well as clinical studies worldwide that focus on outpatients and inpatient clinics, and primary care. According to these studies, pharmacogenomics holds promise for improving patients' health in terms of efficacy and toxicity, as well as in their overall quality of life, while simultaneously can contribute to the minimization of healthcare expenditure.
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5
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van de Ven M, Simons MJHG, Koffijberg H, Joore MA, IJzerman MJ, Retèl VP, van Harten WH. Whole genome sequencing in oncology: using scenario drafting to explore future developments. BMC Cancer 2021; 21:488. [PMID: 33933021 PMCID: PMC8088550 DOI: 10.1186/s12885-021-08214-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background In oncology, Whole Genome Sequencing (WGS) is not yet widely implemented due to uncertainties such as the required infrastructure and expertise, costs and reimbursements, and unknown pan-cancer clinical utility. Therefore, this study aimed to investigate possible future developments facilitating or impeding the use of WGS as a molecular diagnostic in oncology through scenario drafting. Methods A four-step process was adopted for scenario drafting. First, the literature was searched for barriers and facilitators related to the implementation of WGS. Second, they were prioritized by international experts, and third, combined into coherent scenarios. Fourth, the scenarios were implemented in an online survey and their likelihood of taking place within 5 years was elicited from another group of experts. Based on the minimum, maximum, and most likely (mode) parameters, individual Program Evaluation and Review Technique (PERT) probability density functions were determined. Subsequently, individual opinions were aggregated by performing unweighted linear pooling, from which summary statistics were extracted and reported. Results Sixty-two unique barriers and facilitators were extracted from 70 articles. Price, clinical utility, and turnaround time of WGS were ranked as the most important aspects. Nine scenarios were developed and scored on likelihood by 18 experts. The scenario about introducing WGS as a clinical diagnostic with a lower price, shorter turnaround time, and improved degree of actionability, scored the highest likelihood (median: 68.3%). Scenarios with low likelihoods and strong consensus were about better treatment responses to more actionable targets (26.1%), and the effect of centralizing WGS (24.1%). Conclusions Based on current expert opinions, the implementation of WGS as a clinical diagnostic in oncology is heavily dependent on the price, clinical utility (both in terms of identifying actionable targets as in adding sufficient value in subsequent treatment), and turnaround time. These aspects and the optimal way of service provision are the main drivers for the implementation of WGS and should be focused on in further research. More knowledge regarding these factors is needed to inform strategic decision making regarding the implementation of WGS, which warrants support from all relevant stakeholders. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08214-8.
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Affiliation(s)
- Michiel van de Ven
- Technical Medical Centre, University of Twente, Enschede, The Netherlands
| | - Martijn J H G Simons
- Maastricht University Medical Center, Maastricht, The Netherlands.,Maastricht University, Care and Public Health Research Institute (CAPHRI), Maastricht, The Netherlands
| | - Hendrik Koffijberg
- Technical Medical Centre, University of Twente, Enschede, The Netherlands
| | - Manuela A Joore
- Maastricht University Medical Center, Maastricht, The Netherlands.,Maastricht University, Care and Public Health Research Institute (CAPHRI), Maastricht, The Netherlands
| | - Maarten J IJzerman
- Technical Medical Centre, University of Twente, Enschede, The Netherlands.,University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Australia.,Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Valesca P Retèl
- Technical Medical Centre, University of Twente, Enschede, The Netherlands. .,Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam, The Netherlands.
| | - Wim H van Harten
- Technical Medical Centre, University of Twente, Enschede, The Netherlands.,Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam, The Netherlands.,Rijnstate General Hospital, Arnhem, The Netherlands
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6
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Issa AM, Carleton B, Gerhard T, Filipski KK, Freedman AN, Kimmel S, Liu G, Longo C, Maitland-van der Zee AH, Sansbury L, Zhou W, Bartlett G. Pharmacoepidemiology: A time for a new multidisciplinary approach to precision medicine. Pharmacoepidemiol Drug Saf 2021; 30:985-992. [PMID: 33715268 DOI: 10.1002/pds.5226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 03/09/2021] [Indexed: 11/06/2022]
Abstract
The advent of the genomic age has created a rapid increase in complexity for the development and selection of drug treatments. A key component of precision medicine is the use of genetic information to improve therapeutic effectiveness of drugs and prevent potential adverse drug reactions. Pharmacoepidemiology, as a field, uses observational methods to evaluate the safety and effectiveness of drug treatments in populations. Pharmacoepidemiology by virtue of its focus, tradition, and research orientation can provide appropriate study designs and analysis methods for precision medicine. The objective of this manuscript is to demonstrate how pharmacoepidemiology can impact and shape precision medicine and serve as a reference for pharmacoepidemiologists interested in contributing to the science of precision medicine. This paper depicts the state of the science with respect to the need for pharmacoepidemiology and pharmacoepidemiological methods, tools and approaches for precision medicine; the need for and how pharmacoepidemiologists use their skills to engage with the precision medicine community; and recommendations for moving the science of precision medicine pharmacoepidemiology forward. We propose a new integrated multidisciplinary approach dedicated to the emerging science of precision medicine pharmacoepidemiology.
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Affiliation(s)
- Amalia M Issa
- Personalized Precision Medicine & Targeted Therapeutics, Springfield, Pennsylvania, USA.,'Pharmaceutical Sciences' and 'Health Policy', University of the Sciences in Philadelphia, Philadelphia, Pennsylvania, USA.,'Family Medicine' and `Centre of Genomics & Policy'; Faculty of Medicine & Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Bruce Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, and BC Children's Hospital and Research Institute, Vancouver, British Columbia, Canada
| | - Tobias Gerhard
- Center for Pharmacoepidemiology and Treatment Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Kelly K Filipski
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, Maryland, USA
| | - Andrew N Freedman
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, Maryland, USA
| | - Stephen Kimmel
- 'College of Public Health & Health Professions' and 'College of Medicine', University of Florida, Gainesville, Florida, USA
| | - Geoffrey Liu
- Epidemiology; Dalla Lana School of Public Health, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada
| | - Cristina Longo
- Respiratory Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Respiratory Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Leah Sansbury
- Epidemiology, Value Evidence and Outcomes, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - Wei Zhou
- Center for Observational and Real-world Evidence, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Gillian Bartlett
- School of Medicine, University of Missouri, Columbia, Missouri, USA
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7
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Wong M, Previde P, Cole J, Thomas B, Laxmeshwar N, Mallory E, Lever J, Petkovic D, Altman RB, Kulkarni A. Search and visualization of gene-drug-disease interactions for pharmacogenomics and precision medicine research using GeneDive. J Biomed Inform 2021; 117:103732. [PMID: 33737208 DOI: 10.1016/j.jbi.2021.103732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/10/2020] [Accepted: 02/28/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Understanding the relationships between genes, drugs, and disease states is at the core of pharmacogenomics. Two leading approaches for identifying these relationships in medical literature are: human expert led manual curation efforts, and modern data mining based automated approaches. The former generates small amounts of high-quality data, and the latter offers large volumes of mixed quality data. The algorithmically extracted relationships are often accompanied by supporting evidence, such as, confidence scores, source articles, and surrounding contexts (excerpts) from the articles, that can be used as data quality indicators. Tools that can leverage these quality indicators to help the user gain access to larger and high-quality data are needed. APPROACH We introduce GeneDive, a web application for pharmacogenomics researchers and precision medicine practitioners that makes gene, disease, and drug interactions data easily accessible and usable. GeneDive is designed to meet three key objectives: (1) provide functionality to manage information-overload problem and facilitate easy assimilation of supporting evidence, (2) support longitudinal and exploratory research investigations, and (3) offer integration of user-provided interactions data without requiring data sharing. RESULTS GeneDive offers multiple search modalities, visualizations, and other features that guide the user efficiently to the information of their interest. To facilitate exploratory research, GeneDive makes the supporting evidence and context for each interaction readily available and allows the data quality threshold to be controlled by the user as per their risk tolerance level. The interactive search-visualization loop enables relationship discoveries between diseases, genes, and drugs that might not be explicitly described in literature but are emergent from the source medical corpus and deductive reasoning. The ability to utilize user's data either in combination with the GeneDive native datasets or in isolation promotes richer data-driven exploration and discovery. These functionalities along with GeneDive's applicability for precision medicine, bringing the knowledge contained in biomedical literature to bear on particular clinical situations and improving patient care, are illustrated through detailed use cases. CONCLUSION GeneDive is a comprehensive, broad-use biological interactions browser. The GeneDive application and information about its underlying system architecture are available at http://www.genedive.net. GeneDive Docker image is also available for download at this URL, allowing users to (1) import their own interaction data securely and privately; and (2) generate and test hypotheses across their own and other datasets.
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Affiliation(s)
- Mike Wong
- COSE Computing for Life Sciences, San Francisco State University, San Francisco, CA, United States
| | - Paul Previde
- Department of Computer Science, San Francisco State University, San Francisco, CA, United States
| | - Jack Cole
- Department of Computer Science, San Francisco State University, San Francisco, CA, United States
| | - Brook Thomas
- Department of Computer Science, San Francisco State University, San Francisco, CA, United States
| | - Nayana Laxmeshwar
- Department of Computer Science, San Francisco State University, San Francisco, CA, United States
| | - Emily Mallory
- Biomedical Informatics Training Program, Stanford University, Palo Alto, CA, United States
| | - Jake Lever
- Postdoctoral Scholar, Stanford University, Palo Alto, CA, United States
| | - Dragutin Petkovic
- Department of Computer Science, San Francisco State University, San Francisco, CA, United States; COSE Computing for Life Sciences, San Francisco State University, San Francisco, CA, United States
| | - Russ B Altman
- Department of Bioengineering, Department of Genetics, and School of Medicine, Stanford University, Palo Alto, CA, United States
| | - Anagha Kulkarni
- Department of Computer Science, San Francisco State University, San Francisco, CA, United States.
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8
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Roosan D, Hwang A, Roosan MR. Pharmacogenomics cascade testing (PhaCT): a novel approach for preemptive pharmacogenomics testing to optimize medication therapy. THE PHARMACOGENOMICS JOURNAL 2021; 21:1-7. [PMID: 32843688 PMCID: PMC7840503 DOI: 10.1038/s41397-020-00182-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 06/18/2020] [Accepted: 08/12/2020] [Indexed: 11/08/2022]
Abstract
The implementation of pharmacogenomics (PGx) has come a long way since the dawn of utilizing pharmacogenomic data in clinical patient care. However, the potential benefits of sharing PGx results have yet to be explored. In this paper, we explore the willingness of patients to share PGx results, as well as the inclusion of family medication history in identifying potential family members for pharmacogenomics cascade testing (PhaCT). The genetic similarities in families allow for identifying potential gene variants prior to official preemptive testing. Once a candidate patient is determined, PhaCT can be initiated. PhaCT recognizes that further cascade testing throughout a family can serve to improve precision medicine. In order to make PhaCT feasible, we propose a novel shareable HIPAA-compliant informatics platform that will enable patients to manage not only their own test results and medications but also those of their family members. The informatics platform will be an external genomics system with capabilities to integrate with patients' electronic health records. Patients will be given the tools to provide information to and work with clinicians in identifying family members for PhaCT through this platform. Offering patients the tools to share PGx results with their family members for preemptive testing could be the key to empowering patients. Clinicians can utilize PhaCT to potentially improve medication adherence, which may consequently help to distribute the burden of health management between patients, family members, providers, and payers.
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Affiliation(s)
- Don Roosan
- Department of Pharmacy Practice and Administration, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA.
| | - Angela Hwang
- Department of Pharmacy Practice and Administration, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
| | - Moom R Roosan
- Department of Pharmacy Practice, School of Pharmacy, Chapman University, School of Pharmacy, Irvine, CA, USA.
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9
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Slepukhina MA, Ivashchenko DV, Sheina MA, Muradian AA, Blagovestnov DA, Sychev DA. Pain pharmacogenetics. Drug Metab Pers Ther 2020; 35:dmpt-2020-2939. [PMID: 32776897 DOI: 10.1515/dmpt-2020-2939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/16/2020] [Indexed: 11/15/2022]
Abstract
Pain is a significant problem in medicine. The use of PGx markers to personalize postoperative analgesia can increase its effectiveness and avoid undesirable reactions. This article describes the mechanisms of nociception and antinociception and shows the pathophysiological mechanisms of pain in the human body. The main subject of this article is pharmacogenetic approach to the selection of anesthetics. Current review presents data for local and general anesthetics, opioids, and non-steroidal anti-inflammatory drugs. None of the anesthetics currently has clinical guidelines for pharmacogenetic testing. This literature review summarizes the results of original research available, to date, and draws attention to this area.
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Affiliation(s)
| | - Dmitriy V Ivashchenko
- Child Psychiatry and Psychotherapy Department, Department of Personalized Medicine, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Maria A Sheina
- Department of Anesthesiology and Intensive Care, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | | | - Dmitriy A Sychev
- Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
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10
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A Web-Based Pharmacogenomics Search Tool for Precision Medicine in Perioperative Care. J Pers Med 2020; 10:jpm10030065. [PMID: 32708157 PMCID: PMC7564657 DOI: 10.3390/jpm10030065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/05/2020] [Accepted: 07/17/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Precision medicine represents an evolving approach to improve treatment efficacy by modifying it to individual patient's gene variation. Pharmacogenetics, an applicable branch of precision medicine, identifies patient's predisposing genotypes that alter the clinical outcome of the drug, hence preventing serious adverse drug reactions. Pharmacogenetics has been extensively applied to various fields of medicine, but in the field of anesthesiology and preoperative medicine, it has been unexploited. Although the US Food and Drug Administration (FDA) has a table of pharmacogenomics biomarkers and pharmacogenetics, this table only includes general side effects of the included drugs. Thus, the existing FDA table offers limited information on genetic variations that may increase drug side effects. Aims: The purpose of this paper is to provide a web-based pharmacogenomics search tool composed of a comprehensive list of medications that have pharmacogenetic relevance to perioperative medicine that might also have application in other fields of medicine. Method: For this investigation, the FDA table of pharmacogenomics biomarkers in drug labeling was utilized as an in-depth of drugs to construct our pharmacogenetics drug table. We performed a literature search for drug-gene interactions using the unique list of drugs in the FDA table. Publications containing the drug-gene interactions were identified and reviewed. Additional drugs and extracted gene-interactions in the identified publications were added to the constructed drug table. Result: Our tool provides a comprehensive pharmacogenetic drug table including 258 drugs with a total of 461 drug-gene interactions and their corresponding gene variations that might cause modifications in drug efficacy, pharmacokinetics, pharmacodynamics and adverse reactions. This tool is freely accessible online and can be applied as a web-based search instrument for drug-gene interactions in different fields of medicine, including perioperative medicine. Conclusion: In this research, we collected drug-gene interactions in a web-based searchable tool that could be used by physicians to expand their field knowledge in pharmacogenetics and facilitate their clinical decision making. This precision medicine tool could further serve in establishing a comprehensive perioperative pharmacogenomics database that also includes different fields of medicine that could influence the outcome of perioperative medicine.
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11
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Bush WS, Cooke Bailey JN, Beno MF, Crawford DC. Bridging the Gaps in Personalized Medicine Value Assessment: A Review of the Need for Outcome Metrics across Stakeholders and Scientific Disciplines. Public Health Genomics 2019; 22:16-24. [PMID: 31454805 DOI: 10.1159/000501974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/07/2019] [Indexed: 12/14/2022] Open
Abstract
Despite monumental advances in genomics, relatively few health care provider organizations in the United States offer personalized or precision medicine as part of the routine clinical workflow. The gaps between research and applied genomic medicine may be a result of a cultural gap across various stakeholders representing scientists, clinicians, patients, policy makers, and third party payers. Scientists are trained to assess the health care value of genomics by either quantifying population-scale effects, or through the narrow lens of clinical trials where the standard of care is compared with the predictive power of a single or handful of genetic variants. While these metrics are an essential first step in assessing and documenting the clinical utility of genomics, they are rarely followed up with other assessments of health care value that are critical to stakeholders who use different measures to define value. The limited value assessment in both the research and implementation science of precision medicine is likely due to necessary logistical constraints of these teams; engaging bioethicists, health care economists, and individual patient belief systems is incredibly daunting for geneticists and informaticians conducting research. In this narrative review, we concisely describe several definitions of value through various stakeholder viewpoints. We highlight the existing gaps that prevent clinical translation of scientific findings generally as well as more specifically using two present-day, extreme scenarios: (1) genetically guided warfarin dosing representing a handful of genetic markers and more than 10 years of basic and translational research, and (2) next-generation sequencing representing genome-dense data lacking substantial evidence for implementation. These contemporary scenarios highlight the need for various stakeholders to broadly adopt frameworks designed to define and collect multiple value measures across different disciplines to ultimately impact more universal acceptance of and reimbursement for genomic medicine.
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Affiliation(s)
- William S Bush
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jessica N Cooke Bailey
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark F Beno
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dana C Crawford
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA, .,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA, .,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA,
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12
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Wang S, Li L, Shi L. Identification of a key candidate gene‑phenotype network mediated by glycyrrhizic acid using pharmacogenomic analysis. Mol Med Rep 2019; 20:2657-2666. [PMID: 31322195 PMCID: PMC6691250 DOI: 10.3892/mmr.2019.10494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/27/2019] [Indexed: 11/17/2022] Open
Abstract
Glycyrrhizic acid (GA) is primarily used as an anti-inflammatory agent in cases of chronic hepatitis. However, its underlying mechanisms in diverse biological processes and its reported benefits are yet to be fully elucidated. In the current study, an analytical method based on pharmacogenomics was established to mine disease-modulatory activities mediated by GA. Five primary protein targets and 138 functional partners were identified for GA by querying open-source databases, including Drugbank and STRING. Subsequently, GA-associated primary and secondary protein targets were integrated into Cytoscape to construct a protein-protein interaction network to establish connectivity. GA-associated target genes were then clustered based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. The tumor necrosis factor axis was revealed to be a primary module regulated by GA-associated targets. Furthermore, 12 hub genes were queried to assess their potential anti-cancer effects using cBioPortal. The results indicated that pharmacogenomics-based analysis improved understanding of the underlying drug-target events of GA and provided predictive and definitive leads for future studies.
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Affiliation(s)
- Shiqun Wang
- Xiaoshan Biotechnology Center, Yangtze Delta Region Institute of Tsinghua University, Hangzhou, Zhejiang 311231, P.R. China
| | - Lu Li
- Department of Nephrology, Affiliated Children's Hospital of Zhejiang University, Hangzhou, Zhejiang 310052, P.R. China
| | - Long Shi
- Xiaoshan Biotechnology Center, Yangtze Delta Region Institute of Tsinghua University, Hangzhou, Zhejiang 311231, P.R. China
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13
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Genomics and Precision Medicine: Molecular Diagnostics Innovations Shaping the Future of Healthcare in Qatar. ADVANCES IN PUBLIC HEALTH 2019. [DOI: 10.1155/2019/3807032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Unprecedented developments in genomics research and ancillary technologies are creating the potential for astonishing changes in both the healthcare field and the life sciences sector. The innovative genomics applications include the following: (1) embracing next generation sequencing (NGS) in clinical diagnostics setting (applying both whole genome and exome sequencing), (2) single cell sequencing studies, (3) quantifying gene expression changes (including whole transcriptome sequencing), (4) pharmacogenomics, and (5) cell-free DNA blood-based testing. This minireview describes the impact of clinical genomics disruptive innovations on the healthcare system in order to provide better diagnosis and treatment. The observed evolution is not limited to the point-of-care services. Genomics technological breakthroughs are pushing the healthcare environment towards personalized healthcare with the real potential to attain better wellbeing. In this article, we will briefly discuss the Gulf region population-based genome initiatives that intend to improve personalized healthcare by offering better prevention, diagnosis, and therapy for the individual (precision medicine). Qatar’s endeavor in genomics medicine will be underscored including the private Applied Biomedicine Initiative (ABI).
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14
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Zheng LJ, Liu N, Yang K, Wang AF, Tan ZR, Li X. Clinical application and importance of one-step human CYP2C19 genotype detection. J Int Med Res 2018; 46:4965-4973. [PMID: 30360673 PMCID: PMC6300956 DOI: 10.1177/0300060518787718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND To directly achieve cytochrome P450 2C19 gene ( CYP2C19) classification using one-step real-time fluorescent PCR detection and to verify the capabilities of this method with nucleic acid extracted from whole blood samples. METHODS A human CYP2C19 genotyping kit based on one-step real-time fluorescent PCR detection was used to analyze whole blood or genomic DNA samples. This method was compared with pyrosequencing and another quantitative (q)PCR kit for its accuracy, repeatability, detection range analysis, sensitivity, specificity, and anti-interference analysis. RESULTS The one-step real-time PCR method achieved a 100% accuracy rate compared with pyrosequencing and the other qPCR kit. When detecting different concentrations of known genes, concentrations of each sample ranging from 0.2 to 125 ng/µL could be correctly detected. The genotypes of samples treated with anticoagulants, including EDTA and sodium citrate, and chyle blood samples could be correctly detected. CONCLUSION The one-step detection method demonstrated high accuracy and a wide detection range. It also had high levels of repeatability, sensitivity, and specificity for the assessment of genomic DNA test samples.
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Affiliation(s)
- Ling-Jie Zheng
- 1 Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Ning Liu
- 2 Coyote Bioscience Co., Ltd., Haidian District, Beijing, China
| | - Kun Yang
- 2 Coyote Bioscience Co., Ltd., Haidian District, Beijing, China
| | - Ai-Feng Wang
- 1 Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Zhi-Rong Tan
- 3 Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiang Li
- 2 Coyote Bioscience Co., Ltd., Haidian District, Beijing, China
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15
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Kaye AD, Mahakian T, Kaye AJ, Pham AA, Hart BM, Gennuso S, Cornett EM, Gabriel RA, Urman RD. Pharmacogenomics, precision medicine, and implications for anesthesia care. Best Pract Res Clin Anaesthesiol 2018; 32:61-81. [DOI: 10.1016/j.bpa.2018.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/30/2018] [Indexed: 01/28/2023]
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16
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Wang Y, Li G, Ma M, He F, Song Z, Zhang W, Wu C. GT-WGS: an efficient and economic tool for large-scale WGS analyses based on the AWS cloud service. BMC Genomics 2018; 19:959. [PMID: 29363427 PMCID: PMC5780748 DOI: 10.1186/s12864-017-4334-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) plays an increasingly important role in clinical practice and public health. Due to the big data size, WGS data analysis is usually compute-intensive and IO-intensive. Currently it usually takes 30 to 40 h to finish a 50× WGS analysis task, which is far from the ideal speed required by the industry. Furthermore, the high-end infrastructure required by WGS computing is costly in terms of time and money. In this paper, we aim to improve the time efficiency of WGS analysis and minimize the cost by elastic cloud computing. RESULTS We developed a distributed system, GT-WGS, for large-scale WGS analyses utilizing the Amazon Web Services (AWS). Our system won the first prize on the Wind and Cloud challenge held by Genomics and Cloud Technology Alliance conference (GCTA) committee. The system makes full use of the dynamic pricing mechanism of AWS. We evaluate the performance of GT-WGS with a 55× WGS dataset (400GB fastq) provided by the GCTA 2017 competition. In the best case, it only took 18.4 min to finish the analysis and the AWS cost of the whole process is only 16.5 US dollars. The accuracy of GT-WGS is 99.9% consistent with that of the Genome Analysis Toolkit (GATK) best practice. We also evaluated the performance of GT-WGS performance on a real-world dataset provided by the XiangYa hospital, which consists of 5× whole-genome dataset with 500 samples, and on average GT-WGS managed to finish one 5× WGS analysis task in 2.4 min at a cost of $3.6. CONCLUSIONS WGS is already playing an important role in guiding therapeutic intervention. However, its application is limited by the time cost and computing cost. GT-WGS excelled as an efficient and affordable WGS analyses tool to address this problem. The demo video and supplementary materials of GT-WGS can be accessed at https://github.com/Genetalks/wgs_analysis_demo .
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Affiliation(s)
- Yiqi Wang
- School of Computer Science, National University of Defense Technology, Changsha, 410000, China
| | - Gen Li
- Genetalks Biotech. Co., Ltd, Beijing, 100000, China
| | - Mark Ma
- Genetalks Biotech. Co., Ltd, Beijing, 100000, China
| | - Fazhong He
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Zhuo Song
- Genetalks Biotech. Co., Ltd, Beijing, 100000, China.
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410000, China.
| | - Chengkun Wu
- School of Computer Science, National University of Defense Technology, Changsha, 410000, China
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17
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Zhuang B. Fully Integrated Genetic Analysis System. DEVELOPMENT OF A FULLY INTEGRATED “SAMPLE-IN-ANSWER-OUT” SYSTEM FOR AUTOMATIC GENETIC ANALYSIS 2018:89-109. [DOI: 10.1007/978-981-10-4753-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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18
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McAdams D. Resistance diagnosis and the changing economics of antibiotic discovery. Ann N Y Acad Sci 2017; 1388:18-25. [DOI: 10.1111/nyas.13303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/07/2016] [Indexed: 01/01/2023]
Affiliation(s)
- David McAdams
- Fuqua School of Business and Economics Department; Duke University; Durham North Carolina
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19
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Maagdenberg H, Vijverberg SJH, Bierings MB, Carleton BC, Arets HGM, de Boer A, Maitland-van der Zee AH. Pharmacogenomics in Pediatric Patients: Towards Personalized Medicine. Paediatr Drugs 2016; 18:251-60. [PMID: 27142473 PMCID: PMC4920853 DOI: 10.1007/s40272-016-0176-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
It is well known that drug responses differ among patients with regard to dose requirements, efficacy, and adverse drug reactions (ADRs). The differences in drug responses are partially explained by genetic variation. This paper highlights some examples of areas in which the different responses (dose, efficacy, and ADRs) are studied in children, including cancer (cisplatin), thrombosis (vitamin K antagonists), and asthma (long-acting β2 agonists). For childhood cancer, the replication of data is challenging due to a high heterogeneity in study populations, which is mostly due to all the different treatment protocols. For example, the replication cohorts of the association of variants in TPMT and COMT with cisplatin-induced ototoxicity gave conflicting results, possibly as a result of this heterogeneity. For the vitamin K antagonists, the evidence of the association between variants in VKORC1 and CYP2C9 and the dose is clear. Genetic dosing models have been developed, but the implementation is held back by the impossibility of conducting a randomized controlled trial with such a small and diverse population. For the long-acting β2 agonists, there is enough evidence for the association between variant ADRB2 Arg16 and treatment response to start clinical trials to assess clinical value and cost effectiveness of genotyping. However, further research is still needed to define the different asthma phenotypes to study associations in comparable cohorts. These examples show the challenges which are encountered in pediatric pharmacogenomic studies. They also display the importance of collaborations to obtain good quality evidence for the implementation of genetic testing in clinical practice to optimize and personalize treatment.
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Affiliation(s)
- Hedy Maagdenberg
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Susanne J H Vijverberg
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Marc B Bierings
- Department of Pediatric Hematology and Stem Cell Transplantation, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, The Netherlands
| | - Bruce C Carleton
- Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, 4480 Oak Street, Vancouver, BC, Canada
- Pharmaceutical Outcomes Programme, British Columbia Children's Hospital, 4480 Oak Street, Vancouver, BC, Canada
| | - Hubertus G M Arets
- Department of Paediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, The Netherlands
| | - Anthonius de Boer
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Anke H Maitland-van der Zee
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands.
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20
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Bush WS, Crosslin DR, Owusu‐Obeng A, Wallace J, Almoguera B, Basford MA, Bielinski SJ, Carrell DS, Connolly JJ, Crawford D, Doheny KF, Gallego CJ, Gordon AS, Keating B, Kirby J, Kitchner T, Manzi S, Mejia AR, Pan V, Perry CL, Peterson JF, Prows CA, Ralston J, Scott SA, Scrol A, Smith M, Stallings SC, Veldhuizen T, Wolf W, Volpi S, Wiley K, Li R, Manolio T, Bottinger E, Brilliant MH, Carey D, Chisholm RL, Chute CG, Haines JL, Hakonarson H, Harley JB, Holm IA, Kullo IJ, Jarvik GP, Larson EB, McCarty CA, Williams MS, Denny JC, Rasmussen‐Torvik LJ, Roden DM, Ritchie MD. Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network. Clin Pharmacol Ther 2016; 100:160-9. [PMID: 26857349 PMCID: PMC5010878 DOI: 10.1002/cpt.350] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/12/2016] [Accepted: 02/04/2016] [Indexed: 12/20/2022]
Abstract
Genetic variation can affect drug response in multiple ways, although it remains unclear how rare genetic variants affect drug response. The electronic Medical Records and Genomics (eMERGE) Network, collaborating with the Pharmacogenomics Research Network, began eMERGE‐PGx, a targeted sequencing study to assess genetic variation in 82 pharmacogenes critical for implementation of “precision medicine.” The February 2015 eMERGE‐PGx data release includes sequence‐derived data from ∼5,000 clinical subjects. We present the variant frequency spectrum categorized by variant type, ancestry, and predicted function. We found 95.12% of genes have variants with a scaled Combined Annotation‐Dependent Depletion score above 20, and 96.19% of all samples had one or more Clinical Pharmacogenetics Implementation Consortium Level A actionable variants. These data highlight the distribution and scope of genetic variation in relevant pharmacogenes, identifying challenges associated with implementing clinical sequencing for drug treatment at a broader level, underscoring the importance for multifaceted research in the execution of precision medicine.
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21
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Zhuang B, Han J, Xiang G, Gan W, Wang S, Wang D, Wang L, Sun J, Li CX, Liu P. A fully integrated and automated microsystem for rapid pharmacogenetic typing of multiple warfarin-related single-nucleotide polymorphisms. LAB ON A CHIP 2016; 16:86-95. [PMID: 26568290 DOI: 10.1039/c5lc01094b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A fully integrated and automated microsystem consisting of low-cost, disposable plastic chips for DNA extraction and PCR amplification combined with a reusable glass capillary array electrophoresis chip in a modular-based format was successfully developed for warfarin pharmacogenetic testing. DNA extraction was performed by adopting a filter paper-based method, followed by "in situ" PCR that was carried out directly in the same reaction chamber of the chip without elution. PCR products were then co-injected with sizing standards into separation channels for detection using a novel injection electrode. The entire process was automatically conducted on a custom-made compact control and detection instrument. The limit of detection of the microsystem for the singleplex amplification of amelogenin was determined to be 0.625 ng of standard K562 DNA and 0.3 μL of human whole blood. A two-color multiplex allele-specific PCR assay for detecting the warfarin-related single-nucleotide polymorphisms (SNPs) 6853 (-1639G>A) and 6484 (1173C>T) in the VKORC1 gene and the *3 SNP (1075A>C) in the CYP2C9 gene was developed and used for validation studies. The fully automated genetic analysis was completed in two hours with a minimum requirement of 0.5 μL of input blood. Samples from patients with different genotypes were all accurately analyzed. In addition, both dried bloodstains and oral swabs were successfully processed by the microsystem with a simple modification to the DNA extraction and amplification chip. The successful development and operation of this microsystem establish the feasibility of rapid warfarin pharmacogenetic testing in routine clinical practice.
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Affiliation(s)
- Bin Zhuang
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China. and CapitalBio Corporation, Beijing, 102206, China
| | - Junping Han
- Chinese People's Public Security University, Beijing, 100038, China
| | - Guangxin Xiang
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China. and CapitalBio Corporation, Beijing, 102206, China
| | - Wupeng Gan
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China. and CapitalBio Corporation, Beijing, 102206, China
| | - Shuaiqin Wang
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China.
| | - Dong Wang
- CapitalBio Corporation, Beijing, 102206, China and National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, China
| | - Lei Wang
- CapitalBio Corporation, Beijing, 102206, China and National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, China
| | - Jing Sun
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Cai-Xia Li
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Peng Liu
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China.
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22
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Cha EY, Jeong HE, Kim WY, Shin HJ, Kim HS, Shin JG. Brief introduction to current pharmacogenomics research tools. Transl Clin Pharmacol 2016. [DOI: 10.12793/tcp.2016.24.1.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Eun-Young Cha
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
| | - Hye-Eun Jeong
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
| | - Woo-Young Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
| | - Ho Jung Shin
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
| | - Ho-Sook Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
- Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Busan 47392, Korea
| | - Jae-Gook Shin
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
- Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Busan 47392, Korea
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23
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Katsila T, Patrinos GP. Whole genome sequencing in pharmacogenomics. Front Pharmacol 2015; 6:61. [PMID: 25859217 PMCID: PMC4374451 DOI: 10.3389/fphar.2015.00061] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/09/2015] [Indexed: 11/13/2022] Open
Abstract
Pharmacogenomics aims to shed light on the role of genes and genomic variants in clinical treatment response. Although, several drug-gene relationships are characterized to date, many challenges still remain toward the application of pharmacogenomics in the clinic; clinical guidelines for pharmacogenomic testing are still in their infancy, whereas the emerging high throughput genotyping technologies produce a tsunami of new findings. Herein, the potential of whole genome sequencing on pharmacogenomics research and clinical application are highlighted.
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Affiliation(s)
- Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras Patras, Greec
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras Patras, Greec
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