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Leach M, Newman WG, McDermott JH. Rapid point of care testing: the next frontier in pharmacogenomics. Pharmacogenomics 2024:1-3. [PMID: 39041736 DOI: 10.1080/14622416.2024.2366691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/04/2024] [Indexed: 07/24/2024] Open
Affiliation(s)
- Marc Leach
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
- Division of Evolution, Infection & Genomics, School of Biological Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - William G Newman
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
- Division of Evolution, Infection & Genomics, School of Biological Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - John H McDermott
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
- Division of Evolution, Infection & Genomics, School of Biological Sciences, The University of Manchester, Manchester, M13 9PL, UK
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Chen HK, Hsieh YW, Hsu HY, Liu TY, Zhang YT, Lin CD, Tsai FJ. Increased risk of hearing loss associated with MT-RNR1 gene mutations: a real-world investigation among Han Taiwanese Population. BMC Med Genomics 2024; 17:155. [PMID: 38840095 PMCID: PMC11155076 DOI: 10.1186/s12920-024-01921-8] [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] [Received: 04/14/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Previous studies have implicated inherited mutations in mitochondrial DNA (mtDNA) in sensorineural hearing loss (SNHL). However, the definitive association between mitochondrial 12S rRNA (MT-RNR1) variants and hearing loss in the population has not been well established, particularly in Asia. The objective of this retrospective cohort study was to assess the association between MT-RNR1 variants and the risk of SNHL in patients in Taiwan. METHODS The cohort included 306,068 participants from Taiwan between January 2003 and December 2020. Participants were classified based on genetic variants, particularly mitochondrial mutations (rs267606618, rs267606619, rs267606617). MT-RNR1 variant cases were matched 1:10 with non-mutant patients by age, gender, and visit year, excluding those with pre-existing hearing loss. The primary endpoint was SNHL, identified using specific ICD-TM codes with a 90% positive predictive value. Medication exposure history was determined via self-report or electronic medical records in the hospital. Cox proportional hazard regression models were used to assess the association between MT-RNR1 variants and hearing loss, adjusting for various covariates. Kaplan-Meier survival curves and log-rank tests compared hearing loss incidence between groups. RESULTS The mean age of the mtDNA variants group is 32.4 years, with a standard deviation of 19.2 years. The incidence density of hearing loss for the mutation group was 36.42 per 10,000 person-years (95% Confidence Interval [CI], 27.21-47.73), which was higher than the 23.77per 10,000 person-years (95% CI, 21.32-26.42) in the wild-type group (p = 0.0036). Additionally, diabetes mellitus was associated with an increased risk of developing SNHL in individuals with MT-RNR1 variants (adjusted hazard ratio = 1.76 [95% CI, 1.00-3.09], p < 0.05). CONCLUSION This study highlights the increased risk of hearing loss in patients carrying MT-RNR1 variants, particularly those with diabetes mellitus. Future research that integrates genetic and clinical data is crucial for developing more precise interventions to monitor and treat hearing loss in this vulnerable population.
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Affiliation(s)
- Hou-Kuang Chen
- Department of Otorhinolaryngology-Head and Neck Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Yow-Wen Hsieh
- Department of Pharmacy, China Medical University Hospital, Taichung, Taiwan
- School of Pharmacy, College of Pharmacy, China Medical University, Taichung, Taiwan
| | - Hsing-Yu Hsu
- Department of Pharmacy, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Clinical Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ting-Yuan Liu
- Million-person precision medicine initiative, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Ting Zhang
- Department of Pharmacy, China Medical University Hospital, Taichung, Taiwan
| | - Chia-Der Lin
- Department of Otorhinolaryngology-Head and Neck Surgery, China Medical University Hospital, Taichung, Taiwan.
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan.
- Division of Pediatric Genetics, Children's Hospital of China Medical University, Taichung, Taiwan.
- Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan.
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Borzych-Dużałka D, Same R, Neu A, Yap HK, Verrina E, Bakkaloglu SA, Cano F, Patel H, Szczepańska M, Obrycki Ł, Spizzirri AP, Sartz L, Vondrak K, Rebori A, Milosevski-Lomic G, Chan EYH, Basu B, Pezo AL, Zaloszyc A, Chadha V, Schaefer F, Warady BA. Best Practice of Peritoneal Dialysis-Associated Gram-Negative Peritonitis in Children: Insights From the International Pediatric Peritoneal Dialysis Network Registry. Kidney Int Rep 2024; 9:1654-1663. [PMID: 38899186 PMCID: PMC11184244 DOI: 10.1016/j.ekir.2024.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 06/21/2024] Open
Abstract
Introduction Gram-negative peritonitis (GNP) is associated with significant morbidity in children receiving long-term peritoneal dialysis (PD) and current treatment recommendations are based on limited data. Methods Analysis of 379 GNP episodes in 308 children (median age 6.9 years, interquartile range [IQR]: 3.0-13.6) from 45 centers in 28 countries reported to the International Pediatric Peritoneal Dialysis Network registry between 2011 and 2023. Results Overall, 74% of episodes responded well to empiric therapy and full functional recovery (FFR) was achieved in 82% of cases. In vitro bacterial susceptibility to empiric antibiotics and lack of severe abdominal pain at onset were associated with a good initial response. Risk factors for failure to achieve FFR included severe abdominal pain at onset and at 60 to 72 hours from treatment initiation (odds ratio [OR]: 3.81, 95% confidence interval [CI]: 2.01-7.2 and OR: 3.94, 95% CI: 1.06-14.67, respectively), Pseudomonas spp. etiology (OR: 1.73, 95% CI: 1.71-4.21]) and in vitro bacterial resistance to empiric antibiotics (OR: 2.40, 95% CI: 1.21-4.79); the risk was lower with the use of monotherapy as definitive treatment (OR: 0.40, 95% CI: 0.21-0.77). Multivariate analysis showed no benefit of dual antibiotic therapy for treatment of Pseudomonas peritonitis after adjustment for age, presenting symptomatology, 60 to 72-hour treatment response, and treatment duration. Monotherapy with cefazolin in susceptible Enterobacterales peritonitis resulted in a similar FFR rate (91% vs. 93%) as treatment with ceftazidime or cefepime monotherapy. Conclusion Detailed microbiological assessment, consisting of patient-specific and center-specific antimicrobial susceptibility data, should guide empiric treatment. Treatment "deescalation" with the use of monotherapy and narrow spectrum antibiotics according to susceptibility data is not associated with inferior outcomes and should be advocated in the context of emerging bacterial resistance.
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Affiliation(s)
- Dagmara Borzych-Dużałka
- Department for Pediatrics, Nephrology and Hypertension, Medical University of Gdańsk, Gdańsk, Poland
- University Center for Pediatrics and Adolescent Medicine, Heidelberg, Germany
| | - Rebeca Same
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Alicia Neu
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hui Kim Yap
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | - Francisco Cano
- Division of Pediatric Nephrology, Hospital Dr. Luis Calvo Mackenna, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Hiren Patel
- Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Maria Szczepańska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland
| | | | - Ana Paula Spizzirri
- Division of Pediatric Nephrology, Hospital for Maria Ludovica, La Plata, Argentina
| | - Lisa Sartz
- Department of Pediatrics, Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | | | | | - Eugene Yu-hin Chan
- Pediatric Nephrology Centre, Hong Kong Children’s Hospital, Kowloon Bay, Hong Kong SAR
| | | | | | - Ariane Zaloszyc
- Pediatric Nephrology, Pédiatrie 1, Centre Hospitalier Universitaire de Strasbourg, France
| | - Vimal Chadha
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Franz Schaefer
- University Center for Pediatrics and Adolescent Medicine, Heidelberg, Germany
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4
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Arribas C, Decembrino N, Raffaeli G, Amodeo I, González-Caballero JL, Riaza M, Ortiz-Movilla R, Massenzi L, Gizzi C, Araimo G, Cattarelli D, Aversa S, Martinelli S, Frezza S, Orfeo L, Mosca F, Cavallaro G, Garrido F. Ototoxic and nephrotoxic drugs in neonatal intensive care units: results of a Spanish and Italian survey. Eur J Pediatr 2024:10.1007/s00431-024-05467-w. [PMID: 38492032 DOI: 10.1007/s00431-024-05467-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 03/18/2024]
Abstract
Neonates face heightened susceptibility to drug toxicity, often exposed to off-label medications with dosages extrapolated from adult or pediatric studies. Premature infants in Neonatal Intensive Care Units (NICUs) are particularly at risk due to underdeveloped pharmacokinetics and exposure to multiple drugs. The study aimed to survey commonly used medications with a higher risk of ototoxicity and nephrotoxicity in Spanish and Italian neonatal units. A prospective cross-sectional study was conducted in Italian and Spanish neonatal units using a web-based survey with 43 questions. A modified Delphi method involved experts refining the survey through online consensus. Ethical approval was obtained, and responses were collected from January to July 2023. The survey covered various aspects, including drug-related ototoxic and nephrotoxic management, hearing screening, and therapeutic drug monitoring. Responses from 131 participants (35.9% from Spain and 64.1% from Italy) revealed awareness of drug toxicity risks. Varied practices were observed in hearing screening protocols, and a high prevalence of ototoxic and nephrotoxic drug use, including aminoglycosides (100%), vancomycin (70.2%), loop diuretics (63.4%), and ibuprofen (62.6%). Discrepancies existed in guideline availability and adherence, with differences between Italy and Spain in therapeutic drug monitoring practices. CONCLUSIONS The study underscores the need for clinical guidelines and uniform practices in managing ototoxic and nephrotoxic drugs in neonatal units. Awareness is high, but inconsistencies in practices indicate a necessity for standardization, including the implementation of therapeutic drug monitoring and the involvement of clinical pharmacologists. Addressing these issues is crucial for optimizing neonatal care in Southern Europe. WHAT IS KNOWN • Neonates in intensive care face a high risk of nephrotoxicity and ototoxicity from drugs like aminoglycosides, vancomycin, loop diuretics, and ibuprofen. • Therapeutic drug monitoring is key for managing these risks, optimizing dosing for efficacy and minimizing side effects. WHAT IS NEW • NICUs in Spain and Italy show high drug toxicity awareness but differ in ototoxic/nephrotoxic drug management. • Urgent need for standard guidelines and practices to address nephrotoxic risks from aminoglycosides, vancomycin, loop diuretics, and ibuprofen.
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Affiliation(s)
- Cristina Arribas
- Neonatal Intensive Care Unit, Clínica Universidad de Navarra, 28027, Madrid, Spain
| | - Nunzia Decembrino
- Neonatal Intensive Care Unit, AOU Policlinico G. Rodolico San Marco, 95123, Catania, Italy
| | - Genny Raffaeli
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milan, Italy.
| | - Ilaria Amodeo
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milan, Italy
| | | | - Mónica Riaza
- Department of Pediatrics, Clínica Universidad de Navarra, 31008, Pamplona, Spain
| | - Roberto Ortiz-Movilla
- Neonatal Intensive Care Unit, Hospital Universitario Puerta de Hierro-Majadahonda, 28222, Madrid, Spain
| | - Luca Massenzi
- Neonatal Intensive Care Unit, Ospedale Regionale Di Bolzano, 39100, Bolzano, Italy
| | - Camilla Gizzi
- Division of Pediatrics and Neonatology, Sandro Pertini Hospital, 00157, Rome, Italy
| | - Gabriella Araimo
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milan, Italy
| | - Donatella Cattarelli
- Division of Pediatrics and Neonatology, ASST del Garda, 25015, Desenzano del Garda (BS), Italy
| | - Salvatore Aversa
- Neonatal Intensive Care Unit, Children's Hospital, ASST Spedali Civili, 25123, Brescia, Italy
| | - Stefano Martinelli
- Neonatal Intensive Care Unit, ASST Grande Ospedale Metropolitano Niguarda, 20162, Milan, Italy
| | - Simonetta Frezza
- Division of Neonatology, Area of Child Health, Department of Woman, Child Health and Public Health, Fondazione IRCCS Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
| | - Luigi Orfeo
- Neonatal Intensive Care Unit, Isola Tiberina Hospital Gemelli Isola, 00186, Rome, Italy
| | - Fabio Mosca
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milan, Italy
- Department of Clinical Sciences and Community Health, Università Degli Studi Di Milano, 20122, Milan, Italy
| | - Giacomo Cavallaro
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milan, Italy
| | - Felipe Garrido
- Neonatal Intensive Care Unit, Clínica Universidad de Navarra, 28027, Madrid, Spain
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Burgel PR, Southern KW, Addy C, Battezzati A, Berry C, Bouchara JP, Brokaar E, Brown W, Azevedo P, Durieu I, Ekkelenkamp M, Finlayson F, Forton J, Gardecki J, Hodkova P, Hong G, Lowdon J, Madge S, Martin C, McKone E, Munck A, Ooi CY, Perrem L, Piper A, Prayle A, Ratjen F, Rosenfeld M, Sanders DB, Schwarz C, Taccetti G, Wainwright C, West NE, Wilschanski M, Bevan A, Castellani C, Drevinek P, Gartner S, Gramegna A, Lammertyn E, Landau EEC, Plant BJ, Smyth AR, van Koningsbruggen-Rietschel S, Middleton PG. Standards for the care of people with cystic fibrosis (CF); recognising and addressing CF health issues. J Cyst Fibros 2024; 23:187-202. [PMID: 38233247 DOI: 10.1016/j.jcf.2024.01.005] [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] [Received: 11/06/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
This is the third in a series of four papers updating the European Cystic Fibrosis Society (ECFS) standards for the care of people with CF. This paper focuses on recognising and addressing CF health issues. The guidance was produced with wide stakeholder engagement, including people from the CF community, using an evidence-based framework. Authors contributed sections, and summary statements which were reviewed by a Delphi consultation. Monitoring and treating airway infection, inflammation and pulmonary exacerbations remains important, despite the widespread availability of CFTR modulators and their accompanying health improvements. Extrapulmonary CF-specific health issues persist, such as diabetes, liver disease, bone disease, stones and other renal issues, and intestinal obstruction. These health issues require multidisciplinary care with input from the relevant specialists. Cancer is more common in people with CF compared to the general population, and requires regular screening. The CF life journey requires mental and emotional adaptation to psychosocial and physical challenges, with support from the CF team and the CF psychologist. This is particularly important when life gets challenging, with disease progression requiring increased treatments, breathing support and potentially transplantation. Planning for end of life remains a necessary aspect of care and should be discussed openly, honestly, with sensitivity and compassion for the person with CF and their family. CF teams should proactively recognise and address CF-specific health issues, and support mental and emotional wellbeing while accompanying people with CF and their families on their life journey.
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Affiliation(s)
- Pierre-Régis Burgel
- Respiratory Medicine and Cystic Fibrosis National Reference Center, Cochin Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), Institut Cochin, Inserm U1016, Université Paris-Cité, Paris, France
| | - Kevin W Southern
- Department of Women's and Children's Health, Institute in the Park, Alder Hey Children's Hospital, University of Liverpool, Eaton Road, Liverpool L12 2AP, UK.
| | - Charlotte Addy
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff and Vale University Health Board, Cardiff, UK
| | - Alberto Battezzati
- Clinical Nutrition Unit, Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, and ICANS-DIS, Department of Food Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Claire Berry
- Department of Nutrition and Dietetics, Alder Hey Children's NHS Trust, Liverpool, UK
| | - Jean-Philippe Bouchara
- University of Brest, Fungal Respiratory Infections Research Unit, SFR ICAT, University of Angers, Angers, France
| | - Edwin Brokaar
- Department of Pharmacy, Haga Teaching Hospital, The Hague, the Netherlands
| | - Whitney Brown
- Cystic Fibrosis Foundation, Inova Fairfax Hospital, Bethesda, Maryland, USA, Falls Church, VA, USA
| | - Pilar Azevedo
- Cystic Fibrosis Reference Centre-Centro, Hospitalar Universitário Lisboa Norte, Portugal
| | - Isabelle Durieu
- Cystic Fibrosis Reference Center (Constitutif), Service de médecine interne et de pathologie vasculaire, Hospices Civils de Lyon, Hôpital Lyon Sud, RESearch on HealthcAre PErformance (RESHAPE), INSERM U1290, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69373 Lyon Cedex 08, France; ERN-Lung Cystic Fibrosis Network, Frankfurt, Germany
| | - Miquel Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Felicity Finlayson
- Department of Respiratory Medicine, The Alfred Hospital, Melbourne, Australia
| | | | - Johanna Gardecki
- CF Centre at Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pavla Hodkova
- CF Center at University Hospital Motol, Prague, Czech Republic
| | - Gina Hong
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacqueline Lowdon
- Clinical Specialist Paediatric Cystic Fibrosis Dietitian, Leeds Children's Hospital, UK
| | - Su Madge
- Royal Brompton Hospital, Part of Guys and StThomas's Hospital, London, UK
| | - Clémence Martin
- Institut Cochin, Inserm U1016, Université Paris-Cité and National Reference Center for Cystic Fibrosis, Hôpital Cochin AP-HP, ERN-Lung CF Network, Paris 75014, France
| | - Edward McKone
- St.Vincent's University Hospital and University College Dublin School of Medicine, Dublin, Ireland
| | - Anne Munck
- Hospital Necker Enfants-Malades, AP-HP, CF Centre, Université Paris Descartes, Paris, France
| | - Chee Y Ooi
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine & Health, Department of Gastroenterology, Sydney Children's Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Lucy Perrem
- Department of Respiratory Medicine, Children's Health Ireland, Dublin, Ireland
| | - Amanda Piper
- Central Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Andrew Prayle
- Child Health, Lifespan and Population Health & Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Felix Ratjen
- Division of Respiratory Medicine, Department of Pediatrics and Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Margaret Rosenfeld
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA, USA
| | - Don B Sanders
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Carsten Schwarz
- Division Cystic Fibrosis, CF Center, Clinic Westbrandenburg, HMU-Health and Medical University, Potsdam, Germany
| | - Giovanni Taccetti
- Meyer Children's Hospital IRCCS, Cystic Fibrosis Regional Reference Centre, Italy
| | | | - Natalie E West
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Michael Wilschanski
- Pediatric Gastroenterology Unit, CF Center, Hadassah Medical Center, Jerusalem, Israel
| | - Amanda Bevan
- University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Carlo Castellani
- IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, Genova 16147, Italy
| | - Pavel Drevinek
- Department of Medical Microbiology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Silvia Gartner
- Cystic Fibrosis Unit and Pediatric Pulmonology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Andrea Gramegna
- Department of Pathophysiology and Transplantation, Respiratory Unit and Adult Cystic Fibrosis Center, Università degli Studi di Milano, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Elise Lammertyn
- Cystic Fibrosis Europe, Brussels, Belgium and the Belgian CF Association, Brussels, Belgium
| | - Eddie Edwina C Landau
- The Graub CF Center, Pulmonary Institute, Schneider Children's Medical Center, Petah Tikva, Israel
| | - Barry J Plant
- Cork Centre for Cystic Fibrosis (3CF), Cork University Hospital, University College Cork, Ireland
| | - Alan R Smyth
- School of Medicine, Dentistry and Biomedical Sciences, Belfast and NIHR Nottingham Biomedical Research Centre, Queens University Belfast, Nottingham, UK
| | | | - Peter G Middleton
- Westmead Clinical School, Department Respiratory & Sleep Medicine, Westmead Hospital, University of Sydney and CITRICA, Westmead, Australia
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Dawes P, Arru P, Corry R, McDermott JH, Garlick J, Guest H, Howlett E, Jackson I, James R, Keane A, Murray C, Newman W, Visram A, Munro KJ. Patient and public involvement in hearing research: opportunities, impact and reflections with case studies from the Manchester Centre for Audiology and Deafness. Int J Audiol 2024; 63:146-154. [PMID: 36573267 DOI: 10.1080/14992027.2022.2155881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Patient and public involvement (PPI) in research improves relevance to end users and improves processes including recruitment participants. PPI in our research has gone from being non-existent to ubiquitous over a few years. We provide critical reflections on the benefits and challenges of PPI. DESIGN Case studies are reported according to a modified GRIP2 framework; the aims, methodology, impact of PPI and critical reflections on each case and our experiences with PPI in general. STUDY SAMPLE We report five UK projects that included PPI from teenagers, families, people living with dementia, autistic people, and people from South Asian and d/Deaf communities. RESULTS Our experience has progressed from understanding the rationale to grappling methodologies and integrating PPI in our research. PPI took place at all stages of research, although commonly involved input to design including recruitment and development of study materials. Methodologies varied between projects, including PPI co-investigators, advisory panels and online surveys. CONCLUSION On-going challenges include addressing social exclusion from research for people that lack digital access following increasing on-line PPI and involvement from underserved communities. PPI was initially motivated by funders; however the benefits have driven widespread PPI, ensuring our research is relevant to people living with hearing loss.
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Affiliation(s)
- Piers Dawes
- School of Health and Rehabilitation Sciences, University of Queensland, Brisbane, Australia
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK
| | - Paolo Arru
- Vocal, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - John Henry McDermott
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
| | | | - Hannah Guest
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK
| | - Emily Howlett
- Vocal, Manchester University NHS Foundation Trust, Manchester, UK
| | - Iain Jackson
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK
| | - Rachel James
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Annie Keane
- Vocal, Manchester University NHS Foundation Trust, Manchester, UK
| | - Carlyn Murray
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK
| | - William Newman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Anisa Visram
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK
| | - Kevin J Munro
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK
- Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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7
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Zhao M, Luo X, Zhao Q, Yang T, Zhang W, Chen Z, Zeng S, Chen W, Zhang H, Wang Q, Wang W, Zhang X, Zhong T. Characteristics of hearing loss-associated gene mutations: A multi-center study of 119,606 neonates in Gannan. Int J Pediatr Otorhinolaryngol 2023; 174:111744. [PMID: 37801830 DOI: 10.1016/j.ijporl.2023.111744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND HL is the second most common congenital disability in China, and its high incidence brings a serious burden of medical and educational sequelae. HL genetic screening enables the identification of individuals with inherited HL and carriers in a large scale. OBJECTIVE This study aimed to measure the detection rates of hearing loss (HL)-associated gene mutations in the Gannan population. The molecular etiology and risk factors of hereditary HL were also analyzed. METHODS In total, 119,606 newborns from 18 districts of Gannan were enrolled in this multi-center study conducted between April 2019 and April 2021. Otoacoustic Emission (OAE) was used for primary hearing screening 3 days after birth in quiet conditions, and OAE combined with automated auditory brainstem response (AABR) was applied 29-42 days after birth for those who failed or missed the initial screening. Meanwhile, high-throughput sequencing of hotspot HL-associated mutations in GJB2, GJB3, MTRNR1, and SLC26A4 were performed. RESULTS Among the 119,606 newborns, 7796 (6.52%) failed the hearing screening. Genetic screening revealed that 5092 neonates (4.26%) carried HL-associated mutations. The detection rate of GJB2, SLC26A4, MTRNR1 and GJB3 mutations were 2.09%, 1.51%, 0.42% and 0.24%, respectively. The most prevalent variant was GJB2 c.235delC (1.74%). The second most prevalent variant was SLC26A4 c.919-2A > G (0.93%). The population who failed the hearing screening had a lower proportion (24.64%) of SLC26A4 gene variants compared to the population who passed (37.46%). Genetic screening identified 4612 (3.86%) carriers who were normal in hearing screenings. The concurrent hearing and genetic screening identified 480 (0.40%) neonates at high risk for hereditary HL. CONCLUSIONS The results of this study suggest that the concurrent hearing screening and high-throughput genetic screening would greatly improve the effectiveness of newborn HL programs. This integration also facilitates the management of congenital HL, and aids in the prevention of aminoglycoside antibiotics-induced HL.
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Affiliation(s)
- Minghong Zhao
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China; Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China; Laboratory Medicine, Guizhou Aerospace Hospital, Zunyi, China
| | - Xuemei Luo
- Ganzhou Municipal Health Commission, Ganzhou, China
| | - Qinfei Zhao
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Tong Yang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China; Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Wenqian Zhang
- BGI Genomics, Shenzhen, China; Clin Lab, BGI Genomics, Wuhan, China
| | - Zhigang Chen
- BGI Genomics, Shenzhen, China; Clin Lab, BGI Genomics, Wuhan, China
| | - Shaoying Zeng
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Weifeng Chen
- Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Huijuan Zhang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Qi Wang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Weihua Wang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xiaokang Zhang
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, China.
| | - Tianyu Zhong
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China; Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.
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8
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Dohál M, Porvazník I, Solovič I, Mokrý J. Advancing tuberculosis management: the role of predictive, preventive, and personalized medicine. Front Microbiol 2023; 14:1225438. [PMID: 37860132 PMCID: PMC10582268 DOI: 10.3389/fmicb.2023.1225438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023] Open
Abstract
Tuberculosis is a major global health issue, with approximately 10 million people falling ill and 1.4 million dying yearly. One of the most significant challenges to public health is the emergence of drug-resistant tuberculosis. For the last half-century, treating tuberculosis has adhered to a uniform management strategy in most patients. However, treatment ineffectiveness in some individuals with pulmonary tuberculosis presents a major challenge to the global tuberculosis control initiative. Unfavorable outcomes of tuberculosis treatment (including mortality, treatment failure, loss of follow-up, and unevaluated cases) may result in increased transmission of tuberculosis and the emergence of drug-resistant strains. Treatment failure may occur due to drug-resistant strains, non-adherence to medication, inadequate absorption of drugs, or low-quality healthcare. Identifying the underlying cause and adjusting the treatment accordingly to address treatment failure is important. This is where approaches such as artificial intelligence, genetic screening, and whole genome sequencing can play a critical role. In this review, we suggest a set of particular clinical applications of these approaches, which might have the potential to influence decisions regarding the clinical management of tuberculosis patients.
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Affiliation(s)
- Matúš Dohál
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University in Ružomberok, Ružomberok, Slovakia
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University in Ružomberok, Ružomberok, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
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9
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Ramsey LB, Prows CA, Tang Girdwood S, Van Driest S. Current Practices in Pharmacogenomics. Pediatr Clin North Am 2023; 70:995-1011. [PMID: 37704356 PMCID: PMC10865383 DOI: 10.1016/j.pcl.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Pharmacogenomics, where genomic information is used to tailor medication management, is a strategy to maximize drug efficacy and minimize toxicity. Although pediatric evidence is less robust than for adults, medications influenced by pharmacogenomics are prescribed to children and adolescents. Evidence-based guidelines and drug label annotations are available from the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Pharmacogenomics Knowledgebase (PharmGKB). Some pediatric health care facilities use pharmacogenomics to provide dosing recommendations to pediatricians. Herein, we use a case-based approach to illustrate the use of pharmacogenomic data in pediatric clinical care and provide resources for finding and using pharmacogenomic guidelines.
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Affiliation(s)
- Laura B Ramsey
- Division of Clinical Pharmacology, Cincinnati Children's Hospital Medical Center, College of Medicine, University of Cincinnati, 3333 Burnet Avenue, MLC 6018, Cincinnati, OH 45229, USA; Division of Research in Patient Services, Cincinnati Children's Hospital Medical Center, College of Medicine, University of Cincinnati, 3333 Burnet Avenue, MLC 6018, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, MLC 9016, Cincinnati, OH 45529, USA.
| | - Cynthia A Prows
- Division of Human Genetics, Department of Pediatrics and Center for Professional Excellence, Patient Services, Cincinnati Children's Hospital Medical Center, College of Medicine, University of Cincinnati, 3333 Burnet Avenue, MLC 6018, Cincinnati, OH 45229, USA
| | - Sonya Tang Girdwood
- Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, MLC 9016, Cincinnati, OH 45529, USA; Division of Hospital Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 9016, Cincinnati, OH 45529, USA; Division of Clinical Pharmacology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 9016, Cincinnati, OH 45529, USA
| | - Sara Van Driest
- Department of Pediatrics, Vanderbilt University Medical Center, 2200 Children's Way, 8232 DOT, Nashville, TN 37205, USA
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10
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van der Drift D, Simoons M, Koch BCP, Brufau G, Bindels P, Matic M, van Schaik RHN. Implementation of Pharmacogenetics in First-Line Care: Evaluation of Its Use by General Practitioners. Genes (Basel) 2023; 14:1841. [PMID: 37895189 PMCID: PMC10606701 DOI: 10.3390/genes14101841] [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] [Received: 08/28/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Pharmacogenetics (PGx) can explain/predict drug therapy outcomes. There is, however, unclarity about the use and usefulness of PGx in primary care. In this study, we investigated PGx tests ordered by general practitioners (GPs) in 2021 at Dept. Clinical Chemistry, Erasmus MC, and analyzed the gene tests ordered, drugs/drug groups, reasons for testing and single-gene versus panel testing. Additionally, a survey was sent to 90 GPs asking about their experiences and barriers to implementing PGx. In total, 1206 patients and 6300 PGx tests were requested by GPs. CYP2C19 was requested most frequently (17%), and clopidogrel was the most commonly indicated drug (23%). Regarding drug groups, antidepressants (51%) were the main driver for requesting PGx, followed by antihypertensives (26%). Side effects (79%) and non-response (27%) were the main indicators. Panel testing was preferred over single-gene testing. The survey revealed knowledge on when and how to use PGx as one of the main barriers. In conclusion, PGx is currently used by GPs in clinical practice in the Netherlands. Side effects are the main reason for testing, which mostly involves antidepressants. Lack of knowledge is indicated as a major barrier, indicating the need for more education on PGx for GPs.
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Affiliation(s)
- Denise van der Drift
- Department of Clinical Chemistry, Erasmus MC University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Mirjam Simoons
- Department of Hospital Pharmacy, Erasmus MC University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Birgit C. P. Koch
- Department of Hospital Pharmacy, Erasmus MC University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Gemma Brufau
- Department of Clinical Chemistry, Erasmus MC University Medical Center, 3015 GD Rotterdam, The Netherlands
- Department of Clinical Chemistry, Result Laboratory, 3318 AT Dordrecht, The Netherlands
| | - Patrick Bindels
- Department of General Practice, Erasmus MC University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Maja Matic
- Department of Clinical Chemistry, Erasmus MC University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Ron H. N. van Schaik
- Department of Clinical Chemistry, Erasmus MC University Medical Center, 3015 GD Rotterdam, The Netherlands
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11
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Rigobello R, Shaw J, Ilg D, Zimmerman R, Edelmann L, Kornreich R, Scott SA, Cody N. Clinical Pharmacogenomic MT-RNR1 Screening for Aminoglycoside-Induced Ototoxicity and the Post-Test Counseling Conundrum. Clin Pharmacol Ther 2023; 114:262-265. [PMID: 37314952 DOI: 10.1002/cpt.2910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/14/2023] [Indexed: 06/16/2023]
Abstract
Aminoglycoside antibiotic exposure can result in ototoxicity and irreversible hearing loss among individuals that harbor the m.1555A>G variant in the mitochondrial 12S rRNA gene, MT-RNR1. Importantly, pre-emptive m.1555A>G screening has been shown to reduce the prevalence of pediatric aminoglycoside-induced ototoxicity; however, professional guidelines to support and guide post-test pharmacogenomic counseling in this context are not currently available. This Perspective highlights key issues with delivering MT-RNR1 results, including longitudinal familial care considerations and communicating m.1555A>G heteroplasmy.
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Affiliation(s)
| | - Jay Shaw
- GeneDx, Gaithersburg, Maryland, USA
| | | | | | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, California, USA
- Clinical Genomics Laboratory, Stanford Medicine, Palo Alta, California, USA
| | - Neal Cody
- GeneDx, Gaithersburg, Maryland, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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12
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Guo J, Pan Z, Fan L, Zhong Y, Pang R, Su Y. Effect of Three Different Amino Acids Plus Gentamicin Against Methicillin-Resistant Staphylococcus aureus. Infect Drug Resist 2023; 16:4741-4754. [PMID: 37496695 PMCID: PMC10366528 DOI: 10.2147/idr.s411658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Background The issue of methicillin-resistant Staphylococcus aureus (MRSA) resistant to many antibiotics and causing serious infectious diseases is a growing healthcare concern. Purpose In recent years, exogenous administration of metabolites in combination with antibiotics can re-sensitize resistant bacteria to antibiotics; however, their effects vary, and their underlying mechanism of action remains elusive. Methods We assessed the bactericidal effects of the three amino acids in combination with gentamicin in vitro and in vivo. Subsequently, we explored the role of these amino acids on the metabolomics of MRSA using Liquid chromatography-tandem mass spectrometry (LC-MS/MS). Furthermore, we performed the downstream analyses using MetaboAnalyst and Interactive Pathways Explorer. Results Exogenous threonine showed the best bactericidal efficacy with gentamicin, followed by glycine, wherein serine had no effect. Amino acid treatments mainly up-regulated the metabolites, increased the amino acid abundance, and significantly activated metabolisms; these effects were consistent with the bactericidal efficacy of the three amino acids. Most amino acids participated in the tricarboxylic acid cycle, and threonine supplementation increased the activities of citrate synthase, isocitrate dehydrogenase and α-ketoglutarate dehydrogenase, whereas glycine increased activities of citrate synthase and α-ketoglutarate dehydrogenase, and serine did not affect the activities of any of the three key enzymes. We identified 24 biomarkers in the three groups, among which glutamic acid and cysteine showed a gradient decrease and increase, respectively. Subsequent analyses revealed that glutamic acid but not cysteine promoted the bactericidal effect of gentamicin synergistically. Conclusion Threonine has the best synergistic effect in reversing bacterial resistance compared to glycine and serine. We show that different amino acids combined with an antibiotic mainly affect amino acid metabolism and act via different metabolic regulatory mechanisms, which could help develop effective strategies for tackling MRSA infections.
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Affiliation(s)
- Juan Guo
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Zhiyu Pan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Lvyuan Fan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Yilin Zhong
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, People’s Republic of China
| | - Yubin Su
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of China
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13
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Sadee W, Wang D, Hartmann K, Toland AE. Pharmacogenomics: Driving Personalized Medicine. Pharmacol Rev 2023; 75:789-814. [PMID: 36927888 PMCID: PMC10289244 DOI: 10.1124/pharmrev.122.000810] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Personalized medicine tailors therapies, disease prevention, and health maintenance to the individual, with pharmacogenomics serving as a key tool to improve outcomes and prevent adverse effects. Advances in genomics have transformed pharmacogenetics, traditionally focused on single gene-drug pairs, into pharmacogenomics, encompassing all "-omics" fields (e.g., proteomics, transcriptomics, metabolomics, and metagenomics). This review summarizes basic genomics principles relevant to translation into therapies, assessing pharmacogenomics' central role in converging diverse elements of personalized medicine. We discuss genetic variations in pharmacogenes (drug-metabolizing enzymes, drug transporters, and receptors), their clinical relevance as biomarkers, and the legacy of decades of research in pharmacogenetics. All types of therapies, including proteins, nucleic acids, viruses, cells, genes, and irradiation, can benefit from genomics, expanding the role of pharmacogenomics across medicine. Food and Drug Administration approvals of personalized therapeutics involving biomarkers increase rapidly, demonstrating the growing impact of pharmacogenomics. A beacon for all therapeutic approaches, molecularly targeted cancer therapies highlight trends in drug discovery and clinical applications. To account for human complexity, multicomponent biomarker panels encompassing genetic, personal, and environmental factors can guide diagnosis and therapies, increasingly involving artificial intelligence to cope with extreme data complexities. However, clinical application encounters substantial hurdles, such as unknown validity across ethnic groups, underlying bias in health care, and real-world validation. This review address the underlying science and technologies germane to pharmacogenomics and personalized medicine, integrated with economic, ethical, and regulatory issues, providing insights into the current status and future direction of health care. SIGNIFICANCE STATEMENT: Personalized medicine aims to optimize health care for the individual patients with use of predictive biomarkers to improve outcomes and prevent adverse effects. Pharmacogenomics drives biomarker discovery and guides the development of targeted therapeutics. This review addresses basic principles and current trends in pharmacogenomics, with large-scale data repositories accelerating medical advances. The impact of pharmacogenomics is discussed, along with hurdles impeding broad clinical implementation, in the context of clinical care, ethics, economics, and regulatory affairs.
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Affiliation(s)
- Wolfgang Sadee
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Danxin Wang
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Katherine Hartmann
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
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14
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Magavern EF, Caulfield MJ. Equal access to pharmacogenomics testing: The ethical imperative for population-wide access in the UK NHS. Br J Clin Pharmacol 2023; 89:1701-1703. [PMID: 36808131 DOI: 10.1111/bcp.15689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Affiliation(s)
- Emma F Magavern
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
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15
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Anderson JD, Davis BH, Giang G, Jones A, Lee CR, Parker K, Searcy H, Benner K, Limdi N, Guimbellot JS. Pharmacogenetic actionability and medication prescribing in people with cystic fibrosis. Clin Transl Sci 2023; 16:662-672. [PMID: 36760155 PMCID: PMC10087076 DOI: 10.1111/cts.13479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 02/11/2023] Open
Abstract
Although major advancements have been made in the therapeutics for people with cystic fibrosis (PwCF), many still require the use of multiple medications to manage acute exacerbations of disease and maintain health. Iterative trial and error processes of pharmacotherapeutic management can be optimized by assessing and incorporating pharmacogenetics. For 82 PwCF, we reviewed 2 years of medication use and response history and interrogated metabolizer status for common pharmacogenes, revealing 3336 medication exposure events (MEEs) to 286 unique medications. As expected, the more frequent MEEs were those commonly used to treat cystic fibrosis (CF), such as antibiotics and respiratory medications. Antibiotics also comprised 56.7% of the undesirable drug responses. The impact of gene variants on drug responses was assessed using Pharmacogenomics Knowledgebase (PharmGKB) and Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. Thirty-three (11.5%) medications have strong evidence of genetic influence on response as evidenced by gene-based dosing guidelines. 110 (38.5%) unique medications had at least one association with a very important pharmacogene, whereas 143 (50%) were associated with at least one clinical or variant annotation. Over 97% of participants had at least one actionable genotype. Eleven (13.4%) patients with an actionable genotype, taking the impacted medication, had an undesirable drug response described in the CPIC guidelines that could potentially have been mitigated with a priori knowledge of the genotype. PwCF take many medications for disease management, with frequent dose changes to elicit a desired clinical effect. As CF care evolves, implementing pharmacogenetics testing can improve efficiency and safety of prescribing practices using precision selection and dosing at medication initiation.
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Affiliation(s)
- Justin D. Anderson
- Gregory Fleming James Cystic Fibrosis Research CenterUniversity of Alabama at Birmingham (UAB)BirminghamAlabamaUSA
- Division of Pulmonary and Sleep Medicine, Department of PediatricsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Brittney H. Davis
- Department of Neurology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Gracie Giang
- McWhorter School of PharmacySamford UniversityBirminghamAlabamaUSA
| | - April Jones
- McWhorter School of PharmacySamford UniversityBirminghamAlabamaUSA
| | - Cameron R. Lee
- McWhorter School of PharmacySamford UniversityBirminghamAlabamaUSA
| | - Kennedy Parker
- Gregory Fleming James Cystic Fibrosis Research CenterUniversity of Alabama at Birmingham (UAB)BirminghamAlabamaUSA
- Division of Pulmonary and Sleep Medicine, Department of PediatricsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Heather Searcy
- Division of Pulmonary and Sleep Medicine, Department of PediatricsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Kim Benner
- McWhorter School of PharmacySamford UniversityBirminghamAlabamaUSA
| | - Nita A. Limdi
- Department of Neurology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Jennifer S. Guimbellot
- Gregory Fleming James Cystic Fibrosis Research CenterUniversity of Alabama at Birmingham (UAB)BirminghamAlabamaUSA
- Division of Pulmonary and Sleep Medicine, Department of PediatricsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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16
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Huang Q, Liao Y, Yu T, Lei W, Liang H, Wen J, Liu Q, Chen Y, Huang K, Jing L, Huang X, Liu Y, Yu X, Su K, Liu T, Yang L, Huang M. A retrospective analysis of preemptive pharmacogenomic testing in 22,918 individuals from China. J Clin Lab Anal 2023; 37:e24855. [PMID: 36916827 PMCID: PMC10098050 DOI: 10.1002/jcla.24855] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/11/2023] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Pharmacogenomics (PGx) examines the influence of genetic variation on drug responses. With more and more Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines published, PGx is gradually shifting from the reactive testing of single gene toward the preemptive testing of multiple genes. But the profile of PGx genes, especially for the intra-country diversity, is not well understood in China. METHODS We retrospectively collected preemptive PGx testing data of 22,918 participants from 20 provinces of China, analyzed frequencies of alleles, genotypes and phenotypes of pharmacogenes, predicted drug responses for each participant, and performed comparisons between different provinces. RESULTS AND CONCLUSION After analyzing 15 pharmacogenes from CPIC guidelines of 31 drugs, we found that 99.97% of individuals may have an atypical response to at least one drug; the participants carry actionable genotypes leading to atypical dosage recommendation for a median of eight drugs. Over 99% of the participants were recommended a decreased warfarin dose based on genetic factors. There were 20 drugs with high-risk ratios from 0.18% to 58.25%, in which clopidogrel showed the highest high-risk ratio. In addition, the high-risk ratio of rasburicase in GUANGDONG (risk ratio (RR) = 13.17, 95%CI:4.06-33.22, p < 0.001) and GUANGXI (RR = 23.44, 95%CI:8.83-52.85, p < 0.001) were significantly higher than that in all provinces. Furthermore, the diversity we observed among 20 provinces suggests that preemptive PGx testing in different geographical regions in China may need to pay more attention to specific genes. These results emphasize the importance of preemptive PGx testing and provide essential evidence for promoting clinical implementation in China.
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Affiliation(s)
- Quanfei Huang
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuwei Liao
- Precision Medical Lab Center, People's Hospital of Yangjiang, Yangjiang, China
| | - Tao Yu
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Wei Lei
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Hongfeng Liang
- Precision Medical Lab Center, People's Hospital of Yangjiang, Yangjiang, China
| | - Jianxin Wen
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Qing Liu
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Yu Chen
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Kaisheng Huang
- CapitalBio Technology Co. Ltd., Beijing, China.,Guangdong CapitalBio Medical Laboratory, Dongguan, China
| | - Lifang Jing
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Xiaoyan Huang
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Yuanru Liu
- CapitalBio Technology Co. Ltd., Beijing, China.,Guangdong CapitalBio Medical Laboratory, Dongguan, China
| | - Xiaokang Yu
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Kaichan Su
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Tengfei Liu
- CapitalBio Genomics Co., Ltd., Dongguan, China.,CapitalBio Technology Co. Ltd., Beijing, China
| | - Liye Yang
- Precision Medical Lab Center, People's Hospital of Yangjiang, Yangjiang, China
| | - Min Huang
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
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17
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Lopes J, Vidal-Folch N, Lundquist P, Schimmenti LA, Demirel N, Dean V, Olson J, Auth T, Butz M, Reed K, Wylam M, Balcom J, Boczek NJ, Hasadsri L. Aminoglycoside induced ototoxicity risk in the cystic fibrosis population: The utility of large-scale screening. Pediatr Pulmonol 2023; 58:819-824. [PMID: 36437230 DOI: 10.1002/ppul.26259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 10/24/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND MT-RNR1 variants are a well-known cause of aminoglycoside-induced hearing loss (AIHL). Individuals with cystic fibrosis (CF) routinely receive aminoglycosides and are at high risk of AIHL. However, genetic testing before treatment is not routinely performed due to perceived rarity of risk, and cost ineffectiveness with traditional technologies. AIM Assess the utility of large-scale screening for AIHL risk in the CF population, using digital droplet polymerase chain reaction (ddPCR), a novel and scalable low-cost molecular technique. METHODS Using a clinically validated ddPCR assay, we performed retrospective testing on 122 and prospective testing on 32 individuals with CF for the two most common pathogenic variants associated with AIHL, MT-RNR1 m.1555 A > G and m.1494 C > T. Our study screened the largest known cohort of pediatric cases of CF (94/154) for these specific alterations. RESULTS We identified two individuals positive for MT-RNR1 m.1555 A > G and no positives for m.1494 C > T. Of 32 prospective cases, 17 had aminoglycoside exposure. The positive case in our prospective group recently began inhaled tobramycin and denied hearing issues. The clinician adjusted to care for both the patient and sibling with CF (not included in cohort) who is presumed positive for m.1555 A > G due to the nature of mitochondrial inheritance. CONCLUSION Our findings demonstrate the utility of pretreatment screening in the cystic fibrosis population for AIHL risk using ddPCR, a scalable and robust testing methodology at a fraction of the cost as compared to other sequencing-based methods. Therefore, the use of large-scale screening for AIHL risk in the cystic fibrosis community should be re-visited.
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Affiliation(s)
- Jaime Lopes
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Patrick Lundquist
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Nadir Demirel
- Department of Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
| | - Vicki Dean
- Department of Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
| | - Janelle Olson
- Department of Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
| | - Tom Auth
- Department of Research Services, Mayo Clinic, Rochester, Minnesota, USA
| | - Malinda Butz
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Katelyn Reed
- Department of Research Services, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark Wylam
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jessica Balcom
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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18
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Relevance of Pharmacogenomics to the Safe Use of Antimicrobials. Antibiotics (Basel) 2023; 12:antibiotics12030425. [PMID: 36978292 PMCID: PMC10044203 DOI: 10.3390/antibiotics12030425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/11/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
There has been widespread implementation of pharmacogenomic testing to inform drug prescribing in medical specialties such as oncology and cardiology. Progress in using pharmacogenomic tests when prescribing antimicrobials has been more limited, though a relatively large number of pharmacogenomic studies on aspects such as idiosyncratic adverse drug reactions have now been performed for this drug class. Currently, there are recommendations in place from either National Regulatory Agencies and/or specialist Pharmacogenomics Advisory Groups concerning genotyping for specific variants in MT-RNR1 and CYP2C19 before prescribing aminoglycosides and voriconazole, respectively. Numerous additional pharmacogenomic associations have been reported concerning antimicrobial-related idiosyncratic adverse drug reactions, particularly involving specific HLA alleles, but, to date, the cost-effectiveness of genotyping prior to prescription has not been confirmed. Polygenic risk score determination has been investigated to a more limited extent but currently suffers from important limitations. Despite limited progress to date, the future widespread adoption of preemptive genotyping and genome sequencing may provide pharmacogenomic data to prescribers that can be used to inform prescribing and increase the safe use of antimicrobials.
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19
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McDermott JH, Newman WG. Letter to the Editor. J Paediatr Child Health 2023; 59:600. [PMID: 36779317 DOI: 10.1111/jpc.16376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/14/2023]
Affiliation(s)
- John H McDermott
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - William G Newman
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
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20
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Genetic testing for mitochondrial disease: the United Kingdom best practice guidelines. Eur J Hum Genet 2023; 31:148-163. [PMID: 36513735 PMCID: PMC9905091 DOI: 10.1038/s41431-022-01249-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Primary mitochondrial disease describes a diverse group of neuro-metabolic disorders characterised by impaired oxidative phosphorylation. Diagnosis is challenging; >350 genes, both nuclear and mitochondrial DNA (mtDNA) encoded, are known to cause mitochondrial disease, leading to all possible inheritance patterns and further complicated by heteroplasmy of the multicopy mitochondrial genome. Technological advances, particularly next-generation sequencing, have driven a shift in diagnostic practice from 'biopsy first' to genome-wide analyses of blood and/or urine DNA. This has led to the need for a reference framework for laboratories involved in mitochondrial genetic testing to facilitate a consistent high-quality service. In the United Kingdom, consensus guidelines have been prepared by a working group of Clinical Scientists from the NHS Highly Specialised Service followed by national laboratory consultation. These guidelines summarise current recommended technologies and methodologies for the analysis of mtDNA and nuclear-encoded genes in patients with suspected mitochondrial disease. Genetic testing strategies for diagnosis, family testing and reproductive options including prenatal diagnosis are outlined. Importantly, recommendations for the minimum levels of mtDNA testing for the most common referral reasons are included, as well as guidance on appropriate referrals and information on the minimal appropriate gene content of panels when analysing nuclear mitochondrial genes. Finally, variant interpretation and recommendations for reporting of results are discussed, focussing particularly on the challenges of interpreting and reporting mtDNA variants.
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21
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Liu Y, Lin Z, Chen Q, Chen Q, Sang L, Wang Y, Shi L, Guo L, Yu Y. PAnno: A pharmacogenomics annotation tool for clinical genomic testing. Front Pharmacol 2023; 14:1008330. [PMID: 36778023 PMCID: PMC9909284 DOI: 10.3389/fphar.2023.1008330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction: Next-generation sequencing (NGS) technologies have been widely used in clinical genomic testing for drug response phenotypes. However, the inherent limitations of short reads make accurate inference of diplotypes still challenging, which may reduce the effectiveness of genotype-guided drug therapy. Methods: An automated Pharmacogenomics Annotation tool (PAnno) was implemented, which reports prescribing recommendations and phenotypes by parsing the germline variant call format (VCF) file from NGS and the population to which the individual belongs. Results: A ranking model dedicated to inferring diplotypes, developed based on the allele (haplotype) definition and population allele frequency, was introduced in PAnno. The predictive performance was validated in comparison with four similar tools using the consensus diplotype data of the Genetic Testing Reference Materials Coordination Program (GeT-RM) as ground truth. An annotation method was proposed to summarize prescribing recommendations and classify drugs into avoid use, use with caution, and routine use, following the recommendations of the Clinical Pharmacogenetics Implementation Consortium (CPIC), etc. It further predicts phenotypes of specific drugs in terms of toxicity, dosage, efficacy, and metabolism by integrating the high-confidence clinical annotations in the Pharmacogenomics Knowledgebase (PharmGKB). PAnno is available at https://github.com/PreMedKB/PAnno. Discussion: PAnno provides an end-to-end clinical pharmacogenomics decision support solution by resolving, annotating, and reporting germline variants.
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Affiliation(s)
- Yaqing Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zipeng Lin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Leqing Sang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yunjin Wang
- Department of Breast Surgery, Precision Cancer Medicine Center, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Li Guo
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Li Guo, ; Ying Yu,
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China,*Correspondence: Li Guo, ; Ying Yu,
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22
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McDermott JH, Sharma V, Keen J, Newman WG, Pirmohamed M. The Implementation of Pharmacogenetics in the United Kingdom. Handb Exp Pharmacol 2023; 280:3-32. [PMID: 37306816 DOI: 10.1007/164_2023_658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There is considerable inter-individual variability in the effectiveness and safety of pharmaceutical interventions. This phenomenon can be attributed to a multitude of factors; however, it is widely acknowledged that common genetic variation affecting drug absorption or metabolism play a substantial contributory role. This is a concept known as pharmacogenetics. Understanding how common genetic variants influence responses to medications, and using this knowledge to inform prescribing practice, could yield significant advantages for both patients and healthcare systems. Some health services around the world have introduced pharmacogenetics into routine practice, whereas others are less advanced along the implementation pathway. This chapter introduces the field of pharmacogenetics, the existing body of evidence, and discusses barriers to implementation. The chapter will specifically focus on efforts to introduce pharmacogenetics in the NHS, highlighting key challenges related to scale, informatics, and education.
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Affiliation(s)
- John H McDermott
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Videha Sharma
- Division of Informatics, Imaging and Data Science, Centre for Health Informatics, The University of Manchester, Manchester, UK
| | - Jessica Keen
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - William G Newman
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Munir Pirmohamed
- Department of Pharmacology and Therapeutics, Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool, UK.
- Liverpool University Hospital Foundation NHS Trust, Liverpool, UK.
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23
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May ML, Osowicki J, Gaafar D, Suthers G. Using a bedside test to detect genetic susceptibility to aminoglycoside-induced hearing loss: Has the future arrived? J Paediatr Child Health 2023; 59:9-11. [PMID: 36465032 PMCID: PMC10107546 DOI: 10.1111/jpc.16302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/30/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022]
Abstract
Aminoglycosides are among the most commonly prescribed antibiotics in hospitalised Australian adults and children. A proportion of individuals with an underlying genetic predisposition to aminoglycoside-induced hearing loss (AIHL) can develop bilateral sensorineural hearing loss that is immediate and profound after just a single standard dose of an aminoglycoside. A recent publication described the use of a rapid point-of-care test (POCT) in a neonatal nursery in the United Kingdom for real-time detection of infants at risk of AIHL, in whom exposure to aminoglycosides could then be avoided. This proof of concept study should provide a catalyst for further development of similar assays that would be suitable for Australia's genetically diverse population. The barriers to mitigating the impact of AIHL on Australian children are not primarily technical, but involve a lack of data on the prevalence of the MT-RNR1 mutations in our current neonatal and paediatric populations and intensive care nurseries.
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Affiliation(s)
- Meryta L May
- Department of Microbiology, Sullivan Nicolaides Pathology, Sonic Healthcare Australia, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Joshua Osowicki
- Tropical Diseases Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Infectious Diseases Unit, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Duaa Gaafar
- Department of Paediatrics, Ballarat Base Hospital, Ballarat Central, Victoria, Australia.,Murdoch Children's Research Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Graeme Suthers
- Sonic Healthcare Australia - Pathology, Sydney, New South Wales, Australia.,Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
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24
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Huang Q, Liu Y, Lei W, Liang J, Wang Y, Zheng M, Huang X, Liu Y, Huang K, Huang M. Detecting mitochondrial mutations associated with aminoglycoside ototoxicity by noninvasive prenatal testing. J Clin Lab Anal 2022; 37:e24827. [PMID: 36579624 PMCID: PMC9833975 DOI: 10.1002/jcla.24827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/11/2022] [Accepted: 12/18/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Numerous diseases and disorders are associated with mitochondrial DNA (mtDNA) mutations, among which m.1555A > G and m.1494C > T mutations in the 12 S ribosomal RNA gene contribute to aminoglycoside-induced and nonsyndromic hearing loss worldwide. METHODS A total of 76,842 qualified non-invasive prenatal (NIPT) samples were subjected to mtDNA mutation and haplogroup analysis. RESULTS We detected 181 m.1555A > G and m.1494C > T mutations, 151 of which were subsequently sequenced for full-length mitochondrial genome verification. The positive predictive values for the m.1555A > G and m.1494C > T mutations were 90.78% and 90.00%, respectively, a performance comparable to that attained with newborn hearing screening. Furthermore, mitochondrial haplogroup analysis revealed that the 12 S rRNA 1555A > G mutation was enriched in sub-haplotype D5[p = 0, OR = 4.6706(2.81-7.78)]. CONCLUSIONS Our findings indicate that the non-invasive prenatal testing of cell-free DNA obtained from maternal plasma can successfully detect m.1555A > G and m.1494C > T mutations.
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Affiliation(s)
- Quanfei Huang
- Institute of Clinical Pharmacology, School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yanhui Liu
- Dongguan Maternal and Child Health HospitalDongguanChina,Dongguan maternal and Child Health Hospital Affiliated to Southern Medical UniversityDongguanChina
| | - Wei Lei
- CapitalBio Genomics Co., Ltd.DongguanChina,CapitalBio Technology Co., Ltd.BeijingChina
| | - Jiajie Liang
- Dongguan Maternal and Child Health HospitalDongguanChina,Dongguan maternal and Child Health Hospital Affiliated to Southern Medical UniversityDongguanChina
| | - Yang Wang
- CapitalBio Genomics Co., Ltd.DongguanChina,CapitalBio Technology Co., Ltd.BeijingChina
| | - Minhua Zheng
- Dongguan Maternal and Child Health HospitalDongguanChina,Dongguan maternal and Child Health Hospital Affiliated to Southern Medical UniversityDongguanChina
| | - Xiaoyan Huang
- CapitalBio Genomics Co., Ltd.DongguanChina,CapitalBio Technology Co., Ltd.BeijingChina
| | - Yuanru Liu
- CapitalBio Technology Co., Ltd.BeijingChina,Guangdong CapitalBio Medical LaboratoryDongguanChina
| | - Kaisheng Huang
- CapitalBio Technology Co., Ltd.BeijingChina,Guangdong CapitalBio Medical LaboratoryDongguanChina
| | - Min Huang
- Institute of Clinical Pharmacology, School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
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25
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Starosta RT, Shinawi M. Primary Mitochondrial Disorders in the Neonate. Neoreviews 2022; 23:e796-e812. [PMID: 36450643 DOI: 10.1542/neo.23-12-e796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Primary mitochondrial disorders (PMDs) are a heterogeneous group of disorders characterized by functional or structural abnormalities in the mitochondria that lead to a disturbance of cellular energy, reactive oxygen species, and free radical production, as well as impairment of other intracellular metabolic functions, causing single- or multiorgan dysfunction. PMDs are caused by pathogenic variants in nuclear and mitochondrial genes, resulting in distinct modes of inheritance. Onset of disease is variable and can occur in the neonatal period, with a high morbidity and mortality. In this article, we review the most common methods used for the diagnosis of PMDs, as well as their prenatal and neonatal presentations. We highlight the shift in the diagnostic approach for PMDs since the introduction of nontargeted molecular tests into clinical practice, which has significantly reduced the use of invasive studies. We discuss common PMDs that can present in the neonate, including general, nonsyndromic presentations as well as specific syndromic disorders. We also review current treatment advances, including the use of mitochondrial "cocktails" based on limited scientific evidence and theoretical reasoning, as well as the impending arrival of personalized mitochondrial-specific treatments.
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Affiliation(s)
| | - Marwan Shinawi
- Washington University School of Medicine, Saint Louis, MO
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26
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Wittwer NL, Meier CR, Huber CA, Meyer zu Schwabedissen HE, Allemann S, Schneider C. Utilization of Drugs with Pharmacogenetic Dosing Recommendations in Switzerland: A Descriptive Study Using the Helsana Database. Pharmgenomics Pers Med 2022; 15:967-976. [DOI: 10.2147/pgpm.s382214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022] Open
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27
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Brutnell TP, Wang X, Bao J. Integrating pharmacogenomics into clinical trials of hearing disorders. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2022; 152:2828. [PMID: 36456290 PMCID: PMC9648993 DOI: 10.1121/10.0015092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/26/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
In 2019, the U.S. Food and Drug Administration issued guidance to increase the efficiency of drug development and support precision medicine, including tailoring treatments to those patients who will benefit based on genetic variation even in the absence of a documented mechanism of action. Although multiple advancements have been made in the field of pharmacogenetics (PGx) for other disease conditions, there are no approved PGx guidelines in the treatment of hearing disorders. In studies of noise-induced hearing loss (NIHL), some progress has been made in the last several years associating genomic loci with susceptibility to noise damage. However, the power of such studies is limited as the underlying physiological responses may vary considerably among the patient populations. Here, we have summarized previous animal studies to argue that NIHL subtyping is a promising strategy to increase the granularity of audiological assessments. By coupling this enhanced phenotyping capability with genetic association studies, we suggest that drug efficacy will be better predicted, increasing the likelihood of success in clinical trials when populations are stratified based on genetic variation or designed with multidrug combinations to reach a broader segment of individuals suffering or at risk from NIHL.
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Affiliation(s)
| | - Xinwen Wang
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272, USA
| | - Jianxin Bao
- Gateway Biotechnology, St. Louis, Missouri 63132, USA
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28
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Alshabeeb MA, Alyabsi M, Aziz MA, Abohelaika S. Pharmacogenes that demonstrate high association evidence according to CPIC, DPWG, and PharmGKB. Front Med (Lausanne) 2022; 9:1001876. [PMID: 36388934 PMCID: PMC9640910 DOI: 10.3389/fmed.2022.1001876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/22/2022] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Different levels of evidence related to the variable responses of individuals to drug treatment have been reported in various pharmacogenomic (PGx) databases. Identification of gene-drug pairs with strong association evidence can be helpful in prioritizing the implementation of PGx guidelines and focusing on a gene panel. This study aimed to determine the pharmacogenes with the highest evidence-based association and to indicate their involvement in drug-gene interactions. METHODOLOGY The publicly available datasets CPIC, DPWG, and PharmGKB were selected to determine the pharmacogenes with the highest drug outcome associations. The upper two levels of evidence rated by the three scoring methods were specified (levels A-B in CPIC, 3-4 in DPWG, or 1-2 levels in PharmGKB). The identified pharmacogenes were further ranked in this study based on the number of medications they interacted with. RESULTS Fifty pharmacogenes, with high to moderately high evidence of associations with drug response alterations, with potential influence on the therapeutic and/or toxicity outcomes of 152 drugs were identified. CYP2D6, CYP2C9, CYP2C19, G6PD, HLA-B, SLCO1B1, CACNA1S, RYR1, MT-RNR1, and IFNL4 are the top 10 pharmacogenes, where each is predicted to impact patients' responses to ≥5 drugs. CONCLUSION This study identified the most important pharmacogenes based on the highest-ranked association evidence and their frequency of involvement in affecting multiple drugs. The obtained data is useful for customizing a gene panel for PGx testing. Identifying the strength of scientific evidence supporting drug-gene interactions aids drug prescribers in making the best clinical decision.
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Affiliation(s)
- Mohammad A. Alshabeeb
- Population Health Research Section, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Mesnad Alyabsi
- Population Health Research Section, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Mohammad A. Aziz
- Interdisciplinary Nanotechnology Centre, Aligarh Muslim University, Aligarh, India
| | - Salah Abohelaika
- Department of Pharmacy, Qatif Central Hospital, Qatif, Saudi Arabia
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29
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Induced Pluripotent Stem Cells, a Stepping Stone to In Vitro Human Models of Hearing Loss. Cells 2022; 11:cells11203331. [PMID: 36291196 PMCID: PMC9600035 DOI: 10.3390/cells11203331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 10/05/2022] [Accepted: 10/14/2022] [Indexed: 11/28/2022] Open
Abstract
Hearing loss is the most prevalent sensorineural impairment in humans. Yet despite very active research, no effective therapy other than the cochlear implant has reached the clinic. Main reasons for this failure are the multifactorial nature of the disorder, its heterogeneity, and a late onset that hinders the identification of etiological factors. Another problem is the lack of human samples such that practically all the work has been conducted on animals. Although highly valuable data have been obtained from such models, there is the risk that inter-species differences exist that may compromise the relevance of the gathered data. Human-based models are therefore direly needed. The irruption of human induced pluripotent stem cell technologies in the field of hearing research offers the possibility to generate an array of otic cell models of human origin; these may enable the identification of guiding signalling cues during inner ear development and of the mechanisms that lead from genetic alterations to pathology. These models will also be extremely valuable when conducting ototoxicity analyses and when exploring new avenues towards regeneration in the inner ear. This review summarises some of the work that has already been conducted with these cells and contemplates future possibilities.
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30
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Schreeck F, Ahne G, Tremmel R, Schaeffeler E, Schwab M. Pharmacogenomics in pediatric medicine and drug development. Pharmacogenomics 2022; 23:709-712. [PMID: 36004680 DOI: 10.2217/pgs-2022-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Filippa Schreeck
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, 70376, Germany and University of Tuebingen, Tuebingen, 72074, Germany
| | - Gabriele Ahne
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, 70376, Germany and University of Tuebingen, Tuebingen, 72074, Germany.,Department of Paediatrics and Adolescents Medicine, University Hospital Erlangen, Erlangen, 91054, Germany
| | - Roman Tremmel
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, 70376, Germany and University of Tuebingen, Tuebingen, 72074, Germany
| | - Elke Schaeffeler
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, 70376, Germany and University of Tuebingen, Tuebingen, 72074, Germany
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, 70376, Germany and University of Tuebingen, Tuebingen, 72074, Germany.,Departments of Clinical Pharmacology, and Biochemistry and Pharmacy, University of Tuebingen, Tuebingen, 72074, Germany
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31
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McDermott JH, Wright S, Sharma V, Newman WG, Payne K, Wilson P. Characterizing pharmacogenetic programs using the consolidated framework for implementation research: A structured scoping review. Front Med (Lausanne) 2022; 9:945352. [PMID: 36059837 PMCID: PMC9433561 DOI: 10.3389/fmed.2022.945352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/29/2022] [Indexed: 12/11/2022] Open
Abstract
Several healthcare organizations have developed pre-emptive pharmacogenetic testing programs, where testing is undertaken prior to the prescription of a medicine. This review characterizes the barriers and facilitators which influenced the development of these programs. A bidirectional citation searching strategy identified relevant publications before a standardized data extraction approach was applied. Publications were grouped by program and data synthesis was undertaken using the Consolidated Framework for Implementation Research (CFIR). 104 publications were identified from 40 programs and 4 multi-center initiatives. 26 (66%) of the programs were based in the United States and 95% in high-income countries. The programs were heterogeneous in their design and scale. The Characteristics of the Intervention, Inner Setting, and Process domains were referenced by 92.5, 80, and 77.5% of programs, respectively. A positive institutional culture, leadership engagement, engaging stakeholders, and the use of clinical champions were frequently described as facilitators to implementation. Clinician self-efficacy, lack of stakeholder knowledge, and the cost of the intervention were commonly cited barriers. Despite variation between the programs, there were several similarities in approach which could be categorized via the CFIR. These form a resource for organizations planning the development of pharmacogenetic programs, highlighting key facilitators which can be leveraged to promote successful implementation.
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Affiliation(s)
- John H. McDermott
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
- *Correspondence: John H. McDermott,
| | - Stuart Wright
- Division of Population Health, Manchester Centre for Health Economics, Health Services Research and Primary Care, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
| | - Videha Sharma
- Division of Informatics, Centre for Health Informatics, Imaging and Data Science, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
| | - William G. Newman
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - Katherine Payne
- Division of Population Health, Manchester Centre for Health Economics, Health Services Research and Primary Care, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
| | - Paul Wilson
- Division of Population Health, Centre for Primary Care and Health Services Research, Health Services Research and Primary Care, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
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Li MM, Tayoun AA, DiStefano M, Pandya A, Rehm HL, Robin NH, Schaefer AM, Yoshinaga-Itano C. Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:1392-1406. [PMID: 35802133 DOI: 10.1016/j.gim.2022.03.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/26/2022] Open
Abstract
Hearing loss is a common and complex condition that can occur at any age, can be inherited or acquired, and is associated with a remarkably wide array of etiologies. The diverse causes of hearing loss, combined with the highly variable and often overlapping presentations of different forms of hearing loss, challenge the ability of traditional clinical evaluations to arrive at an etiologic diagnosis for many deaf and hard-of-hearing individuals. However, identifying the etiology of hearing loss may affect clinical management, improve prognostic accuracy, and refine genetic counseling and assessment of the likelihood of recurrence for relatives of deaf and hard-of-hearing individuals. Linguistic and cultural identities associated with being deaf or hard-of-hearing can complicate access to and the effectiveness of clinical care. These concerns can be minimized when genetic and other health care services are provided in a linguistically and culturally sensitive manner. This clinical practice resource offers information about the frequency, causes, and presentations of hearing loss and suggests approaches to the clinical and genetic evaluation of deaf and hard-of-hearing individuals aimed at identifying an etiologic diagnosis and providing informative and effective patient education and genetic counseling.
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Affiliation(s)
- Marilyn M Li
- Department of Pathology and Laboratory Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Mohammed Bin Rashid University, Dubai, United Arab Emirates
| | | | - Arti Pandya
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Nathaniel H Robin
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Amanda M Schaefer
- Department of Otolaryngology-Head & Neck Surgery, Molecular Otolaryngology and Renal Research Laboratories, University of Iowa, Iowa City, IA
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Swift CG. Personalised future prescribing using pharmacogenomics: A resumé of a joint Royal College of Physicians / British Pharmacological Society working party report. Future Healthc J 2022; 9:174-178. [DOI: 10.7861/fhj.rev-9.2.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Prevalence of exposure to pharmacogenetic drugs by the Saudis treated at the health care centers of the Ministry of National Guard. Saudi Pharm J 2022; 30:1181-1192. [PMID: 36164570 PMCID: PMC9508627 DOI: 10.1016/j.jsps.2022.06.013] [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: 08/31/2021] [Accepted: 06/17/2022] [Indexed: 12/02/2022] Open
Abstract
Background The drugs impacted by genetic variants are known as pharmacogenetic (PGx) drugs. Patients’ responses to these drugs may vary according to the variability in patients’ genetic makeup. Hence, exploring the pharmacogenes that affect drug treatment is vital to ensure optimal therapy and patients’ safety. This study aimed to describe the usage rate of PGx drugs and the frequency of relevant variants in the Saudi population. Methodology Prescription patterns over seven years (2015–2021) for Saudi patients on PGx drugs treated at the Ministry of National Guard-Health Affairs (MNG-HA) were investigated. Only registered drugs in the MNG-HA formulary (n = 78) were included. The patients were subgrouped into four age groups: ≤24, 25–44, 45–64, and ≥65 years. Further subgrouping was made according to gender and drugs’ therapeutic categories following anatomical therapeutic chemical (ATC) classification. Furthermore, an online searching was carried out to identify the pharmacogenes reported in the literature among healthy Saudis. The search included 45 genes that may affect drug outcomes based on evidence rated by either CPIC (A-B levels) or PharmGKB (1–2 levels). Results The screened patients were 1,483,905. Patients on PGx drugs accounted for 46.7% (n = 693,077 patients). The analgesic group was the most prescribed drug category (47%), which included ibuprofen (20.5%), celecoxib (6.3%), tramadol (5.8%), and others. Cardiovascular agents were the second-most utilized drug class (24.4%). Omeprazole was the second most commonly used medication (11.1%) but ranked third as a class (gastroenterology). Females used PGx drugs more frequently than males (53.5% versus 46.5%) and a higher usage rate by patients aged 45–64 years (31.3%) was noted. The cytochrome P450 genes (CYP2C9, CYP2C19, and CYP2D6) were estimated to impact responses of 54.3% (n = 1,156,113) of the used drugs (27.2% are possibly affected by CYP2C9, 12.8% by CYP2C19, and 14.3% by CYP2D6). Thirty-five pharmacogenes that characterize Saudi population and their variants’ allele frequencies were identified from previous reports. This study presents the largest reported number of genes that may affect drug therapies among Saudis. Conclusion This study confirmed that a high percentage of Saudi patients use PGx drugs and various genotypes of certain pharmacogenes are inherited by the Saudi population.
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Klanderman BJ, Koch C, Machini K, Parpattedar SS, Bandyadka S, Lin CF, Hynes E, Lebo MS, Amr SS. Automated Pharmacogenomic Reports for Clinical Genome Sequencing. J Mol Diagn 2022; 24:205-218. [PMID: 35041930 DOI: 10.1016/j.jmoldx.2021.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/09/2021] [Accepted: 12/07/2021] [Indexed: 11/26/2022] Open
Abstract
Clinical laboratories offering genome sequencing have the opportunity to return pharmacogenomic findings to patients, providing the added benefit of preemptive testing that could help inform medication selection or dosing throughout the lifespan. Implementation of pharmacogenomic reporting must address several challenges, including inherent limitations in short-read genome sequencing methods, gene and variant selection, standardization of genotype and phenotype nomenclature, and choice of guidelines and drugs to report. An automated pipeline, lmPGX, was developed as an end-to-end solution that produces two versions of a pharmacogenomic report, presenting either Clinical Pharmacogenetics Implementation Consortium or US Food and Drug Administration guidelines for 12 genes. The pipeline was validated for performance using reference samples and pharmacogenetic data from the Genetic Testing Reference Materials Coordination Program. To determine performance and limitations, lmPGX was compared with three additional publicly available pharmacogenomic pipelines. The lmPGX pipeline offers clinical laboratories an opportunity for seamless integration of pharmacogenomic results with genome reporting.
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Affiliation(s)
- Barbara J Klanderman
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Kalotina Machini
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Deparment of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Shruti S Parpattedar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Shruthi Bandyadka
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Chiao-Feng Lin
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elizabeth Hynes
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Deparment of Pathology, Harvard Medical School, Boston, Massachusetts; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
| | - Sami S Amr
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Deparment of Pathology, Harvard Medical School, Boston, Massachusetts.
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Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders. Curr Issues Mol Biol 2022; 44:1127-1148. [PMID: 35723297 PMCID: PMC8947152 DOI: 10.3390/cimb44030074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/06/2022] Open
Abstract
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs’s cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications.
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Neumann E, Schreeck F, Herberg J, Jacqz Aigrain E, Maitland-van der Zee AH, Pérez-Martínez A, Hawcutt DB, Schaeffeler E, Rane A, de Wildt SN, Schwab M. How paediatric drug development and use could benefit from OMICs: a c4c expert group white paper. Br J Clin Pharmacol 2022; 88:5017-5033. [PMID: 34997627 DOI: 10.1111/bcp.15216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/01/2022] Open
Abstract
The safety and efficacy of pharmacotherapy in children, particularly preterms, neonates, and infants, is limited by a paucity of good quality data from prospective clinical drug trials. A specific challenge is the establishment of valid biomarkers. OMICs technologies may support these efforts, by complementary information about targeted and non-targeted molecules through systematic characterization and quantitation of biological samples. OMICs technologies comprise at least genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomics in addition to the patient's phenotype. OMICs technologies are in part hypothesis-generating allowing an in depth understanding of disease pathophysiology and pharmacological mechanisms. Application of OMICs technologies in paediatrics faces major challenges before routine adoption. First, developmental processes need to be considered, including a sub-division into specific age groups as developmental changes clearly impact OMICs data. Second, compared to the adult population, the number of patients is limited as well as type and amount of necessary biomaterial, especially in neonates and preterms. Thus, advanced trial designs and biostatistical methods, non-invasive biomarkers, innovative biobanking concepts including data and samples from healthy children, as well as analytical approaches (e.g. liquid biopsies) should be addressed to overcome these obstacles. The ultimate goal is to link OMICs technologies with innovative analysis tools, like artificial intelligence at an early stage. The use of OMICs data based on a feasible approach will contribute to identify complex phenotypes and subpopulations of patients to improve development of medicines for children with potential economic advantages.
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Affiliation(s)
- Eva Neumann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Filippa Schreeck
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Jethro Herberg
- Department of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Evelyne Jacqz Aigrain
- Pediatric Pharmacology and Pharmacogenetics, Hopital Universitaire Saint-Louis, Paris, France.,Clinical Investigation Center CIC1426, Hôpital Robert Debre, Paris, France.,Pharmacology, University of Paris, Paris, France
| | | | - Antonio Pérez-Martínez
- Institute for Health Research (IdiPAZ), La Paz University Hospital, Madrid, Spain.,Pediatric Onco-Hematology Department, La Paz University Hospital, Madrid, Spain.,Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Daniel B Hawcutt
- Department of Women's and Children's Health, University of Liverpool, UK.,NIHR Alder Hey Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, UK
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Anders Rane
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Saskia N de Wildt
- Department of Pharmacology and Toxicology, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands.,Intensive Care and Department of Paediatric Surgery, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany.,Departments of Clinical Pharmacology, and of Biochemistry and Pharmacy, University of Tuebingen, Tuebingen, Germany
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Pham VH, Nguyen VL, Jung HE, Cho YS, Shin JG. The frequency of the known mitochondrial variants associated with drug-induced toxicity in a Korean population. BMC Med Genomics 2022; 15:3. [PMID: 34980117 PMCID: PMC8722126 DOI: 10.1186/s12920-021-01153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Few studies have annotated the whole mitochondrial DNA (mtDNA) genome associated with drug responses in Asian populations. This study aimed to characterize mtDNA genetic profiles, especially the distribution and frequency of well-known genetic biomarkers associated with diseases and drug-induced toxicity in a Korean population. METHOD Whole mitochondrial genome was sequenced for 118 Korean subjects by using a next-generation sequencing approach. The bioinformatic pipeline was constructed for variant calling, haplogroup classification and annotation of mitochondrial mutation. RESULTS A total of 681 variants was identified among all subjects. The MT-TRNP gene and displacement loop showed the highest numbers of variants (113 and 74 variants, respectively). The m.16189T > C allele, which is known to reduce the mtDNA copy number in human cells was detected in 25.4% of subjects. The variants (m.2706A > G, m.3010A > G, and m.1095T > C), which are associated with drug-induced toxicity, were observed with the frequency of 99.15%, 30.51%, and 0.08%, respectively. The m.2150T > A, a genotype associated with highly disruptive effects on mitochondrial ribosomes, was identified in five subjects. The D and M groups were the most dominant groups with the frequency of 34.74% and 16.1%, respectively. CONCLUSIONS Our finding was consistent with Korean Genome Project and well reflected the unique profile of mitochondrial haplogroup distribution. It was the first study to annotate the whole mitochondrial genome with drug-induced toxicity to predict the ADRs event in clinical implementation for Korean subjects. This approach could be extended for further study for validation of the potential ethnic-specific mitochondrial genetic biomarkers in the Korean population.
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Affiliation(s)
- Vinh Hoa Pham
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea
| | - Van Lam Nguyen
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea
| | - Hye-Eun Jung
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea.,Department of Precision Medicine, SPMED Co., Ltd., Busan, 46508, Republic of Korea
| | - Yong-Soon Cho
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea.,Department of Pharmacology and Clinical Pharmacology, PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Jae-Gook Shin
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea. .,Department of Pharmacology and Clinical Pharmacology, PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea. .,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea.
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An Investigation of the Knowledge Overlap between Pharmacogenomics and Disease Genetics. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022; 27:385-396. [PMID: 34890165 PMCID: PMC8772060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Precision medicine faces many challenges, including the gap of knowledge between disease genetics and pharmacogenomics (PGx). Disease genetics interprets the pathogenicity of genetic variants for diagnostic purposes, while PGx investigates the genetic influences on drug responses. Ideally, the quality of health care would be improved from the point of disease diagnosis to drug prescribing if PGx is integrated with disease genetics in clinical care. However, PGx genes or variants are usually not reported as a secondary finding even if they are included in a clinical genetic test for diagnostic purposes. This happens even though the detection of PGx variants can provide valuable drug prescribing recommendations. One underlying reason is the lack of systematic classification of the knowledge overlap between PGx and disease genetics. Here, we address this issue by analyzing gene and genetic variant annotations from multiple expert-curated knowledge databases, including PharmGKB, CPIC, ClinGen and ClinVar. We further classified genes based on the strength of evidence supporting a gene's pathogenic role or PGx effect as well as the level of clinical actionability of a gene. Twenty-six genes were found to have pathogenic variation associated with germline diseases as well as strong evidence for a PGx association. These genes were classified into four sub-categories based on the distinct connection between the gene's pathogenic role and PGx effect. Moreover, we have also found thirteen RYR1 genetic variants that were annotated as pathogenic and at the same time whose PGx effect was supported by a preponderance of evidence and given drug prescribing recommendations. Overall, we identified a nontrivial number of gene and genetic variant overlaps between disease genetics and PGx, which laid out a foundation for combining PGx and disease genetics to improve clinical care from disease diagnoses to drug prescribing and adherence.
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Coffin AB, Boney R, Hill J, Tian C, Steyger PS. Detecting Novel Ototoxins and Potentiation of Ototoxicity by Disease Settings. Front Neurol 2021; 12:725566. [PMID: 34489859 PMCID: PMC8418111 DOI: 10.3389/fneur.2021.725566] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Over 100 drugs and chemicals are associated with permanent hearing loss, tinnitus, and vestibular deficits, collectively known as ototoxicity. The ototoxic potential of drugs is rarely assessed in pre-clinical drug development or during clinical trials, so this debilitating side-effect is often discovered as patients begin to report hearing loss. Furthermore, drug-induced ototoxicity in adults, and particularly in elderly patients, may go unrecognized due to hearing loss from a variety of etiologies because of a lack of baseline assessments immediately prior to novel therapeutic treatment. During the current pandemic, there is an intense effort to identify new drugs or repurpose FDA-approved drugs to treat COVID-19. Several potential COVID-19 therapeutics are known ototoxins, including chloroquine (CQ) and lopinavir-ritonavir, demonstrating the necessity to identify ototoxic potential in existing and novel medicines. Furthermore, several factors are emerging as potentiators of ototoxicity, such as inflammation (a hallmark of COVID-19), genetic polymorphisms, and ototoxic synergy with co-therapeutics, increasing the necessity to evaluate a drug's potential to induce ototoxicity under varying conditions. Here, we review the potential of COVID-19 therapies to induce ototoxicity and factors that may compound their ototoxic effects. We then discuss two models for rapidly detecting the potential for ototoxicity: mammalian auditory cell lines and the larval zebrafish lateral line. These models offer considerable value for pre-clinical drug development, including development of COVID-19 therapies. Finally, we show the validity of in silico screening for ototoxic potential using a computational model that compares structural similarity of compounds of interest with a database of known ototoxins and non-ototoxins. Preclinical screening at in silico, in vitro, and in vivo levels can provide an earlier indication of the potential for ototoxicity and identify the subset of candidate therapeutics for treating COVID-19 that need to be monitored for ototoxicity as for other widely-used clinical therapeutics, like aminoglycosides and cisplatin.
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Affiliation(s)
| | | | - Jordan Hill
- Washington State University Vancouver, Vancouver, WA, United States
| | - Cong Tian
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, United States
| | - Peter S. Steyger
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, United States
- National Center for Rehabilitative Auditory Research, Portland, OR, United States
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