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Gill EE, Jia B, Murall CL, Poujol R, Anwar MZ, John NS, Richardsson J, Hobb A, Olabode AS, Lepsa A, Duggan AT, Tyler AD, N'Guessan A, Kachru A, Chan B, Yoshida C, Yung CK, Bujold D, Andric D, Su E, Griffiths EJ, Domselaar GV, Jolly GW, Ward HKE, Feher H, Baker J, Simpson JT, Uddin J, Ragoussis J, Eubank J, Fritz JH, Gálvez JH, Fang K, Cullion K, Rivera L, Xiang L, Croxen MA, Shiell M, Prystajecky N, Quirion PO, Bajari R, Rich S, Mubareka S, Moreira S, Cain S, Sutcliffe SG, Kraemer SA, Joly Y, Alturmessov Y, Consortium C, Consortium C, Academic VDP, Network H, Fiume M, Snutch TP, Bell C, Lopez-Correa C, Hussin JG, Joy JB, Colijn C, Gordon PMK, Hsiao WWL, Poon AFY, Knox NC, Courtot M, Stein L, Otto SP, Bourque G, Shapiro BJ, Brinkman FSL. The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. ArXiv 2024:arXiv:2405.04734v1. [PMID: 38764594 PMCID: PMC11100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). The Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. Here we also highlight Duotang, a web platform that presents genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.
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Skantharajah N, Baichoo S, Boughtwood TF, Casas-Silva E, Chandrasekharan S, Dave SM, Fakhro KA, Falcon de Vargas AB, Gayle SS, Gupta VK, Hendricks-Sturrup R, Hobb AE, Li S, Llamas B, Lopez-Correa C, Machirori M, Melendez-Zajgla J, Millner MA, Page AJ, Paglione LD, Raven-Adams MC, Smith L, Thomas EM, Kumuthini J, Corpas M. Equity, diversity, and inclusion at the Global Alliance for Genomics and Health. Cell Genom 2023; 3:100386. [PMID: 37868041 PMCID: PMC10589617 DOI: 10.1016/j.xgen.2023.100386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
A lack of diversity in genomics for health continues to hinder equitable leadership and access to precision medicine approaches for underrepresented populations. To avoid perpetuating biases within the genomics workforce and genomic data collection practices, equity, diversity, and inclusion (EDI) must be addressed. This paper documents the journey taken by the Global Alliance for Genomics and Health (a genomics-based standard-setting and policy-framing organization) to create a more equitable, diverse, and inclusive environment for its standards and members. Initial steps include the creation of two groups: the Equity, Diversity, and Inclusion Advisory Group and the Regulatory and Ethics Diversity Group. Following a framework that we call "Reflected in our Teams, Reflected in our Standards," both groups address EDI at different stages in their policy development process.
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Affiliation(s)
- Neerjah Skantharajah
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | | | | | - Sanjay M. Dave
- Department of Biotechnology, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Khalid A. Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha, Qatar
| | - Aida B. Falcon de Vargas
- Hospital Vargas de Caracas, Vargas Medical School, Universidad Central de Venezuela, Caracas, Venezuela
- Hospital de Clínicas Caracas, Caracas, Venezuela
| | | | - Vivek K. Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | | | | | - Stephanie Li
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Broad Institute, Cambridge, MA, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
| | | | - Mavis Machirori
- Ada Lovelace Institute, London, UK
- PEALS, Newcastle University, Newcastle Upon Tyne, UK
| | | | - Mareike A. Millner
- Maastricht University, Health Law and Governance Group, Maastricht, the Netherlands
| | - Angela J.H. Page
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Broad Institute, Cambridge, MA, USA
| | - Laura D. Paglione
- Spherical Cow Group, New York, NY, USA
- Laura Paglione LLC, New York, NY, USA
| | - Maili C. Raven-Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | - Lindsay Smith
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Ericka M. Thomas
- The All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Judit Kumuthini
- South African National Bioinformatics Institute, University of Western Cape, Cape Town, South Africa
| | - Manuel Corpas
- School of Life Sciences, University of Westminster, London, UK
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Mitropoulos K, Cooper DN, Mitropoulou C, Agathos S, Reichardt JKV, Al-Maskari F, Chantratita W, Wonkam A, Dandara C, Katsila T, Lopez-Correa C, Ali BR, Patrinos GP. Genomic Medicine Without Borders: Which Strategies Should Developing Countries Employ to Invest in Precision Medicine? A New "Fast-Second Winner" Strategy. OMICS 2018; 21:647-657. [PMID: 29140767 DOI: 10.1089/omi.2017.0141] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Genomic medicine has greatly matured in terms of its technical capabilities, but the diffusion of genomic innovations worldwide faces significant barriers beyond mere access to technology. New global development strategies are sorely needed for biotechnologies such as genomics and their applications toward precision medicine without borders. Moreover, diffusion of genomic medicine globally cannot adhere to a "one-size-fits-all-countries" development strategy, in the same way that drug treatments should be customized. This begs a timely, difficult but crucial question: How should developing countries, and the resource-limited regions of developed countries, invest in genomic medicine? Although a full-scale investment in infrastructure from discovery to the translational implementation of genomic science is ideal, this may not always be feasible in all countries at all times. A simple "transplantation of genomics" from developed to developing countries is unlikely to be feasible. Nor should developing countries be seen as simple recipients and beneficiaries of genomic medicine developed elsewhere because important advances in genomic medicine have materialized in developing countries as well. There are several noteworthy examples of genomic medicine success stories involving resource-limited settings that are contextualized and described in this global genomic medicine innovation analysis. In addition, we outline here a new long-term development strategy for global genomic medicine in a way that recognizes the individual country's pressing public health priorities and disease burdens. We term this approach the "Fast-Second Winner" model of innovation that supports innovation commencing not only "upstream" of discovery science but also "mid-stream," building on emerging highly promising biomarker and diagnostic candidates from the global science discovery pipeline, based on the unique needs of each country. A mid-stream entry into innovation can enhance collective learning from other innovators' mistakes upstream in discovery science and boost the probability of success for translation and implementation when resources are limited. This à la carte model of global innovation and development strategy offers multiple entry points into the global genomics innovation ecosystem for developing countries, whether or not extensive and expensive discovery infrastructures are already in place. Ultimately, broadening our thinking beyond the linear model of innovation will help us to enable the vision and practice of genomics without borders in both developed and resource-limited settings.
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Affiliation(s)
| | - David N Cooper
- 2 Institute of Medical Genetics, School of Medicine, Cardiff University , Cardiff, United Kingdom
| | | | - Spiros Agathos
- 4 Yachay Tech University , San Miguel de Urcuquí, Ecuador
| | | | - Fatima Al-Maskari
- 5 Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates .,6 Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates
| | - Wasun Chantratita
- 7 Department of Pathology, Medical Genomic Center, Ramathibodi Hospital, Faculty of Medicine, Mahidol University , Bangkok, Thailand
| | - Ambroise Wonkam
- 8 Division of Human Genetics, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Collet Dandara
- 8 Division of Human Genetics, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Theodora Katsila
- 9 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
| | | | - Bassam R Ali
- 5 Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates .,6 Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates
| | - George P Patrinos
- 5 Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates .,6 Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates .,9 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
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Mitropoulos K, Al Jaibeji H, Forero DA, Laissue P, Wonkam A, Lopez-Correa C, Mohamed Z, Chantratita W, Lee MTM, Llerena A, Brand A, Ali BR, Patrinos GP. Success stories in genomic medicine from resource-limited countries. Hum Genomics 2015; 9:11. [PMID: 26081768 PMCID: PMC4485996 DOI: 10.1186/s40246-015-0033-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/09/2015] [Indexed: 02/08/2023] Open
Abstract
In recent years, the translation of genomic discoveries into mainstream medical practice and public health has gained momentum, facilitated by the advent of new technologies. However, there are often major discrepancies in the pace of implementation of genomic medicine between developed and developing/resource-limited countries. The main reason does not only lie in the limitation of resources but also in the slow pace of adoption of the new findings and the poor understanding of the potential that this new discipline offers to rationalize medical diagnosis and treatment. Here, we present and critically discuss examples from the successful implementation of genomic medicine in resource-limited countries, focusing on pharmacogenomics, genome informatics, and public health genomics, emphasizing in the latter case genomic education, stakeholder analysis, and economics in pharmacogenomics. These examples can be considered as model cases and be readily replicated for the wide implementation of pharmacogenomics and genomic medicine in other resource-limited environments.
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Affiliation(s)
| | - Hayat Al Jaibeji
- University of Maastricht, Maastricht, The Netherlands. .,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
| | - Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.
| | - Paul Laissue
- Unidad de Genética, Grupo GENIUROS, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia.
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | | | - Zahurin Mohamed
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Wasun Chantratita
- Department of Pathology, Medical Genomic Center, Ramathibodi Hospital, Faculty of Medicine, Mahidol University, Bangkok, Thailand.
| | - Ming Ta Michael Lee
- Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. .,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Adrian Llerena
- CICAB Clinical Research Center, Extremadura University Hospital and Medical School, Badajoz, Spain.
| | - Angela Brand
- University of Maastricht, Maastricht, The Netherlands.
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
| | - George P Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece.
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Bromley CM, Close S, Cohen N, Favis R, Fijal B, Gheyas F, Liu W, Lopez-Correa C, Prokop A, Singer JB, Snapir A, Tchelet A, Wang D, Goldstaub D. Designing pharmacogenetic projects in industry: practical design perspectives from the Industry Pharmacogenomics Working Group. Pharmacogenomics J 2008; 9:14-22. [PMID: 18794908 DOI: 10.1038/tpj.2008.11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pharmacogenetic association studies have the potential to identify variations in DNA sequence which impact drug response. Identifying these DNA variants can help to explain interindividual variability in drug response; this is the first step in personalizing dosing and treatment regimes to a patient's needs. There are many intricacies in the design and analysis of pharmacogenetic association studies, including having adequate power, selecting proper endpoints, detecting and correcting the effects of population stratification, modeling genetic and nongenetic covariates accurately, and validating the results. At this point there are no formal guidelines on the design and analysis of pharmacogenetic studies. The Industry Pharmacogenomics Working Group has initiated discussions regarding potential guidelines for pharmacogenetic study design and analyses (http://i-pwg.org) and the results from these discussions are presented in this paper.
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Affiliation(s)
- C M Bromley
- BioStat Solutions Inc., Mount Airy, MD 21771, USA.
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De Raedt T, Brems H, Lopez-Correa C, Vermeesch JR, Marynen P, Legius E. Genomic organization and evolution of the NF1 microdeletion region☆. Genomics 2004; 84:346-60. [PMID: 15233998 DOI: 10.1016/j.ygeno.2004.03.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Revised: 03/02/2004] [Accepted: 03/26/2004] [Indexed: 11/22/2022]
Abstract
Five to 10% of neurofibromatosis type 1 (NF1) individuals have a microdeletion (1.5 Mb) encompassing the entire NF1 region and neighboring genes. Microdeletion patients have a distinct phenotype with a more severe tumor burden. Most of the microdeletion breakpoints cluster in flanking paralogous regions (NF1REPs). We describe the complete genomic region covering the NF1 microdeletion and an extensive analysis of the genomic and transcriptional organization of the NF1REPs. The flanking NF1REPs have a total length of about 75 kb and are composed of several fragments. One of these fragments originated from chromosome 19 and contains a hot spot for microdeletion breakpoints. The analysis of the genomic organization of the NF1 microdeletion region and of the NF1REPs in particular is important for understanding the mechanism by which NF1 microdeletions are formed. This analysis will also help to identify loci potentially involved in the pathogenesis of the increased tumor load and malignancy risk observed in NF1 microdeletion patients.
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Affiliation(s)
- Thomas De Raedt
- Center of Human Genetics, KULeuven, Herestraat 49, 3000 Louvain, Belgium
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