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 Findings from the Section on Bioinformatics and Translational Informatics

2017 ◽  
Vol 26 (01) ◽  
pp. 188-192 ◽  
Author(s):  
H. Dauchel ◽  
T. Lecroq
Keyword(s):  
Intelligent Systems ◽  
Large Scale ◽  
Cancer Genomics ◽  
Clinical Care ◽  
Evaluation Process ◽  
Omics Data ◽  
Health Domain ◽  
Medical Genomics ◽  
Research Activities ◽  
Translational Informatics

Summary Objective: To summarize excellent current research and propose a selection of best papers published in 2016 in the field of Bioinformatics and Translational Informatics with applications in the health domain and clinical care. Methods: We provide a synopsis of the articles selected for the IMIA Yearbook 2017, from which we attempt to derive a synthetic overview of current and future activities in the field. As in 2016, 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 coverage. Each section editor evaluated separately the set of 951 articles returned and evaluation results were merged for retaining 15 candidate best papers for peer-review. Results: The selection and evaluation process of papers published in the Bioinformatics and Translational Informatics field yielded four excellent articles focusing this year on the secondary use and massive integration of multi-omics data for cancer genomics and non-cancer complex diseases. Papers present methods to study the functional impact of genetic variations, either at the level of the transcription or at the levels of pathway and network. Conclusions: Current research activities in Bioinformatics and Translational Informatics with applications in the health domain continue to explore new algorithms and statistical models to manage, integrate, and interpret large-scale genomic datasets. As addressed by some of the selected papers, future trends would include the question of the international collaborative sharing of clinical and omics data, and the implementation of intelligent systems to enhance routine medical genomics.

scholarly journals Findings from the Section on Bioinformatics and Translational Informatics

2017 ◽  
Vol 26 (01) ◽  
pp. 188-191
Author(s):  
H. Dauchel ◽  
T. Lecroq
Keyword(s):  
Intelligent Systems ◽  
Large Scale ◽  
Cancer Genomics ◽  
Clinical Care ◽  
Evaluation Process ◽  
Omics Data ◽  
Health Domain ◽  
Medical Genomics ◽  
Research Activities ◽  
Translational Informatics

Summary Objective: To summarize excellent current research and propose a selection of best papers published in 2016 in the field of Bioinformatics and Translational Informatics with applications in the health domain and clinical care. Methods: We provide a synopsis of the articles selected for the IMIA Yearbook 2017, from which we attempt to derive a synthetic overview of current and future activities in the field. As in 2016, 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 coverage. Each section editor evaluated separately the set of 951 articles returned and evaluation results were merged for retaining 15 candidate best papers for peer-review. Results: The selection and evaluation process of papers published in the Bioinformatics and Translational Informatics field yielded four excellent articles focusing this year on the secondary use and massive integration of multi-omics data for cancer genomics and non-cancer complex diseases. Papers present methods to study the functional impact of genetic variations, either at the level of the transcription or at the levels of pathway and network. Conclusions: Current research activities in Bioinformatics and Translational Informatics with applications in the health domain continue to explore new algorithms and statistical models to manage, integrate, and interpret large-scale genomic datasets. As addressed by some of the selected papers, future trends would include the question of the international collaborative sharing of clinical and omics data, and the implementation of intelligent systems to enhance routine medical genomics.

scholarly journals Managing Large-Scale Genomic Datasets and Translation into Clinical Practice

2014 ◽  
Vol 23 (01) ◽  
pp. 212-214 ◽  
Author(s):  
L. F. Soualmia ◽  
T. Lecroq ◽  
Keyword(s):  
Large Scale ◽  
Genomic Data ◽  
Evaluation Process ◽  
Daily Practice ◽  
Supervised Machine Learning ◽  
Complex Data ◽  
Genome Medicine ◽  
Tumor Subtypes ◽  
Research Activities ◽  
Translational Informatics

Summary Objective:To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain. Method: We provide a synopsis of the articles selected for the IMIA Yearbook 2014, from which we attempt to derive a synthetic overview of current and future activities in the field. 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 evaluated independently the set of 1,851 articles and 15 articles were retained for peer-review. Results: The selection and evaluation process of this Yearbook’s section on Bioinformatics and Translational Informatics yielded three excellent articles regarding data management and genome medicine. In the first article, the authors present VEST (Variant Effect Scoring Tool) which is a supervised machine learning tool for prioritizing variants found in exome sequencing projects that are more likely involved in human Mendelian diseases. In the second article, the authors show how to infer surnames of male individuals by crossing anonymous publicly available genomic data from the Y chromosome and public genealogy data banks. The third article presents a statistical framework called iCluster+ that can perform pattern discovery in integrated cancer genomic data. This framework was able to determine different tumor subtypes in colon cancer. Conclusions: The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on large-scale biological, genomic, and Electronic Health Records data. Indeed, there is a need for powerful tools for managing and interpreting complex data, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and development efforts are contributing to the challenge of impacting clinically the results and even going towards a personalized medicine in the near future.

scholarly journals Bioinformatics Methods and Tools to Advance Clinical Care

2015 ◽  
Vol 24 (01) ◽  
pp. 170-173 ◽  
Author(s):  
T. Lecroq ◽  
L. F. Soualmia ◽  
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Cancer Survival ◽  
High Resolution Mass Spectrometry ◽  
Clinical Care ◽  
Evaluation Process ◽  
Daily Practice ◽  
High Coverage ◽  
Research Activities ◽  
Translational Informatics

Summary Objectives: To summarize excellent current research 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 2015, 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 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. Results: The selection and evaluation process of this Yearbook’s section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. Conclusions: The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and development efforts contribute to the challenge of impacting clinically the obtained results towards a personalized medicine.

scholarly journals A deliberative study of public attitudes towards sharing genomic data within NHS genomic medicine services in England

2020 ◽  
Vol 29 (7) ◽  
pp. 702-717
Author(s):  
Lamiece Hassan ◽  
Ann Dalton ◽  
Carrie Hammond ◽  
Mary Patricia Tully
Keyword(s):  
Public Attitudes ◽  
Clinical Care ◽  
Genomic Medicine ◽  
Genomic Data ◽  
Routine Care ◽  
Service Development ◽  
The Public ◽  
Research Activities ◽  
Share Data

Whole genome (DNA) sequencing is becoming part of routine care healthcare in England. Genomic data are most useful when pooled with other patients’ data, meaning that clinicians may need to share data to effectively treat patients. We ran deliberative focus groups to explore views among 44 patients and members of the public about proposals for wider genomic data sharing for clinical care. Participants were briefed about genomic medicine and engaged in group and individual exercises to deliberate on the benefits and risks of using genomic data. Findings showed that participants supported wider sharing of genomic data within health services and naturally linked care and research activities. Nonetheless, they were concerned about managing flows of information to protect patient confidentiality and guard against unauthorised uses, now and over the long-term. Ongoing conversations with the public are needed to determine appropriate uses of genomic data and safeguards to inform service development.

scholarly journals Efficient Results in Semantic Interoperability for Health Care

2016 ◽  
Vol 25 (01) ◽  
pp. 184-187
Author(s):  
J. Charlet ◽  
L. F. Soualmia ◽  
Keyword(s):  
Health Care ◽  
Semantic Web ◽  
Knowledge Representation ◽  
Large Scale ◽  
Recommendation System ◽  
Clinical Care ◽  
Knowledge Bases ◽  
Semantic Interoperability ◽  
The Third ◽  
Research Activities

Summary Objectives: To summarize excellent current research in the field of Knowledge Representation and Management (KRM) within the health and medical care domain. Method: We provide a synopsis of the 2016 IMIA selected articles as well as a related synthetic overview of the current and future field activities. A first step of the selection was performed through MEDLINE querying with a list of MeSH descriptors completed by a list of terms adapted to the KRM section. The second step of the selection was completed by the two section editors who separately evaluated the set of 1,432 articles. The third step of the selection consisted of a collective work that merged the evaluation results to retain 15 articles for peer-review. Results: The selection and evaluation process of this Yearbook’s section on Knowledge Representation and Management has yielded four excellent and interesting articles regarding semantic interoperability for health care by gathering heterogeneous sources (knowledge and data) and auditing ontologies. In the first article, the authors present a solution based on standards and Semantic Web technologies to access distributed and heterogeneous datasets in the domain of breast cancer clinical trials. The second article describes a knowledge-based recommendation system that relies on ontologies and Semantic Web rules in the context of chronic diseases dietary. The third article is related to concept-recognition and text-mining to derive common human diseases model and a phenotypic network of common diseases. In the fourth article, the authors highlight the need for auditing the SNOMED CT. They propose to use a crowd-based method for ontology engineering. Conclusions: The current research activities further illustrate the continuous convergence of Knowledge Representation and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care by proposing solutions to cope with the problem of semantic interoperability. Indeed, there is a need for powerful tools able to manage and interpret complex, large-scale and distributed datasets and knowledge bases, but also a need for user-friendly tools developed for the clinicians in their daily practice.

scholarly journals From Genome Sequencing to Bedside

2013 ◽  
Vol 22 (01) ◽  
pp. 175-177 ◽  
Author(s):  
L. F. Soualmia ◽  
T. Lecroq
Keyword(s):  
Genome Sequencing ◽  
High Throughput Sequencing ◽  
Health Management ◽  
Complex Diseases ◽  
Evaluation Process ◽  
Blood Analysis ◽  
Sequencing Technologies ◽  
Research Activities ◽  
Rare Gene ◽  
Translational Informatics

Summary Objectives: To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and evidence-based medicine. Method: We provide a synopsis of the articles selected for the IMIA Yearbook 2013, from which we attempt to derive a synthetic overview of current and future activities in the field. Three steps of selection were performed by querying PubMed and Web of Science. A first set of 5,549 articles was refined into a second set of 1,272 articles from which 15 articles were retained for peer-review. Results: The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding the Human Genome and Medicine. Exploiting genomic data depends on having the appropriate reference annotation available. In the first article, the goal of the GENCODE Consortium is to produce and publish The GENCODE human reference gene set. As a result it is composed by merged manual and automatic annotations, which are frequently updated from public experimental databases. The quality of genome sequencing is platform-dependant. In the second article, a generic database independent from the sequencing technologies, Huvariome, can help to identify errors and inconsistencies in sequencing. To understand complex diseases of patients it will be of great importance to detect rare gene variants. This is the aim of the third study. Finally, in the last article, the plasma's DNA of healthy individual and patients suffering from cancer is compared. Conclusions: The current research activities attest to the continuous convergence of Bioinformatics and Medical Informatics for clinical practice. For instance, a direct use of high throughput sequencing technologies for patients could aid the diagnosis of complex diseases (such as cancer) without invasive surgery (such as biopsy) but only with blood analysis. However, ongoing genomic tests will generate massive amounts of data and will imply new trends in the near future: “Big Data” and smart health management.

scholarly journals Barriers to Implementing Clinical Pharmacogenetics Testing in Sub-Saharan Africa. A Critical Review

Pharmaceutics ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 809
Author(s):  
Emiliene B. Tata ◽  
Melvin A. Ambele ◽  
Michael S. Pepper
Keyword(s):  
Health Care ◽  
Large Scale ◽  
Ethical Issues ◽  
Care Delivery ◽  
Clinical Care ◽  
Cost Effective ◽  
Communicable Diseases ◽  
Sub Saharan Africa ◽  
Successful Implementation ◽  
Sub Saharan

Clinical research in high-income countries is increasingly demonstrating the cost- effectiveness of clinical pharmacogenetic (PGx) testing in reducing the incidence of adverse drug reactions and improving overall patient care. Medications are prescribed based on an individual’s genotype (pharmacogenes), which underlies a specific phenotypic drug response. The advent of cost-effective high-throughput genotyping techniques coupled with the existence of Clinical Pharmacogenetics Implementation Consortium (CPIC) dosing guidelines for pharmacogenetic “actionable variants” have increased the clinical applicability of PGx testing. The implementation of clinical PGx testing in sub-Saharan African (SSA) countries can significantly improve health care delivery, considering the high incidence of communicable diseases, the increasing incidence of non-communicable diseases, and the high degree of genetic diversity in these populations. However, the implementation of PGx testing has been sluggish in SSA, prompting this review, the aim of which is to document the existing barriers. These include under-resourced clinical care logistics, a paucity of pharmacogenetics clinical trials, scientific and technical barriers to genotyping pharmacogene variants, and socio-cultural as well as ethical issues regarding health-care stakeholders, among other barriers. Investing in large-scale SSA PGx research and governance, establishing biobanks/bio-databases coupled with clinical electronic health systems, and encouraging the uptake of PGx knowledge by health-care stakeholders, will ensure the successful implementation of pharmacogenetically guided treatment in SSA.

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 Containment of COVID-19 in Ethiopia and implications for tuberculosis care and research

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Hussen Mohammed ◽  
Lemessa Oljira ◽  
Kedir Teji Roba ◽  
Getnet Yimer ◽  
Abebaw Fekadu ◽  
...  
Keyword(s):  
Clinical Care ◽  
Economic Security ◽  
Sub Saharan Africa ◽  
Infection Prevention And Control ◽  
System Response ◽  
Security Threat ◽  
African Countries ◽  
Irregular Migrants ◽  
Research Activities ◽  
And Control

Abstract Background The coronavirus disease 2019 (COVID-19) has emerged as a global health and economic security threat with staggering cumulative incidence worldwide. Given the severity of projections, hospitals across the globe are creating additional critical care surge capacity and limiting patient routine access to care for other diseases like tuberculosis (TB). The outbreak fuels panic in sub-Saharan Africa where the healthcare system is fragile in withstanding the disease. Here, we looked over the COVID-19 containment measures in Ethiopia in context from reliable sources and put forth recommendations that leverage the health system response to COVID-19 and TB. Main text Ethiopia shares a major proportion of the global burden of infectious diseases, while the patterns of COVID-19 are still at an earlier stage of the epidemiology curve. The Ethiopian government exerted tremendous efforts to curb the disease. It limited public gatherings, ordered school closures, directed high-risk civil servants to work from home, and closed borders. It suspended flights to 120 countries and restricted mass transports. It declared a five-month national state of emergency and granted a pardon for 20 402 prisoners. It officially postponed parliamentary and presidential elections. It launched the ‘PM Abiy-Jack Ma initiative’, which supports African countries with COVID-19 diagnostics and infection prevention and control commodities. It expanded its COVID-19 testing capacity to 38 countrywide laboratories. Many institutions are made available to provide clinical care and quarantine. However, the outbreak still has the potential for greater loss of life in Ethiopia if the community is unable to shape the regular behavioral and sociocultural norms that would facilitate the spread of the disease. The government needs to keep cautious that irregular migrants would fuel the disease. A robust testing capacity is needed to figure out the actual status of the disease. The pandemic has reduced TB care and research activities significantly and these need due attention. Conclusions Ethiopia took several steps to detect, manage, and control COVID-19. More efforts are needed to increase testing capacity and bring about behavioral changes in the community. The country needs to put in place alternative options to mitigate interruptions of essential healthcare services and scientific researches of significant impact.

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