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Maillard M, Louveau B, Vilquin P, Goldwirt L, Thomas F, Mourah S. Pharmacogenomics in solid cancers and hematologic malignancies: Improving personalized drug prescription. Therapie 2021; 77:171-183. [PMID: 34922740 DOI: 10.1016/j.therap.2021.11.003] [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: 09/11/2021] [Accepted: 09/29/2021] [Indexed: 11/30/2022]
Abstract
The discovery of molecular alterations involved in oncogenesis is evolving rapidly and has led to the development of new innovative targeted therapies in oncology. High-throughput sequencing techniques help to identify genomic targets and to provide predictive molecular biomarkers of response to guide alternative therapeutic strategies. Besides the emergence of these theranostic markers for the new targeted treatments, pharmacogenetic markers (corresponding to genetic variants existing in the constitutional DNA, i.e., the host genome) can help to optimize the use of chemotherapy. In this review, we present the current clinical applications of constitutional PG and the recent concepts and advances in pharmacogenomics, a rapidly evolving field that focuses on various molecular alterations identified on constitutional or somatic (tumor) genome.
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Affiliation(s)
- Maud Maillard
- Institut Claudius-Regaud, Institut universitaire du cancer de Toulouse, IUCT-Oncopole, 31059 Toulouse, France; Centre de recherches en cancérologie de Toulouse CRCT, 31037 Toulouse, France; Université Paul-Sabatier Toulouse III, 31062 Toulouse, France
| | - Baptiste Louveau
- Inserm, UMR_S976, 75475 Paris, France; Université de Paris, 75010 Paris, France; Pharmacogenomics department, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
| | - Paul Vilquin
- Inserm, UMR_S976, 75475 Paris, France; Université de Paris, 75010 Paris, France; Pharmacogenomics department, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
| | - Lauriane Goldwirt
- Inserm, UMR_S976, 75475 Paris, France; Université de Paris, 75010 Paris, France; Pharmacogenomics department, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
| | - Fabienne Thomas
- Institut Claudius-Regaud, Institut universitaire du cancer de Toulouse, IUCT-Oncopole, 31059 Toulouse, France; Centre de recherches en cancérologie de Toulouse CRCT, 31037 Toulouse, France; Université Paul-Sabatier Toulouse III, 31062 Toulouse, France
| | - Samia Mourah
- Inserm, UMR_S976, 75475 Paris, France; Université de Paris, 75010 Paris, France; Pharmacogenomics department, Hôpital Saint-Louis, AP-HP, 75010 Paris, France.
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Ren A, Prassas I, Sugumar V, Soosaipillai A, Bernardini M, Diamandis EP, Kulasingam V. Comparison of two multiplexed technologies for profiling >1,000 serum proteins that may associate with tumor burden. F1000Res 2021; 10:509. [PMID: 34868557 PMCID: PMC8609392 DOI: 10.12688/f1000research.53364.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background: In this pilot study, we perform a preliminary comparison of two targeted multiplex proteomics technologies for discerning serum protein concentration changes that may correlate to tumor burden in ovarian cancer (OC) patients. Methods: Using the proximity extension assay (PEA) and Quantibody® Kiloplex Array (QKA), we measured >1,000 proteins in the pre-surgical and post-surgical serum from nine OC patients (N=18 samples). We expect that proteins that have decreased significantly in the post-surgical serum concentration may correlate to tumor burden in each patient. Duplicate sera from two healthy individuals were used as controls (N=4 samples). We employed in-house ELISAs to measure five proteins with large serum concentration changes in pre- and post-surgical sera, from four of the original nine patients and the two original controls. Results: Both platforms showed a weak correlation with clinical cancer antigen 125 (CA125) data. The two multiplexed platforms showed a significant correlation with each other for >400 overlapping proteins. PEA uncovered 15 proteins, while QKA revealed 11 proteins, with more than a two-fold post-surgical decrease in at least six of the nine patients. Validation using single enzyme-linked immunosorbent assays (ELISAs) showed at least a two-fold post-surgical decrease in serum concentration of the same patients, as indicated by the two multiplex assays. Conclusion: Both methods identified proteins that had significantly decreased in post-surgical serum concentration, as well as recognizing proteins that had been implicated in OC patients. Our findings from a limited sample size suggest that novel targeted proteomics platforms are promising tools for identifying candidate serological tumor-related proteins. However further studies are essential for the improvement of accuracy and avoidance of false results.
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Affiliation(s)
- Annie Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ioannis Prassas
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Vijithan Sugumar
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Antoninus Soosaipillai
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Marcus Bernardini
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Gynecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
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Menyhárt O, Győrffy B. Multi-omics approaches in cancer research with applications in tumor subtyping, prognosis, and diagnosis. Comput Struct Biotechnol J 2021; 19:949-960. [PMID: 33613862 PMCID: PMC7868685 DOI: 10.1016/j.csbj.2021.01.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 12/17/2022] Open
Abstract
While cost-effective high-throughput technologies provide an increasing amount of data, the analyses of single layers of data seldom provide causal relations. Multi-omics data integration strategies across different cellular function levels, including genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes offer unparalleled opportunities to understand the underlying biology of complex diseases, such as cancer. We review some of the most frequently used data integration methods and outline research areas where multi-omics significantly benefit our understanding of the process and outcome of the malignant transformation. We discuss algorithmic frameworks developed to reveal cancer subtypes, disease mechanisms, and methods for identifying driver genomic alterations and consider the significance of multi-omics in tumor classifications, diagnostics, and prognostications. We provide a comprehensive summary of each omics strategy's most recent advances within the clinical context and discuss the main challenges facing their clinical implementations. Despite its unparalleled advantages, multi-omics data integration is slow to enter everyday clinics. One major obstacle is the uneven maturity of different omics approaches and the growing gap between generating large volumes of data compared to data processing capacity. Progressive initiatives to enforce the standardization of sample processing and analytical pipelines, multidisciplinary training of experts for data analysis and interpretation are vital to facilitate the translatability of theoretical findings.
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Affiliation(s)
- Otília Menyhárt
- Semmelweis University, Department of Bioinformatics and 2 Department of Pediatrics, H-1094 Budapest, Hungary
- Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
| | - Balázs Győrffy
- Semmelweis University, Department of Bioinformatics and 2 Department of Pediatrics, H-1094 Budapest, Hungary
- Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
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Bugada D, Lorini LF, Fumagalli R, Allegri M. Genetics and Opioids: Towards More Appropriate Prescription in Cancer Pain. Cancers (Basel) 2020; 12:cancers12071951. [PMID: 32708424 PMCID: PMC7409018 DOI: 10.3390/cancers12071951] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/16/2020] [Indexed: 12/26/2022] Open
Abstract
Opioids are extensively used in patients with cancer pain; despite their efficacy, several patients can experience ineffective analgesia and/or side effects. Pharmacogenetics is a new approach to drug prescription based on the “personalized-medicine” concept, i.e., the ability of tailoring treatments to each individual’s genetic/genomic profile. Pharmacogenetics aims to identify specific genetic variants that influence pharmacokinetics and pharmacodynamics of drugs, better determining their effectiveness/safety profile. Opioid response is a complex scenario, but some gene variants have shown a correlation with pain sensitivity, as well as with opioid metabolism and clinical efficacy/adverse events. Although questions remain unanswered, some of these gene variants may already be used to identify specific patients’ phenotypes that are more prone to experience better clinical response (i.e., better analgesia and/or less adverse events). Once adopted, this approach to opioid prescription may improve a patient’s outcome. This review summarizes the available data on genetic variants and opioid response: we will focus on basic pharmacogenetic and its impact in the clinical scenario discussing how they may lead to more appropriate opioid prescription in cancer patients.
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Affiliation(s)
- Dario Bugada
- Emergency and Intensive Care Department, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy;
- Italian Pain Group;
- Correspondence:
| | - Luca F. Lorini
- Emergency and Intensive Care Department, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy;
| | - Roberto Fumagalli
- School of Medicine and Surgery, University of Milan-Bicocca, 20900 Monza, Italy;
- Department of Anesthesiology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy
| | - Massimo Allegri
- Italian Pain Group;
- Pain Therapy Service—Fondazione Policlinico Monza, 20900 Monza, Italy
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Barin-Le Guellec C, Picard N, Alarcan H, Barreau M, Becquemont L, Quaranta S, Boyer JC, Loriot MA. [Pharmacogenetics for patient care in France: A discipline that evolves!]. Therapie 2019; 75:459-470. [PMID: 31767126 DOI: 10.1016/j.therap.2019.09.006] [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: 05/15/2019] [Revised: 08/12/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022]
Abstract
Pharmacogenetics, which concepts are known for a long time, is entering a new period at least as far as its practical applications for patients are concerned. In recent years there have been more and more initiatives to promote widespread dissemination, and health authorities are increasingly incorporating these concepts into drug labels. In France, the national network of pharmacogenetics (RNPGx) works to promote these activities, both with health actors (biologists, clinicians) and health authorities. This article reviews the current situation in France and the milestones of the year 2018. It highlights recent advances in this field, in terms of currently recommended analyses, sharing of information or technological developments, and the prospects for future developments in the near future from targeted pharmacogenetics to eventually preemptive approaches.
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Affiliation(s)
- Chantal Barin-Le Guellec
- Inserm U1248, laboratoire de biochimie et biologie moléculaire, université de Tours, CHU de tours, 2, boulevard Tonnellé, 37044 Tours cedex, France.
| | - Nicolas Picard
- Inserm U1248, service de pharmacologie et toxicologie, université de Limoges, CHU de Limoges, 87042 Limoges, France
| | - Hugo Alarcan
- Inserm U1248, laboratoire de biochimie et biologie moléculaire, université de Tours, CHU de tours, 2, boulevard Tonnellé, 37044 Tours cedex, France
| | - Melody Barreau
- Inserm U1107, Service de pharmacologie, université d'Auvergne, CHU de Clermont-Ferrand, 63001 Clermont-Ferrand, France
| | - Laurent Becquemont
- CESP/Inserm U1018, Centre de recherche clinique, hôpital Bicêtre, université Paris Sud, 94275 Le Kremlin-Bicêtre, France
| | - Sylvie Quaranta
- Laboratoire de pharmacocinétique et toxicologie, CHU Timone, 13005 Marseille, France
| | | | - Marie-Anne Loriot
- Inserm U1144, service de biochimie, hôpital européen Georges-Pompidou, université Paris Descartes, 75015 Paris, France
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Hasanzad M, Sarhangi N, Aghaei Meybodi HR, Nikfar S, Khatami F, Larijani B. Precision Medicine in Non Communicable Diseases. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2019; 8:1-18. [PMID: 32351905 PMCID: PMC7175610 DOI: 10.22088/ijmcm.bums.8.2.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/20/2019] [Indexed: 12/12/2022]
Abstract
Non-communicable diseases (NCDs) are the leading cause of death and disease burden globally, cardiovascular diseases (CVDs) account for the major part of death related to NCDs followed by different types of cancer, chronic obstructive pulmonary disease (COPD), and diabetes. As the World Health Organization (WHO) and the United Nations have announced a 25% reduction in mortality of NCDs by 2025, different communities need to adopt preventive strategies for achieving this goal. Personalized medicine approach as a predictive and preventive strategy aims for a better therapeutic goal to the patients to maximize benefits and reduce harms. The clinical benefits of this approach are already realized in cancer targeted therapy, and its impact on other conditions needs more studies in different societies. In this review, we essentially describe the concept of personalized (or precision) medicine in association with NCDs and the future of precision medicine in prediction, prevention, and personalized treatment.
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Affiliation(s)
- Mandana Hasanzad
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.,Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Negar Sarhangi
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Aghaei Meybodi
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Shekoufeh Nikfar
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Khatami
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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Lapeyre-Mestre M, Montastruc F. Interest of pharmacoepidemiology for pharmacodynamics and analysis of the mechanism of action of drugs. Therapie 2019; 74:209-214. [PMID: 30792079 DOI: 10.1016/j.therap.2018.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/31/2018] [Indexed: 01/07/2023]
Abstract
Pharmacology is often divided in separate branches, such as molecular and cellular pharmacology, pharmacokinetics, pharmacodynamics, experimental and/or preclinical pharmacology, clinical pharmacology (and therapeutics), pharmacogenetics, pharmacogenomics, pharmacovigilance, pharmacoepidemiology, pharmacoeconomics… This enumeration gives a global picture of different scientific areas, which are however dealing with the same question. Another mindset should be a global interactive and continuous approach, which could be designed as "human pharmacology". An original and attractive way to illustrate this continuous approach is to combine pharmacodynamics and pharmacovigilance and/or pharmacoepidemiologic data. Coupling disproportionality analyses in pharmacovigilance databases or computerized health databases, with pharmacological characteristics of drugs (receptor affinity, for example) allows investigating in humans, the mechanism of adverse drug reactions. Examples of such analyses investigating the risk of movement disorders, diabetes related to psychoactive drugs, or the risk of adverse cardiac outcomes with different drugs (classical drugs or protein kinase inhibitors) are given. The increasing number of research works investigating this topic underlines the importance of this relatively new approach, which gives significant inputs for the better knowledge of drug safety.
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Affiliation(s)
- Maryse Lapeyre-Mestre
- Service of medical and clinical pharmacology, faculty of medicine, university hospital center, 31000 Toulouse, France; UMR 1027 pharmacoepidemiology, assessment of drug utilization and drug safety, Inserm, university Paul-Sabatier Toulouse III, 31000 Toulouse, France.
| | - François Montastruc
- Service of medical and clinical pharmacology, faculty of medicine, university hospital center, 31000 Toulouse, France; UMR 1027 pharmacoepidemiology, assessment of drug utilization and drug safety, Inserm, university Paul-Sabatier Toulouse III, 31000 Toulouse, France
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Yoo BC, Kim KH, Woo SM, Myung JK. Clinical multi-omics strategies for the effective cancer management. J Proteomics 2017; 188:97-106. [PMID: 28821459 DOI: 10.1016/j.jprot.2017.08.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 02/06/2023]
Abstract
Cancer is a global health issue as a multi-factorial complex disease, and early detection and novel therapeutic strategies are required for more effective cancer management. With the development of systemic analytical -omics strategies, the therapeutic approach and study of the molecular mechanisms of carcinogenesis and cancer progression have moved from hypothesis-driven targeted investigations to data-driven untargeted investigations focusing on the integrated diagnosis, treatment, and prevention of cancer in individual patients. Predictive, preventive, and personalized medicine (PPPM) is a promising new approach to reduce the burden of cancer and facilitate more accurate prognosis, diagnosis, as well as effective treatment. Here we review the fundamentals of, and new developments in, -omics technologies, together with the key role of a variety of practical -omics strategies in PPPM for cancer treatment and diagnosis. BIOLOGICAL SIGNIFICANCE In this review, a comprehensive and critical overview of the systematic strategy for predictive, preventive, and personalized medicine (PPPM) for cancer disease was described in a view of cancer prognostic prediction, diagnostics, and prevention as well as cancer therapy and drug responses. We have discussed multi-dimensional data obtained from various resources and integration of multisciplinary -omics strategies with computational method which could contribute the more effective PPPM for cancer. This review has provided the novel insights of the current applications of each and combined -omics technologies, which showed their powerful potential for the establishment of PPPM for cancer.
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Affiliation(s)
- Byong Chul Yoo
- Biomarker Branch, Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Kyung-Hee Kim
- Biomarker Branch, Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, Republic of Korea; Omics Core Laboratory, Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Sang Myung Woo
- Biomarker Branch, Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, Republic of Korea; Center for Liver Cancer, Hospital, National Cancer Center, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Jae Kyung Myung
- Department of Cancer Biomedical System, National Cancer Centre Graduate School of Cancer Science and Policy, Goyang-si, Gyeonggi-do, Republic of Korea.
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Agarwal D, Udoji MA, Trescot A. Genetic Testing for Opioid Pain Management: A Primer. Pain Ther 2017; 6:93-105. [PMID: 28409480 PMCID: PMC5447546 DOI: 10.1007/s40122-017-0069-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Indexed: 01/01/2023] Open
Abstract
Patients see their primary care physicians (PCPs) for a variety of medical conditions, chronic pain being one of the most common. An increased use of prescription medications (especially opioids) has led to an increase in adverse drug reactions and has heightened our awareness of the variability in response to medications. Opioids and other pain adjuvants are widely used, and drug-drug interactions involving these analgesics can be problematic and potentially lethal. Pharmacogenetics has improved our understanding of drug efficacy and response, opened doors to individual tailoring of medical management, and created a series of ethical and economic considerations. Since it is a relatively new field, genetic testing has not been fully integrated into the primary care setting. The purpose of this paper is to review the metabolism of commonly prescribed opioids, discuss the economic and ethical issues, and provide PCPs with an understanding of how to incorporate genetic testing into routine use to improve clinical practice and patient management.
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Affiliation(s)
- Deepti Agarwal
- Department of Anesthesiology, Advocate Illinois Masonic Medical Center, Chicago, IL, USA
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