scholarly journals Patient-focused pathogen genetic counselling—has the time come?

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Angeline S Ferdinand ◽  
Jane S Hocking ◽  
Justin T. Denholm ◽  
Benjamin P. Howden ◽  
Deborah A. Williamson
Keyword(s):  
Genetic Counselling ◽  
Healthcare Professionals ◽  
Genomic Data ◽  
Reporting Guidelines ◽  
Genomic Information ◽  
Healthcare Ethics ◽  
Media Reporting ◽  
Ethical Frameworks ◽  
Genomic Results

AbstractEnsuring accordance with principles of healthcare ethics requires improved communication of pathogen genomic data. This could include educating healthcare professionals in communicating pathogen genomic information to individuals, developing ethical frameworks for reporting pathogen genomic results to individuals, responsible media reporting guidelines, and counselling for individuals (‘pathogen genetic counselling’).

scholarly journals Newspaper Adherence to Media Reporting Guidelines for the Suicide Deaths of Kate Spade and Anthony Bourdain

2019 ◽  
Vol 2 (11) ◽  
pp. e1914517 ◽  
Author(s):  
Arielle H. Sheftall ◽  
Jaclyn L. Tissue ◽  
Paige Schlagbaum ◽  
Jonathan B. Singer ◽  
Nerissa Young ◽  
...  
Keyword(s):  
Reporting Guidelines ◽  
Media Reporting

scholarly journals Imaging of Cellular Oxidoreductase Activity Suggests Mixotrophic Metabolisms in Thiomargarita spp

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Jake V. Bailey ◽  
Beverly E. Flood ◽  
Elizabeth Ricci ◽  
Nathalie Delherbe
Keyword(s):  
Organic Carbon ◽  
Time Course ◽  
Genomic Data ◽  
Metabolic Potential ◽  
Oxidoreductase Activity ◽  
Metabolic Plasticity ◽  
Hypoxic Conditions ◽  
Genomic Studies ◽  
Genomic Results ◽  
Carbon Degradation

ABSTRACT The largest known bacteria, Thiomargarita spp., have yet to be isolated in pure culture, but their large size allows for individual cells to be monitored in time course experiments or to be individually sorted for omics-based investigations. Here we investigated the metabolism of individual cells of Thiomargarita spp. by using a novel application of a tetrazolium-based dye that measures oxidoreductase activity. When coupled with microscopy, staining of the cells with a tetrazolium-formazan dye allows metabolic responses in Thiomargarita spp. to be to be tracked in the absence of observable cell division. Additionally, the metabolic activity of Thiomargarita sp. cells can be differentiated from the metabolism of other microbes in specimens that contain adherent bacteria. The results of our redox dye-based assay suggest that Thiomargarita is the most metabolically versatile under anoxic conditions, where it appears to express cellular oxidoreductase activity in response to the electron donors succinate, acetate, citrate, formate, thiosulfate, H2, and H2S. Under hypoxic conditions, formazan staining results suggest the metabolism of succinate and likely acetate, citrate, and H2S. Cells incubated under oxic conditions showed the weakest formazan staining response, and then only to H2S, citrate, and perhaps succinate. These results provide experimental validation of recent genomic studies of Candidatus Thiomargarita nelsonii that suggest metabolic plasticity and mixotrophic metabolism. The cellular oxidoreductase response of bacteria attached to the exterior of Thiomargarita also supports the possibility of trophic interactions between these largest of known bacteria and attached epibionts. IMPORTANCE The metabolic potential of many microorganisms that cannot be grown in the laboratory is known only from genomic data. Genomes of Thiomargarita spp. suggest that these largest of known bacteria are mixotrophs, combining lithotrophic metabolism with organic carbon degradation. Our use of a redox-sensitive tetrazolium dye to query the metabolism of these bacteria provides an independent line of evidence that corroborates the apparent metabolic plasticity of Thiomargarita observed in recently produced genomes. Finding new cultivation-independent means of testing genomic results is critical to testing genome-derived hypotheses on the metabolic potentials of uncultivated microorganisms. IMPORTANCE The metabolic potential of many microorganisms that cannot be grown in the laboratory is known only from genomic data. Genomes of Thiomargarita spp. suggest that these largest of known bacteria are mixotrophs, combining lithotrophic metabolism with organic carbon degradation. Our use of a redox-sensitive tetrazolium dye to query the metabolism of these bacteria provides an independent line of evidence that corroborates the apparent metabolic plasticity of Thiomargarita observed in recently produced genomes. Finding new cultivation-independent means of testing genomic results is critical to testing genome-derived hypotheses on the metabolic potentials of uncultivated microorganisms.

scholarly journals ImaGene: a convolutional neural network to quantify natural selection from genomic data

2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Luis Torada ◽  
Lucrezia Lorenzon ◽  
Alice Beddis ◽  
Ulas Isildak ◽  
Linda Pattini ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Natural Selection ◽  
Convolutional Neural Network ◽  
Positive Selection ◽  
Genomic Data ◽  
Demographic Model ◽  
Genomic Information ◽  
Joint Inference ◽  
Genetic Bases

Abstract Background The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms underpinning human phenotypes. Popular methods of detecting such signals rely on compressing genomic information into summary statistics, resulting in the loss of information. Furthermore, few methods are able to quantify the strength of selection. Here we explored the use of deep learning in evolutionary biology and implemented a program, called , to apply convolutional neural networks on population genomic data for the detection and quantification of natural selection. Results enables genomic information from multiple individuals to be represented as abstract images. Each image is created by stacking aligned genomic data and encoding distinct alleles into separate colors. To detect and quantify signatures of positive selection, implements a convolutional neural network which is trained using simulations. We show how the method implemented in can be affected by data manipulation and learning strategies. In particular, we show how sorting images by row and column leads to accurate predictions. We also demonstrate how the misspecification of the correct demographic model for producing training data can influence the quantification of positive selection. We finally illustrate an approach to estimate the selection coefficient, a continuous variable, using multiclass classification techniques. Conclusions While the use of deep learning in evolutionary genomics is in its infancy, here we demonstrated its potential to detect informative patterns from large-scale genomic data. We implemented methods to process genomic data for deep learning in a user-friendly program called . The joint inference of the evolutionary history of mutations and their functional impact will facilitate mapping studies and provide novel insights into the molecular mechanisms associated with human phenotypes.

scholarly journals 333 Animal –GRIN a platform for animal genetic information

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 49-49
Author(s):  
Harvey D Blackburn ◽  
Ted Manahan ◽  
Carrie S Wilson ◽  
Wenkai Fu ◽  
Eduardo Cajueiro ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Genomic Data ◽  
Gene Bank ◽  
Genomic Information ◽  
Landscape Genomics ◽  
Bank Managers ◽  
On Line ◽  
The U.S ◽  
Ruby On Rails

Abstract An information system, Animal-GRIN, has been constructed as part of the U.S., Brazilian, and Canadian livestock genetic resource programs. It is designed to provide information to gene bank managers, the research community, and livestock producers about livestock breeds and subpopulations acquired in gene bank collections. The system was developed using a range of free software tools, including: MySQL, Ruby on Rails, Java Script, etc. The system is dynamic and publically accessible (https://nrrc.ars.usda.gov/A-GRIN). Exemplary information in Animal-GRIN consists of: animal identifiers, number and type of samples in the collection, pedigrees, coefficients of genetic relationships between animals within a breed, breeding values, phenotypes, and geographic source. To meet the national need for the long term archiving of genomic information developed with public funds, Animal-GRIN was expanded to store and make publically available genomic information (SNP) from any SNP chip, including custom products. Researchers are encouraged to submit their data upon completion of their publically funded projects. With the drill down concept, users can search the database for genomic information, physical samples associated with the genomic information, and phenotypic information on specific animals. Once animals of interest are found, on-line tools enable users to request either germplasm samples or genomic data. Progress in meeting genetic security for a breed’s collection can also be viewed. To date the U.S. collection has 52,639 animals with almost a million samples representing 36 species, 167 breeds, and 331 subpopulations and these have been entered into Animal-GRIN. Genomic data has been acquired on 1,899 animals representing 36 breeds. The next phase of Animal-GRIN development will be development of landscape genomics components. Acquisition of germplasm samples and associated genomic information are a continuing effort.

scholarly journals A Model for Genome-First Care: Returning Secondary Genomic Findings to Participants and Their Healthcare Providers in a Large Research Cohort

2017 ◽  
Author(s):  
Marci L. B. Schwartz ◽  
Cara Zayac McCormick ◽  
Amanda L. Lazzeri ◽  
D’Andra M. Lindbuchler ◽  
Miranda L. G. Hallquist ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Gene List ◽  
Healthcare Providers ◽  
Secondary Analysis ◽  
Direct Interaction ◽  
Genomic Data ◽  
Sequencing Data ◽  
Discovery Research ◽  
Monogenic Diseases ◽  
Genomic Results

ABSTRACTBackgroundResearch cohorts with linked genomic data exist, or are being developed, at many research centers. Within any such “sequenced cohort” of more than 100 participants, it is likely that there are participants with previously undisclosed risk for life-threatening monogenic diseases that could be identified with targeted analysis of their existing data. Identification of such disease-associated findings are not usually primary to the enrollment research goals. At Geisinger Health System, MyCode® Community Health Initiative (MyCode) participants represent one such large sequenced cohort. Since 2013, MyCode participants in discovery research have been consented for secondary analysis of their existing research genomic sequences to allow delivery of medically actionable findings to them and their healthcare providers. This return of genomic results program was developed to manage an anticipated 3.5% of MyCode participants who will receive clinically confirmed genomic variants from an approved gene list out of more than 150,000 total participants. Risk-associated DNA sequences alone without any clinical parameter, prompt “genome-first” follow-up encounters.MethodsThis article describes our process for generating clinical grade results from research-based genomic sequencing data, delivering results to patients and their providers, facilitating targeted clinical evaluations of patients and promoting cascade testing of at-risk relatives. We also summarize our early data about the results generated during this process and our ability to contact patients and their providers to disclose the information.ResultsThis process has been used to generate 343 results on 339 patients. 93% of patients with a result have been successfully contacted about their results as evidenced by direct interaction about their result with the research team or a healthcare provider. 222 healthcare providers have been notified of a result on one or more patient through this result delivery process.ConclusionsHere we describe the existing GHS model to deliver genomic data into the electronic medical record and the clinical interactions that are prompted and supported. Elements of this genome-first care model can be applied in other healthcare settings and in national efforts, such as “All of Us”, that wish to establish programs for returning genomic results to research participants.

scholarly journals Linking Ethical Standards for Healthcare Professionals with Indian Cultural Values

2021 ◽  
Vol 16 (3) ◽  
pp. 49-58
Author(s):  
Jaya Mathew ◽  
Phathara-On Wesarat
Keyword(s):  
Cultural Values ◽  
Healthcare Professionals ◽  
Ethical Decision Making ◽  
Healthcare Sector ◽  
Ethical Standards ◽  
Competing Values ◽  
Healthcare Ethics ◽  
Community Values ◽  
Working Lives ◽  
Ethical Conflicts

Ethical standards of healthcare sector are important to the lives of people because healthcare is a profession that impacts the lives of people, their families and society. Healthcare professionals are inevitably involved in ethical decision-making in their working lives and address a conflict regarding competing values such as personal, organizational, professional, and community values. India is a country in South Asia where people are diverse in ethnicity, religion, and culture. So, revealing commonly accepted ethical standards for resolving ethical conflicts for healthcare professionals becomes more relevant for India. However, the research on this issue is limited. Therefore, the purpose of this paper is to reveal the link between ethical standards for healthcare professionals in general and Indian cultural values such as Dharma, Nishkama Karma and Jnana. This paper used a scoping review to screen the relevant articles which were selected from the Scopus and Google Scholar databases. The keywords used for searching the research articles were “ethical standard”, “ethics”, “healthcare ethics”, and “Indian cultural values”. Then, the constructs of healthcare ethics were identified and the relevant ethical standards for each construct were not only evaluated based on the two key theoretical viewpoints namely deontology and teleology, but also justified by Indian cultural values.

scholarly journals Parental Access to Children's Raw Genomic Data in Canada: Legal Rights and Professional Responsibility

2021 ◽  
Vol 12 ◽  
Author(s):  
Michael J. S. Beauvais ◽  
Adrian M. Thorogood ◽  
Michael J. Szego ◽  
Karine Sénécal ◽  
M'an H. Zawati ◽  
...  
Keyword(s):  
Healthcare Professionals ◽  
Personal Information ◽  
Personal Data ◽  
Genomic Data ◽  
Public Institution ◽  
Best Interests ◽  
Legal Rights ◽  
The European Union ◽  
The Right ◽  
Right Of Access

Children with rare and common diseases now undergo whole genome sequencing (WGS) in clinical and research contexts. Parents sometimes request access to their child's raw genomic data, to pursue their own analyses or for onward sharing with health professionals and researchers. These requests raise legal, ethical, and practical issues for professionals and parents alike. The advent of widespread WGS in pediatrics occurs in a context where privacy and data protection law remains focused on giving individuals control-oriented rights with respect to their personal information. Acting in their child's stead and in their best interests, parents are generally the ones who will be exercising these informational rights on behalf of the child. In this paper, we map the contours of parental authority to access their child's raw genomic data. We consider three use cases: hospital-based researchers, healthcare professionals acting in a clinical-diagnostic capacity, and “pure” academic researchers at a public institution. Our research seeks to answer two principal questions: Do parents have a right of access to their child's raw WGS data? If so, what are the limits of this right? Primarily focused on the laws of Ontario, Canada's most populous province, with a secondary focus on Canada's three other most populous provinces (Quebec, British Columbia, and Alberta) and the European Union, our principal findings include (1) parents have a general right of access to information about their children, but that the access right is more capacious in the clinical context than in the research context; (2) the right of access extends to personal data in raw form; (3) a consideration of the best interests of the child may materially limit the legal rights of parents to access data about their child; (4) the ability to exercise rights of access are transferred from parents to children when they gain decision-making capacity in both the clinical and research contexts, but with more nuance in the former. With these findings in mind, we argue that professional guidelines, which are concerned with obligations to interpret and return results, may assist in furthering a child's best interests in the context of legal access rights. We conclude by crafting recommendations for healthcare professionals in the clinical and research contexts when faced with a parental request for a child's raw genomic data.

scholarly journals Ethical practice in medicine: a review

2020 ◽  
Author(s):  
Kasaw Adane ◽  
Ligabaw Worku ◽  
Teshiwal Deress ◽  
Adino Tesfahun
Keyword(s):  
Medical Ethics ◽  
Healthcare Professionals ◽  
Code Of Ethics ◽  
Healthcare Delivery ◽  
Healthcare Services ◽  
Physical Contact ◽  
Ethical Practice ◽  
Minimum Level ◽  
Healthcare Ethics ◽  
Moral Standards

Abstract Objective A patient with health problems seek healthcare services from healthcare professionals. Their patient-provider relationships are usually affected by roles, gifts, services, and physical contact. The major ethical healthcare practices focus on respecting patient’s freedom and basic human rights. However, there are only limited references materials issued on medical ethics and ethical medical practices. Hence, this review article tries to describe the important aspects of ethical practices in healthcare delivery. Methods Initially, idea conceptualization, planning and keyword defining were for the development of this material. The keywords were medical ethics, code of ethics, bioethics, ethical practice, quality service and healthcare ethics. Result Then, two authors independently assessed published materials using EndNote® program from PubMed (NML) and Google Scholar databases. Finally, from a total of 721 full-text articles downloaded, 34 published article meeting inclusion criteria were included in this article. Conclusion Adherence to high ethical and moral standards, responding to societal needs and reflection social contract, subordinating self-interest to the interest of others and the manifestation of the core human values are all expected from healthcare professionals. Ethical and legal dimensions of medicine are very important. Hence, providing high-quality patient care at low cost and compliance with ethical and moral standards is the most common reason for the incompliance with medical ethics. Hence, healthcare professionals are expected to have a minimum level of knowledge on ethical concepts, favorable attitude, and a minimum level of skill to comply with regulatory and ethical requirements in all situations.

scholarly journals Social Media Responses to Online Suicide-Related News Articles

Crisis ◽  
2020 ◽  
pp. 1-5
Author(s):  
Tiana Edwards ◽  
Michelle Torok ◽  
Lauren McGillivray ◽  
Trent Ford ◽  
Katherine Mok ◽  
...  
Keyword(s):  
Social Media ◽  
Random Sample ◽  
Primary Source ◽  
Reporting Guidelines ◽  
Online Media ◽  
Media Reporting ◽  
Factors Associated ◽  
Contagion Effects ◽  
Digital News ◽  
Media Responses

Abstract. Background: Responsible media reporting of suicide is important to prevent contagion effects. Online media reporting is increasingly becoming the primary source of news information for many people. Aims: This study aimed to assess compliance with responsible media reporting guidelines, and whether social media responses were associated with compliance. Method: A random sample of Australian digital news articles over a 9-month period were coded for compliance to Mindframe suicide reporting guidelines. Social media responses (number of shares and number of comments) were collected via Facebook. Results: From the sample of 275 articles, articles were compliant with a median of seven of the nine recommendations. Articles compliant with more than seven recommendations were shared more frequently (median: 93 vs. 38 shares, p = .017) but no difference was observed in the number of comments (median: 0 vs. 0, p = .340). Limitations: Other factors associated with individual events and articles are also likely to contribute to the response on social media. Although no difference in the number of comments was observed, the nature of these comments may differ. Conclusion: Improved understanding of how to maximize dissemination of positive messages may help minimize contagion effects.

scholarly journals MOSGA 2: Comparative genomics and validation tools

2021 ◽  
Author(s):  
Roman Martin ◽  
Hagen Dreßler ◽  
Georges Hattab ◽  
Thomas Hackl ◽  
Matthias G Fischer ◽  
...  
Keyword(s):  
Quality Control ◽  
Comparative Genomics ◽  
Data Quality ◽  
Genomic Data ◽  
Data Sets ◽  
Genomic Information ◽  
High Quality ◽  
Genome Annotations ◽  
Genome Assemblies ◽  
Annotation Quality

Due to the highly growing number of available genomic information, the need for accessible and easy-to-use analysis tools is increasing. To facilitate eukaryotic genome annotations, we created MOSGA. In this work, we show how MOSGA~2 is developed by including several advanced analyses for genomic data. Since the genomic data quality greatly impacts the annotation quality, we included multiple tools to validate and ensure high-quality user-submitted genome assemblies. Moreover, thanks to the integration of comparative genomics methods, users can benefit from a broader genomic view by analyzing multiple genomic data sets simultaneously. Further, we demonstrate the new functionalities of MOSGA~2 by different use-cases and practical examples. MOSGA~2 extends the already established application to the quality control of the genomic data and integrates and analyzes multiple genomes in a larger context, e.g., by phylogenetics.

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