scholarly journals Rethinking the ethical principles of genomic medicine services

2019 ◽  
Vol 28 (2) ◽  
pp. 147-154 ◽  
Author(s):  
Stephanie B. Johnson ◽  
Ingrid Slade ◽  
Alberto Giubilini ◽  
Mackenzie Graham
Keyword(s):  
Large Scale ◽  
Genomic Medicine ◽  
Medical Knowledge ◽  
Genomic Data ◽  
Ethical Principles ◽  
Clinical Services ◽  
Genomic Dataset ◽  
Regulatory Processes ◽  
Societal Benefits ◽  
Explicit Consent

Abstract Clinical genome and exome sequencing is currently used in only a small fraction of patients, yet large scale genomic initiatives are becoming more embedded in clinical services. This paper examines the ethical principles that should guide regulatory processes regarding consent and data sharing in this context. We argue that a genomic dataset administered by the health system carries substantial societal benefits, and that the collective nature of this initiative means that at least those patients who benefit from genome sequencing have an ethical obligation to share their health information. This obligation is grounded in considerations of fairness. Furthermore, we argue that the use of genomic data for the advancement of medical knowledge should be permitted without explicit consent and that international and other bodies should be granted access to these data, provided certain conditions are satisfied.

scholarly journals Findings from the Section on Bioinformatics and Translational Informatics

2016 ◽  
Vol 25 (01) ◽  
pp. 207-210
Author(s):  
T. Lecroq ◽  
H. Dauchel ◽  
Keyword(s):  
Large Scale ◽  
Clinical Care ◽  
Genomic Medicine ◽  
Genomic Data ◽  
Evaluation Process ◽  
The Cancer Genome Atlas ◽  
Sub Saharan Africa ◽  
Health Domain ◽  
Research Activities ◽  
Translational Informatics

Summary Objectives : To summarize excellent current research and propose a selection of best papers published in 2015 in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. Method : We provide a synopsis of the articles selected for the IMIA Yearbook 2016, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,566 articles and the evaluation results were merged for retaining 14 articles for peer-review. Results : The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles focusing this year on data management of large-scale datasets and genomic medicine that are mainly new method-based papers. Three articles explore the high potential of the re-analysis of previously collected data, here from The Cancer Genome Atlas project (TCGA) and one article presents an original analysis of genomic data from sub-Saharan Africa populations. Conclusions : The current research activities in Bioinformatics and Translational Informatics with application in the health domain continues to explore new algorithms and statistical models to manage and interpret large-scale genomic datasets. From population wide genome sequencing for cataloging genomic variants to the comprehension of functional impact on pathways and molecular interactions regarding a given pathology, making sense of large genomic data requires a necessary effort to address the issue of clinical translation for precise diagnostic and personalized medicine.

scholarly journals Psychiatric disorders in China: strengths and challenges of contemporary research and clinical services

2021 ◽  
pp. 1-14
Author(s):  
Xiao Chang ◽  
Qiyong Gong ◽  
Chunbo Li ◽  
Weihua Yue ◽  
Xin Yu ◽  
...  
Keyword(s):  
Psychiatric Disorders ◽  
Disease Burden ◽  
Large Scale ◽  
Well Being ◽  
Research Quality ◽  
Psychiatric Research ◽  
Clinical Services ◽  
Contributing Factors ◽  
Brain Functions ◽  
Neuroscience Research

Abstract China accounts for 17% of the global disease burden attributable to mental, neurological and substance use disorders. As a country undergoing profound societal change, China faces growing challenges to reduce the disease burden caused by psychiatric disorders. In this review, we aim to present an overview of progress in neuroscience research and clinical services for psychiatric disorders in China during the past three decades, analysing contributing factors and potential challenges to the field development. We first review studies in the epidemiological, genetic and neuroimaging fields as examples to illustrate a growing contribution of studies from China to the neuroscience research. Next, we introduce large-scale, open-access imaging genetic cohorts and recently initiated brain banks in China as platforms to study healthy brain functions and brain disorders. Then, we show progress in clinical services, including an integration of hospital and community-based healthcare systems and early intervention schemes. We finally discuss opportunities and existing challenges: achievements in research and clinical services are indispensable to the growing funding investment and continued engagement in international collaborations. The unique aspect of traditional Chinese medicine may provide insights to develop a novel treatment for psychiatric disorders. Yet obstacles still remain to promote research quality and to provide ubiquitous clinical services to vulnerable populations. Taken together, we expect to see a sustained advancement in psychiatric research and healthcare system in China. These achievements will contribute to the global efforts to realize good physical, mental and social well-being for all individuals.

scholarly journals ‘CTRL’: an online, Dynamic Consent and participant engagement platform working towards solving the complexities of consent in genomic research

2021 ◽  
Author(s):  
Matilda A. Haas ◽  
Harriet Teare ◽  
Megan Prictor ◽  
Gabi Ceregra ◽  
Miranda E. Vidgen ◽  
...  
Keyword(s):  
Large Scale ◽  
Genomic Medicine ◽  
International Standards ◽  
Security And Privacy ◽  
Genomic Research ◽  
Return Of Results ◽  
Future Research ◽  
Design And Development ◽  
Participant Engagement ◽  
Dynamic Consent

AbstractThe complexities of the informed consent process for participating in research in genomic medicine are well-documented. Inspired by the potential for Dynamic Consent to increase participant choice and autonomy in decision-making, as well as the opportunities for ongoing participant engagement it affords, we wanted to trial Dynamic Consent and to do so developed our own web-based application (web app) called CTRL (control). This paper documents the design and development of CTRL, for use in the Australian Genomics study: a health services research project building evidence to inform the integration of genomic medicine into mainstream healthcare. Australian Genomics brought together a multi-disciplinary team to develop CTRL. The design and development process considered user experience; security and privacy; the application of international standards in data sharing; IT, operational and ethical issues. The CTRL tool is now being offered to participants in the study, who can use CTRL to keep personal and contact details up to date; make consent choices (including indicate preferences for return of results and future research use of biological samples, genomic and health data); follow their progress through the study; complete surveys, contact the researchers and access study news and information. While there are remaining challenges to implementing Dynamic Consent in genomic research, this study demonstrates the feasibility of building such a tool, and its ongoing use will provide evidence about the value of Dynamic Consent in large-scale genomic research programs.

scholarly journals Cloud-based intelligent self-diagnosis and department recommendation service using Chinese medical BERT

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Junshu Wang ◽  
Guoming Zhang ◽  
Wei Wang ◽  
Ka Zhang ◽  
Yehua Sheng
Keyword(s):  
Cloud Computing ◽  
Large Scale ◽  
Medical Service ◽  
Rapid Development ◽  
Medical Knowledge ◽  
Language Models ◽  
Computing Environment ◽  
Computing Power ◽  
Cloud Computing Environment ◽  
Proposed Model

AbstractWith the rapid development of hospital informatization and Internet medical service in recent years, most hospitals have launched online hospital appointment registration systems to remove patient queues and improve the efficiency of medical services. However, most of the patients lack professional medical knowledge and have no idea of how to choose department when registering. To instruct the patients to seek medical care and register effectively, we proposed CIDRS, an intelligent self-diagnosis and department recommendation framework based on Chinese medical Bidirectional Encoder Representations from Transformers (BERT) in the cloud computing environment. We also established a Chinese BERT model (CHMBERT) trained on a large-scale Chinese medical text corpus. This model was used to optimize self-diagnosis and department recommendation tasks. To solve the limited computing power of terminals, we deployed the proposed framework in a cloud computing environment based on container and micro-service technologies. Real-world medical datasets from hospitals were used in the experiments, and results showed that the proposed model was superior to the traditional deep learning models and other pre-trained language models in terms of performance.

scholarly journals Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

2008 ◽  
Vol 40 (7) ◽  
pp. 854-861 ◽  
Author(s):  
Jun Zhu ◽  
Bin Zhang ◽  
Erin N Smith ◽  
Becky Drees ◽  
Rachel B Brem ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Large Scale ◽  
Genomic Data ◽  
Functional Genomic ◽  
Functional Genomic Data

scholarly journals Identifying Aspects of Public Attitudes Toward Whole Genome Sequencing to Inform the Integration of Genomics into Care

2021 ◽  
pp. 1-12
Author(s):  
Holly Etchegary ◽  
Daryl Pullman ◽  
Charlene Simmonds ◽  
Zoha Rabie ◽  
Proton Rahman
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Online Survey ◽  
Public Attitudes ◽  
Genetic Counselor ◽  
Genomic Medicine ◽  
Genomic Data ◽  
Whole Genome ◽  
The Public ◽  
Genomic Test

<b><i>Introduction:</i></b> The growth of global sequencing initiatives and commercial genomic test offerings suggests the public will increasingly be confronted with decisions about sequencing. Understanding public attitudes can assist efforts to integrate sequencing into care and inform the development of public education and outreach strategies. <b><i>Methods:</i></b> A 48-item online survey was advertised on Facebook in Eastern Canada and hosted on SurveyMonkey in late 2018. The survey measured public interest in whole genome sequencing and attitudes toward various aspects of sequencing using vignettes, scaled, and open-ended items. <b><i>Results:</i></b> While interest in sequencing was high, critical attitudes were observed. In particular, items measuring features of patient control and choice regarding genomic data were strongly endorsed by respondents. Majority wanted to specify upfront how their data could be used, retain the ability to withdraw their sample at a later date, sign a written consent form, and speak to a genetic counselor prior to sequencing. Concerns about privacy and unauthorized access to data were frequently observed. Education level was the sociodemographic variable most often related to attitude statements such that those with higher levels of education generally displayed more critical attitudes. <b><i>Conclusions:</i></b> Attitudes identified here could be used to inform the development of implementation strategies for genomic medicine. Findings suggest health systems must address patient concerns about privacy, consent practices, and the strong desire to control what happens to their genomic data through public outreach and education. Specific oversight procedures and policies that are clearly communicated to the public will be required.

Genomic Medicine Frontier in Human Solid Tumors: Prospects and Challenges

2013 ◽  
Vol 31 (15) ◽  
pp. 1874-1884 ◽  
Author(s):  
Rodrigo Dienstmann ◽  
Jordi Rodon ◽  
Jordi Barretina ◽  
Josep Tabernero
Keyword(s):  
Solid Tumors ◽  
Cancer Progression ◽  
Cancer Genomics ◽  
Genomic Medicine ◽  
Genomic Data ◽  
Cost Effective ◽  
Assessment Model ◽  
Historical View ◽  
Systemic Treatments ◽  
Human Solid Tumors

Recent discoveries of genomic alterations that underlie and promote the malignant phenotype, together with an expanded repertoire of targeted agents, have provided many opportunities to conduct hypothesis-driven clinical trials. The ability to profile each unique cancer for actionable aberrations by using high-throughput technologies in a cost-effective way provides unprecedented opportunities for using matched therapies in a selected patient population. The major challenges are to integrate and make biologic sense of the substantial genomic data derived from multiple platforms. We define two different approaches for the analysis, interpretation, and clinical applicability of genomic data: (1) the genomically stratified model originates from the “one test-one drug” paradigm and is currently being expanded with an upfront multicategorical approach following recent advances in multiplexed genotyping platforms; and (2) the comprehensive assessment model is based on whole-genome, -exome, and -transcriptome data and allows identification of novel drivers and subsequent therapies in the experimental setting. Tumor heterogeneity and evolution of the diverse populations of cancer cells during cancer progression, influenced by the effects of systemic treatments, will need to be addressed in the new scenario of early drug development. Logistical issues related to prescreening strategies and trial allocation, in addition to concerns in the economic and ethical domains, must be taken into consideration. Here we present a historical view of how increased understanding of cancer genomics has been translated to the clinic and discuss the prospects and challenges for further implementation of a personalized treatment strategy for human solid tumors.

scholarly journals The theory on and software simulating large-scale genomic data for genotype-by-environment interactions

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiujin Li ◽  
Hailiang Song ◽  
Zhe Zhang ◽  
Yunmao Huang ◽  
Qin Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Simulated Data ◽  
Genomic Data ◽  
Efficient Tool ◽  
Phenotypic Data ◽  
Genotype By Environment Interactions ◽  
Genotype By Environment ◽  
Threshold Trait ◽  
Genome Wide ◽  
Increasing Demand

Abstract Background With the emphasis on analysing genotype-by-environment interactions within the framework of genomic selection and genome-wide association analysis, there is an increasing demand for reliable tools that can be used to simulate large-scale genomic data in order to assess related approaches. Results We proposed a theory to simulate large-scale genomic data on genotype-by-environment interactions and added this new function to our developed tool GPOPSIM. Additionally, a simulated threshold trait with large-scale genomic data was also added. The validation of the simulated data indicated that GPOSPIM2.0 is an efficient tool for mimicking the phenotypic data of quantitative traits, threshold traits, and genetically correlated traits with large-scale genomic data while taking genotype-by-environment interactions into account. Conclusions This tool is useful for assessing genotype-by-environment interactions and threshold traits methods.

scholarly journals Leveraging Implementation Science to Address Health Disparities in Genomic Medicine: Examples from the Field

2019 ◽  
Vol 29 (Suppl 1) ◽  
pp. 187-192
Author(s):  
Megan C. Roberts ◽  
George A. Mensah ◽  
Muin J. Khoury
Keyword(s):  
Public Health ◽  
Implementation Science ◽  
Population Health ◽  
Public Health Practice ◽  
Genomic Medicine ◽  
Genomic Data ◽  
Health Impact ◽  
Cancer Syndrome ◽  
Public Health Agencies ◽  
Multi Stakeholder

The integration of genomic data into screen­ing, prevention, diagnosis, and treatment for clinical and public health practices has been slow and challenging. Implementa­tion science can be applied in tackling the barriers and challenges as well as exploring opportunities and best practices for integrat­ing genomic data into routine clinical and public health practice. In this article, we de­fine the state of disparities in genomic medi­cine and focus predominantly on late-stage research findings. We use case studies from genetic testing for cardiovascular diseases (familial hypercholesterolemia) and cancer (Lynch syndrome and hereditary breast and ovarian cancer syndrome) in high-risk populations to consider current disparities and related barriers in turning genomic advances into population health impact to advance health equity. Finally, we address how implementation science can address these translational barriers and we discuss the strategic importance of collaborative multi-stakeholder approaches that engage public health agencies, professional societ­ies, academic health and research centers, community clinics, and patients and their families to work collectively to improve population health and reduce or eliminate health inequities.Ethn Dis. 2019;29(Suppl 1):187-192; doi:10.18865/ed.29.S1.187.

scholarly journals Frequent birth-and-death events throughout perforin-1 evolution

2020 ◽  
Author(s):  
Miguel Araujo-Voces ◽  
Victor Quesada
Keyword(s):  
Preliminary Analysis ◽  
Large Scale ◽  
Mammalian Species ◽  
Genomic Data ◽  
Start Codon ◽  
High Similarity ◽  
Gene Encoding ◽  
Coding Sequences ◽  
Copy Numbers ◽  
Multiple Species

Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

Sign in / Sign up

Export Citation Format

Share Document