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Capps B, Chadwick R, Lederman Z, Lysaght T, Mills C, Mulvihill JJ, Oetting WS, Winship I. The Human Genome Organisation (HUGO) and a vision for Ecogenomics: the Ecological Genome Project. Hum Genomics 2023; 17:115. [PMID: 38111041 PMCID: PMC10726505 DOI: 10.1186/s40246-023-00560-x] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND The following outlines ethical reasons for widening the Human Genome Organisation's (HUGO) mandate to include ecological genomics. MAIN: The environment influences an organism's genome through ambient factors in the biosphere (e.g. climate and UV radiation), as well as the agents it comes into contact with, i.e. the epigenetic and mutagenic effects of inanimate chemicals and pollution, and pathogenic organisms. Emerging scientific consensus is that social determinants of health, environmental conditions and genetic factors work together to influence the risk of many complex illnesses. That paradigm can also explain the environmental and ecological determinants of health as factors that underlie the (un)healthy ecosystems on which communities rely. We suggest that The Ecological Genome Project is an aspirational opportunity to explore connections between the human genome and nature. We propose consolidating a view of Ecogenomics to provide a blueprint to respond to the environmental challenges that societies face. This can only be achieved by interdisciplinary engagement between genomics and the broad field of ecology and related practice of conservation. In this respect, the One Health approach is a model for environmental orientated work. The idea of Ecogenomics-a term that has been used to relate to a scientific field of ecological genomics-becomes the conceptual study of genomes within the social and natural environment. CONCLUSION The HUGO Committee on Ethics, Law and Society (CELS) recommends that an interdisciplinary One Health approach should be adopted in genomic sciences to promote ethical environmentalism. This perspective has been reviewed and endorsed by the HUGO CELS and the HUGO Executive Board.
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Affiliation(s)
- Benjamin Capps
- Department of Bioethics, Dalhousie University, 5849 University Avenue, CRC Building, Room C-312, PO Box 15000, Halifax, NS, B3H 4R2, Canada.
| | | | | | - Tamra Lysaght
- National University of Singapore, Singapore, Singapore
| | | | - John J Mulvihill
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
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Cipri S, Abenavoli L, Boccuto L, Del Baldo G, Mastronuzzi A. How Genetics and Genomics Advances Are Rewriting Pediatric Cancer Research and Clinical Care. Medicina (B Aires) 2022; 58:1386. [PMID: 36295546 DOI: 10.3390/medicina58101386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
In the last two decades, thanks to the data that have been obtained from the Human Genome Project and the development of next-generation sequencing (NGS) technologies, research in oncology has produced extremely important results in understanding the genomic landscape of pediatric cancers, which are the main cause of death during childhood. NGS has provided significant advances in medicine by detecting germline and somatic driver variants that determine the development and progression of many types of cancers, allowing a distinction between hereditary and non-hereditary cancers, characterizing resistance mechanisms that are also related to alterations of the epigenetic apparatus, and quantifying the mutational burden of tumor cells. A combined approach of next-generation technologies allows us to investigate the numerous molecular features of the cancer cell and the effects of the environment on it, discovering and following the path of personalized therapy to defeat an "ancient" disease that has had victories and defeats. In this paper, we provide an overview of the results that have been obtained in the last decade from genomic studies that were carried out on pediatric cancer and their contribution to the more accurate and faster diagnosis in the stratification of patients and the development of new precision therapies.
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Hescheler DA, Hartmann MJM, Riemann B, Michel M, Bruns CJ, Alakus H, Chiapponi C. Targeted Therapy for Adrenocortical Carcinoma: A Genomic-Based Search for Available and Emerging Options. Cancers (Basel) 2022; 14:2721. [PMID: 35681700 DOI: 10.3390/cancers14112721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/22/2022] [Accepted: 05/27/2022] [Indexed: 12/07/2022] Open
Abstract
In rare diseases such as adrenocortical carcinoma (ACC), in silico analysis can help select promising therapy options. We screened all drugs approved by the FDA and those in current clinical studies to identify drugs that target genomic alterations, also known to be present in patients with ACC. We identified FDA-approved drugs in the My Cancer Genome and National Cancer Institute databases and identified genetic alterations that could predict drug response. In total, 155 FDA-approved drugs and 905 drugs in clinical trials were identified and linked to 375 genes of 89 TCGA patients. The most frequent potentially targetable genetic alterations included TP53 (20%), BRD9 (13%), TERT (13%), CTNNB1 (13%), CDK4 (7%), FLT4 (7%), and MDM2 (7%). We identified TP53-modulating drugs to be possibly effective in 20-26% of patients, followed by the Wnt signaling pathway inhibitors (15%), Telomelysin and INO5401 (13%), FHD-609 (13%), etc. According to our data, 67% of ACC patients exhibited genomic alterations that might be targeted by FDA-approved drugs or drugs being tested in current clinical trials. Although there are not many current therapy options directly targeting reported ACC alterations, this study identifies emerging options that could be tested in clinical trials.
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Masys DR, Benson DA. Don Lindberg and the Creation of the National Center for Biotechnology Information. Stud Health Technol Inform 2022; 288:113-121. [PMID: 35102833 DOI: 10.3233/shti210986] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The highest priority new initiative resulting from the 1985-86 National Library of Medicine Long Range Planning exercise initiated by NLM Director Dr. Donald A.B. Lindberg was the creation of new information resources and services related to molecular biology and genetics, termed "biotechnology information". Beginning with existing NLM resources and research projects associated with molecular data, and with Lindberg's enthusiastic support, the institution launched a Congressionally-mandated Center that has become an essential part of 21st century biomedical science.
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Abstract
The reference human genome sequence is inarguably the most important and widely used resource in the fields of human genetics and genomics. It has transformed the conduct of biomedical sciences and brought invaluable benefits to the understanding and improvement of human health. However, the commonly used reference sequence has profound limitations, because across much of its span, it represents the sequence of just one human haplotype. This single, monoploid reference structure presents a critical barrier to representing the broad genomic diversity in the human population. In this review, we discuss the modernization of the reference human genome sequence to a more complete reference of human genomic diversity, known as a human pangenome.
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Affiliation(s)
- Karen H Miga
- UC Santa Cruz Genomics Institute and Department of Biomedical Engineering, University of California, Santa Cruz, California 95064, USA;
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genome Sciences and Systems Biology, and McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
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Lindeboom RGH, Regev A, Teichmann SA. Towards a Human Cell Atlas: Taking Notes from the Past. Trends Genet 2021; 37:625-630. [PMID: 33879355 DOI: 10.1016/j.tig.2021.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/15/2021] [Accepted: 03/19/2021] [Indexed: 12/20/2022]
Abstract
Comprehensively characterizing the cellular composition and organization of tissues has been a long-term scientific challenge that has limited our ability to study fundamental and clinical aspects of human physiology. The Human Cell Atlas (HCA) is a global collaborative effort to create a reference map of all human cells as a basis for both understanding human health and diagnosing, monitoring, and treating disease. Many aspects of the HCA are analogous to the Human Genome Project (HGP), whose completion presents a major milestone in modern biology. To commemorate the HGP's 20-year anniversary of completion, we discuss the launch of the HCA in light of the HGP, and highlight recent progress by the HCA consortium.
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Affiliation(s)
- Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Current Address: Genentech, South San Francisco, CA, USA
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Cavendish Laboratory, JJ Thomson Avenue, University of Cambridge, Cambridge, UK
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McGonigle I, Schuster SC. Global science meets ethnic diversity: Ian McGonigle interviews GenomeAsia100K Scientific Chairman Stephan Schuster. Genet Res (Camb) 2019; 101:e5. [PMID: 30912487 DOI: 10.1017/S001667231800006X] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
GenomeAsia100K is a human genome project based at Nanyang Technological University in Singapore that aims to sequence one hundred thousand Asian genomes in an effort that addresses an ethnic bias towards Western populations in previous genomic research. GenomeAsia100K consists of a team of bioinformaticians, statisticians and population geneticists, and was initiated by the Nanyang Technological University in collaboration with industrial partners MedGenome (an Indian R&D company specializing in genomic data), the California Biotech company Genentech, and Macrogen, a genome sequencing company from Korea. The GenomeAsia100K project is amongst the most ambitious precision medicine projects to date but it is not clear how the project will challenge or reshape understandings of ethnic and racial differences in Asian populations. Ian McGonigle, a scientist and cultural anthropologist, sat down with geneticist Stephan C. Schuster, the scientific chairman of GenomeAsia100K, to discuss the project and the implications of genomics for social identity in the 21st century.
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SAKAKI Y. A Japanese history of the Human Genome Project. Proc Jpn Acad Ser B Phys Biol Sci 2019; 95:441-458. [PMID: 31611500 PMCID: PMC6819149 DOI: 10.2183/pjab.95.031] [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] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/04/2019] [Indexed: 06/10/2023]
Abstract
The Human Genome Project (HGP) is one of the most important international achievements in life sciences, to which Japanese scientists made remarkable contributions. In the early 1980s, Akiyoshi Wada pioneered the first project for the automation of DNA sequencing technology. Ken-ichi Matsubara exhibited exceptional leadership to launch the comprehensive human genome program in Japan. Hideki Kambara made a major contribution by developing a key device for high-speed DNA sequencers, which enabled scientists to construct human genome draft sequences. The RIKEN team led by Yoshiyuki Sakaki (the author) played remarkable roles in the draft sequencing and completion of chromosomes 21, 18, and 11. Additionally, the Keio University team led by Nobuyoshi Shimizu made noteworthy contributions to the completion of chromosomes 22, 21, and 8. In April 2003, the Japanese team joined the international consortium in declaring the completion of the human genome sequence. Consistent with the HGP mandate, Japan has successfully developed a wide range of ambitious genomic sciences.
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Affiliation(s)
- Yoshiyuki SAKAKI
- Emeritus Professor, The University of Tokyo, Tokyo, Japan
- Emeritus Professor, Kyushu University, Fukuoka, Japan
- Emeritus Researcher, RIKEN, Wako, Saitama, Japan
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Aworunse OS, Adeniji O, Oyesola OL, Isewon I, Oyelade J, Obembe OO. Genomic Interventions in Medicine. Bioinform Biol Insights 2018; 12:1177932218816100. [PMID: 30546257 PMCID: PMC6287307 DOI: 10.1177/1177932218816100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 12/31/2022] Open
Abstract
Lately, the term "genomics" has become ubiquitous in many scientific articles. It is a rapidly growing aspect of the biomedical sciences that studies the genome. The human genome contains a torrent of information that gives clues about human origin, evolution, biological function, and diseases. In a bid to demystify the workings of the genome, the Human Genome Project (HGP) was initiated in 1990, with the chief goal of sequencing the approximately 3 billion nucleotide base pairs of the human DNA. Since its completion in 2003, the HGP has opened new avenues for the application of genomics in clinical practice. This review attempts to overview some milestone discoveries that paved way for the initiation of the HGP, remarkable revelations from the HGP, and how genomics is influencing a paradigm shift in routine clinical practice. It further highlights the challenges facing the implementation of genomic medicine, particularly in Africa. Possible solutions are also discussed.
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Affiliation(s)
| | | | - Olusola L Oyesola
- Department of Biological Sciences, Covenant University, Ota, Nigeria
| | - Itunuoluwa Isewon
- Department of Computer & Information Sciences, Covenant University, Ota, Nigeria
| | - Jelili Oyelade
- Department of Computer & Information Sciences, Covenant University, Ota, Nigeria
| | - Olawole O Obembe
- Department of Biological Sciences, Covenant University, Ota, Nigeria
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Abstract
The genomics community has frequently compared advances in sequencing to advances in microelectronics. Lately there have been many claims, including by the National Human Genome Research Institute (NHGRI), that genomics is outpacing developments in computing as measured by Moore's law - the notion that computers double in processing capability per dollar spent every 18-24 months. Celebrations of the "$1000 genome" and other speed-related sequencing milestones might be dismissed as a distraction from genomics' slowness in delivering clinical breakthroughs, but the fact that such celebrations have been persistently encouraged by the NHGRI reveals a great deal about the priorities and expectations of the American general public, the intended audience of the genomics-computing comparison. By delving into the history of speculative thinking about sequencing and computing, this article demonstrates just how much more receptive to high-risk/high-payoff ventures the NIH and the general public have become. The article also provides access to some of the roots and consequences of the association of "innovation talk" with genomics, and the means to look past that association to the less glamorous (but arguably much more important) contributions of the NHGRI to building the field of genomics.
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Affiliation(s)
- Joseph November
- Department of History, University of South Carolina, Columbia, SC, USA.
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Abstract
This paper addresses the cultural impact of genomics and the Human Genome Project (HGP) on human self-understanding. Notably, it addresses the claim made by Francis Collins (director of the HGP) that the genome is the language of God and the claim made by Max Delbrück (founding father of molecular life sciences research) that Aristotle must be credited with having predicted DNA as the soul that organises bio-matter. From a continental philosophical perspective I will argue that human existence results from a dialectical interaction between two types of texts: the language of molecular biology and the language of civilisation; the language of the genome and the language of our socio-cultural, symbolic ambiance. Whereas the former ultimately builds on the alphabets of genes and nucleotides, the latter is informed by primordial texts such as the Bible and the Quran. In applied bioethics deliberations on genomics, science is easily framed as liberating and progressive, religious world-views as conservative and restrictive (Zwart 1993). This paper focusses on the broader cultural ambiance of the debate to discern how the bi-textuality of human existence is currently undergoing a transition, as not only the physiological, but also the normative dimension is being reframed in biomolecular and terabyte terms.
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Affiliation(s)
- H A E Hub Zwart
- a Department of Philosophy and Science Studies (Chair), Faculty of Science , Radboud University Nijmegen , Nijmegen , Netherlands.,b Institute for Science in Society (ISiS) (Director) , Nijmegen , Netherlands
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Abstract
Over its 30 or so years of existence, the genomic commons-the worldwide collection of publicly accessible repositories of human and nonhuman genomic data-has enjoyed remarkable, perhaps unprecedented, success. Thanks to the rapid public data release policies initiated by the Human Genome Project, free access to a vast array of scientific data is now the norm, not only in genomics, but in scientific disciplines of all descriptions. And far from being a monolithic creation of bureaucratic fiat, the genomic commons is an exemplar of polycentric, multistakeholder governance. But like all dynamic and rapidly evolving systems, the genomic commons is not without its challenges. Issues involving scientific priority, intellectual property, individual privacy, and informed consent, in an environment of data sets of exponentially expanding size and complexity, must be addressed in the near term. In this review, we describe the characteristics and unique history of the genomic commons, then address some of the trends, challenges, and opportunities that we envision for this valuable public resource in the years to come.
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Affiliation(s)
- Jorge L Contreras
- S.J. Quinney College of Law and School of Medicine, University of Utah, Salt Lake City, Utah 84112, USA;
| | - Bartha M Knoppers
- Centre of Genomics and Policy and Department of Medicine, McGill University, Montreal, Quebec H3A 0G1, Canada;
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Abstract
The Human Genome Project in 2003 has resulted in the complete sequence of ~99% of the human genome paving the road for the Human Proteome Project (HPP) assessing the full characterization of the translated protein map of the 20,300 protein-coding genes. Consequently, the emerging of the proteomics field has successfully been adopted as the method of choice for the proteome characterization. Proteomics is a term that is used to encompass multidisciplinary approaches combining different technologies that aim to study the entire spectrum of protein changes at a specific physiological condition. Proteomics research has shown excellent outcomes in different fields, among which is neuroscience; however, the complexity of the nervous systems necessitated the genesis of a new subdiscipline of proteomics termed as "neuroproteomics." Neuroproteomics studies involve assessing the quantitative and qualitative aspects of nervous system components encompassing global dynamic events underlying various brain-related disorders ranging from neuropsychiatric disorders, degenerative disorders, mental illness, and most importantly brain-specific neurotrauma-related injuries. In this introductory chapter, we will provide a brief historical perspective on the field of neuroproteomics. In doing so, we will highlight on the recent applications of neuroproteomics in the areas of neurotrauma, an area that has benefitted from neuroproteomics in terms of biomarker research, spatiotemporal injury mechanism, and its use to translate its findings from experimental settings to human translational applications. Importantly, this chapter will include some recommendation to the general studies in the area of neuroproteomics and the need to move from this field from being a descriptive, hypothesis-free approach to being an independent mature scientific discipline.
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Affiliation(s)
- Naify Ramadan
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hussein Ghazale
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Mohamad El-Haress
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
| | - Firas H Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
- Department of Psychiatry, Center for Neuroproteomics and Biomarkers Research, University of Florida, Gainesville, FL, USA.
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Park ST, Kim J. Trends in Next-Generation Sequencing and a New Era for Whole Genome Sequencing. Int Neurourol J 2016; 20:S76-83. [PMID: 27915479 DOI: 10.5213/inj.1632742.371] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 12/28/2022] Open
Abstract
This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields. De novo genome assembly and large scale DNA resequencing to understand genomic variations are popular genomic research tools for processing a tremendous amount of data at low cost. Studies on transcriptomes are now available, from previous-hybridization based microarray methods. Epigenetic studies are also available with NGS applications such as whole genome methylation sequencing and chromatin immunoprecipitation followed by sequencing. Human genetics has faced a new paradigm of research and medical genomics by sequencing technologies since the Human Genome Project. The trend of NGS technologies in human genomics has brought a new era of WGS by enabling the building of human genomes databases and providing appropriate human reference genomes, which is a necessary component of personalized medicine and precision medicine.
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Abstract
OBJECTIVES To examine the empirical literature related to the incorporation of genetic research and genetic competency needed by the nurse in practice. DESIGN Literature review. DATA SOURCES This article will explore published research within the past seven years of 2008-2015 that address the need for the increased incorporation of genetic content in nursing practice in addition to the need for the nurse to effectively screen the patient at risk of a genetic disorder. This literature review specifically focuses on the inadequacy of nurses in addressing genomic health compromise and serving as advocates for patients and families facing genetic disorders. METHODS A review of the literature published from 2008 to 2015 related to the incorporation of genetics in nursing practice and the role of the nurse as a patient advocate for families facing genetic disorders with resulting genomic health compromise. RESULTS The research exposes the lack of adequate preparation of nurses to incorporate and utilize the recent advances in genomic healthcare. Practicing nurses lack understating and skill in the application of genetics and genomic technologies to patient care. The nursing profession, including nursing academia, need to enhance the integration of genetic and genomic content into nursing curriculum and practice. CONCLUSION Practicing nurses are inadequately prepared to apply genetic advancements in screening at risk patients and addressing the needs of the patient or family facing a genomic health compromise.
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Affiliation(s)
- Deborah Jacks Camak
- Dishman Department of Nursing, Lamar University, 4400 MLK Blvd, P.O. Box 10009, Beaumont, TX 77710, United States.
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Shaw J. Documenting genomics: Applying archival theory to preserving the records of the Human Genome Project. Stud Hist Philos Biol Biomed Sci 2016; 55:61-9. [PMID: 26388555 PMCID: PMC4736235 DOI: 10.1016/j.shpsc.2015.08.005] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 05/11/2023]
Abstract
The Human Genome Archive Project (HGAP) aimed to preserve the documentary heritage of the UK's contribution to the Human Genome Project (HGP) by using archival theory to develop a suitable methodology for capturing the results of modern, collaborative science. After assessing past projects and different archival theories, the HGAP used an approach based on the theory of documentation strategy to try to capture the records of a scientific project that had an influence beyond the purely scientific sphere. The HGAP was an archival survey that ran for two years. It led to ninety scientists being contacted and has, so far, led to six collections being deposited in the Wellcome Library, with additional collections being deposited in other UK repositories. In applying documentation strategy the HGAP was attempting to move away from traditional archival approaches to science, which have generally focused on retired Nobel Prize winners. It has been partially successful in this aim, having managed to secure collections from people who are not 'big names', but who made an important contribution to the HGP. However, the attempt to redress the gender imbalance in scientific collections and to improve record-keeping in scientific organisations has continued to be difficult to achieve.
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Affiliation(s)
- Jennifer Shaw
- Wellcome Library, 215 Euston Road, London, NW1 2BE, UK.
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Mina T, Amini-Bavil-Olyaee S, Tacke F, Maes P, Van Ranst M, Pourkarim MR. Genomic Diversity of Hepatitis B Virus Infection Associated With Fulminant Hepatitis B Development. Hepat Mon 2015; 15:e29477. [PMID: 26288637 PMCID: PMC4533131 DOI: 10.5812/hepatmon.29477v2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/25/2015] [Indexed: 12/11/2022]
Abstract
CONTEXT After five decades of Hepatitis B Virus (HBV) vaccine discovery, HBV is still a major public health problem. Due to the high genetic diversity of HBV and selective pressure of the host immune system, intra-host evolution of this virus in different clinical manifestations is a hot topic of research. HBV infection causes a range of clinical manifestations from acute to chronic infection, cirrhosis and hepatocellular carcinoma. Among all forms of HBV infection manifestations, fulminant hepatitis B infection possesses the highest fatality rate. Almost 1% of the acutely infected patients develop fulminant hepatitis B, in which the mortality rate is around 70%. EVIDENCE ACQUISITION All published papers deposited in Genbank, on the topic of fulminant hepatitis were reviewed and their virological aspects were investigated. In this review, we highlight the genomic diversity of HBV reported from patients with fulminant HBV infection. RESULTS The most commonly detected diversities affect regulatory motifs of HBV in the core and S region, indicating that these alterations may convert the virus to an aggressive strain. Moreover, mutations at T-cell and B-cell epitopes located in pre-S1 and pre-S2 proteins may lead to an immune evasion of the virus, likely favoring a more severe clinical course of infection. Furthermore, point and frame shift mutations in the core region increase the viral replication of HBV and help virus to evade from immune system and guarantee its persistence. CONCLUSIONS Fulminant hepatitis B is associated with distinct mutational patterns of HBV, underlining that genomic diversity of the virus is an important factor determining its pathogenicity.
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Affiliation(s)
- Thomas Mina
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Samad Amini-Bavil-Olyaee
- Department of Molecular Microbiology and Immunology, Harlyne J. Norris Cancer Research Tower, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Frank Tacke
- Department of Medicine III, RWTH-University Hospital Aachen, Aachen, Germany
| | - Piet Maes
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran, IR Iran
- Corresponding Author: Mahmoud Reza Pourkarim, Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, P. O. Box: BE-3000, Leuven, Belgium. Tel: +32-16332145, Fax: +32-16332141, E-mail:
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Affiliation(s)
- N A Holtzman
- Department of Pediatrics, Johns Hopkins Medical Institutions, Baltimore, Md
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Fox CS, Hall JL, Arnett DK, Ashley EA, Delles C, Engler MB, Freeman MW, Johnson JA, Lanfear DE, Liggett SB, Lusis AJ, Loscalzo J, MacRae CA, Musunuru K, Newby LK, O'Donnell CJ, Rich SS, Terzic A. Future translational applications from the contemporary genomics era: a scientific statement from the American Heart Association. Circulation 2015; 131:1715-36. [PMID: 25882488 DOI: 10.1161/cir.0000000000000211] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardiovascular clinical care. In brief, this scientific statement assesses the current timeline for effective translation of basic discoveries to clinical advances, highlighting past successes. Current discoveries in the area of genetics and genomics are covered next, followed by future expectations, tools, and competencies for achieving the goal of improving clinical care.
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Hoyt R, Linnville S, Chung HM, Hutfless B, Rice C. Digital family histories for data mining. Perspect Health Inf Manag 2013; 10:1a. [PMID: 24159269 PMCID: PMC3797548] [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] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
As we move closer to ubiquitous electronic health records (EHRs), genetic, familial, and clinical information will need to be incorporated into EHRs as structured data that can be used for data mining and clinical decision support. While the Human Genome Project has produced new and exciting genomic data, the cost to sequence the human personal genome is high, and significant controversies regarding how to interpret genomic data exist. Many experts feel that the family history is a surrogate marker for genetic information and should be part of any paper-based or electronic health record. A digital family history is now part of the Meaningful Use Stage 2 menu objectives for EHR reimbursement, projected for 2014. In this study, a secure online family history questionnaire was designed to collect data on a unique cohort of Vietnam-era repatriated male veterans and a comparison group in order to compare participant and family disease rates on common medical disorders with a genetic component. This article describes our approach to create the digital questionnaire and the results of analyzing family history data on 319 male participants.
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Affiliation(s)
- Robert Hoyt
- Robert Hoyt, MD, FACP, is the Director of the Medical Informatics Program in the School of Allied Health and Life Sciences at the University of West Florida in Pensacola, FL. He is also a clinical researcher at the Robert E. Mitchell Center for Prisoner of War Studies in Pensacola, FL
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Bromberg Y. Building a genome analysis pipeline to predict disease risk and prevent disease. J Mol Biol 2013; 425:3993-4005. [PMID: 23928561 DOI: 10.1016/j.jmb.2013.07.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/26/2013] [Accepted: 07/28/2013] [Indexed: 12/24/2022]
Abstract
Reduced costs and increased speed and accuracy of sequencing can bring the genome-based evaluation of individual disease risk to the bedside. While past efforts have identified a number of actionable mutations, the bulk of genetic risk remains hidden in sequence data. The biggest challenge facing genomic medicine today is the development of new techniques to predict the specifics of a given human phenome (set of all expressed phenotypes) encoded by each individual variome (full set of genome variants) in the context of the given environment. Numerous tools exist for the computational identification of the functional effects of a single variant. However, the pipelines taking advantage of full genomic, exomic, transcriptomic (and other) sequences have only recently become a reality. This review looks at the building of methodologies for predicting "variome"-defined disease risk. It also discusses some of the challenges for incorporating such a pipeline into everyday medical practice.
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Affiliation(s)
- Y Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08873, USA.
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Ikegawa S. A short history of the genome-wide association study: where we were and where we are going. Genomics Inform 2012; 10:220-5. [PMID: 23346033 PMCID: PMC3543921 DOI: 10.5808/gi.2012.10.4.220] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 10/31/2012] [Accepted: 11/01/2012] [Indexed: 01/03/2023] Open
Abstract
Recent rapid advances in genetic research are ushering us into the genome sequence era, where an individual's genome information is utilized for clinical practice. The most spectacular results of the human genome study have been provided by genome-wide association studies (GWASs). This is a review of the history of GWASs as related to my work. Further efforts are necessary to make full use of its potential power to medicine.
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Affiliation(s)
- Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Genomic Medicine, RIKEN, Tokyo 108-8639, Japan
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Abstract
Are new concepts in biomedical ethics required to keep pace with the developments in post-Human Genome Project (HGP) genomics? This paper traces the place of ethics in the post-HGP landscape. The need for a revision of the approach taken by biomedical ethics toward questions in genomics has been appreciated for years. Traditional biomedical ethics, led by the protection paradigm, was devised to serve a very different context. Today, compelling ethical questions arise from the tension between individual and collective interests in the context of population-based data collection and research. The collection of phenotype data, and the development of new sequencing technologies, raises burning questions that call for innovative tools and models in ethics. Future developments that will likely include the routine availability of personal genome information, and the advent of systems biology as a framework for interpretation, will require ongoing flexibility and a creative approach.
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Affiliation(s)
- Jeantine E Lunshof
- VU university medical center, Department of Clinical Genetics & Human Genetics, Section Community Genetics, EMGO Institute, Van der Boechorststraat 7, PO Box 7057, 1007 MB Amsterdam, The Netherlands.
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26
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Looney B. Should genes be patented? The gene patenting controversy: legal, ethical, and policy foundations of an international agreement. Law Policy Int Bus 2002; 26:231-72. [PMID: 11979605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Abstract
This article seeks to highlight some of the more important ethical and legal issues raised by the Human Genome Project. It is recognized that hithertofore ethical control over the pace and scope of scientific progress has been only partly successful, due largely to the resistance of the professionals involved to outside interference and to the ineffectiveness of self-monitoring. The Human Genome Project has the potential to alter the lives of individuals and the structure of human society as a whole. It is essential therefore that individuals be empowered through the application and development of existing heads of liability in constitutional and private law to effect at least some of the necessary control. The transnational aspects of the project and the ethical and legal issues which it raises are also stressed.
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Sprunger SA, Julian-Arnold G. Promoting and managing genome innovation. Risk 2001; 7:197-200. [PMID: 11655074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Davis DS. Legal trends in bioethics. J Clin Ethics 2001; 11:94-5. [PMID: 11645768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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31
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Annas GJ. Mapping the human genome and the meaning of monster mythology. Emory Law J 2001; 39:629-64. [PMID: 11653904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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32
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Lockwood B. Genetics and the law: bibliography. Emory Law J 2001; 39:875-936. [PMID: 11653911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Deftos LJ. Genomic torts: the law of the future -- the duty of physicians to disclose the presence of a genetic disease to the relatives of their patients with the disease. Univ San Francisco Law Rev 2001; 32:105-37. [PMID: 11660530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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34
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Friedland SI. The criminal law implications of the Human Genome Project: reimagining a genetically oriented criminal justice system. KY Law J 2001; 86:303-66. [PMID: 11660630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Greene VW. Fourth International Congress of Ethics in Medicine (Jerusalem, 13-18 October 1991). Int Dig Health Legis 2001; 43:860-5. [PMID: 11659639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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36
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Arizona State University Center for the Study of Law, Science and Technology. The Human Genome Project: bibliography of ethical, social, legal, and scientific aspects. Jurimetrics 1992; 32:223-311. [PMID: 11659418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Abstract
The Human Genome Project has raised many issues regarding the contributions of genetics to a variety of diseases and societal conditions. With genetic testing now easily conducted with lowered costs in nonmedical domains, a variety of privacy issues must be considered. Such testing will result in the loss of significant privacy rights for the individual. Society must now consider such issues as the ownership of genetic data, confidentiality rights to such information, limits placed on genetic screening, and legislation to control genetic testing and its applications. There is often a conflict between individual rights to privacy and the need for societal protection.
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International Workshop on Legal Aspects of the Human Genome Project (Bilbao, 24-26 May 1993) adopts Bilbao Declaration. Int Dig Health Legis 1994; 45:234-7. [PMID: 11659960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Elsas LJ. A clinical approach to legal and ethical problems in human genetics. Emory Law J 2001; 39:811-53. [PMID: 11653909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Karjala DS. A legal research agenda for the Human Genome Initiative. Jurimetrics 2001; 32:121-222. [PMID: 11659417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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O'Hara S. The use of genetic testing in the health insurance industry: the creation of a "biologic underclass". Southwest Univ Law Rev 2001; 22:1211-28. [PMID: 11659756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Goerlich A, Krannich M. The gene politics of the European Community. Reprod Genet Eng 2001; 2:201-18. [PMID: 11652004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Withers WW, Kenworthy PG. Biotechnology: can a new technology survive? St Louis Univ Law J 2001; 31:673-97. [PMID: 11650845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Draper E. Privacy rights, stigma, and genetic screening. Forum Appl Res Public Policy 2001; 8:19-22. [PMID: 11652660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Iles AT. The Human Genome Project: a challenge to the human rights framework. Harv Hum Rights J 2001; 9:27-60. [PMID: 11660498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Berry RM. The Human Genome Project and the end of insurance. Univ Fla J Law Public Policy 2001; 7:205-56. [PMID: 11660500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Grisolía S. Ethical and social aspects of the Human Genome Project. Impact Sci Soc 2001; 41[1:37-43. [PMID: 11660526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Malpede K. Notes on the writing and reception of the stage play Better People. Issues Reprod Genet Eng 2001; 4:155-69. [PMID: 11651374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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