scholarly journals PGP-UK: a research and citizen science hybrid project in support of personalized medicine

2018 ◽  
Author(s):  
◽  
Stephan Beck ◽  
Alison M Berner ◽  
Graham Bignell ◽  
Maggie Bond ◽  
...  
Keyword(s):  
Personalized Medicine ◽  
Citizen Science ◽  
Public Awareness ◽  
Open Data ◽  
Genome Project ◽  
Personal Genome ◽  
The Public ◽  
Open Consent ◽  
Free Open Source ◽  
And Personalized Medicine

AbstractMolecular analyses such as whole-genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is, however, not without challenges, and multiple studies are ongoing to identify what these are and explore how they can be addressed. Defined as a research project, the Personal Genome Project UK (PGP-UK) is part of the global PGP network and focuses on open data sharing and citizen science to advance and accelerate personalized genomics and medicine. Here we report our findings on using an open consent recruitment protocol, active participant involvement, open access release of personal genome, methylome and transcriptome data and associated analyses, including 47 new variants predicted to affect gene function and innovative reports based on the analysis of genetic and epigenetic variants. For this pilot study, we recruited ten participants willing to actively engage as citizen scientists with the project. In addition, we introduce Genome Donation as a novel mechanism for openly sharing previously restricted data and discuss the first three donations received. Lastly, we present GenoME, a free, open-source educational app suitable for the lay public to allow exploration of personal genomes. Our findings demonstrate that citizen science-based approaches like PGP-UK have an important role to play in the public awareness, acceptance and implementation of genomics and personalized medicine.

scholarly journals Introducing Pharmacogenetics and Personalized Medicine via a Weblog

2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Kaitlin Bova ◽  
Sara Bova ◽  
Kevin Hill ◽  
Mark Dixon ◽  
Diana Ivankovich ◽  
...  
Keyword(s):  
Personalized Medicine ◽  
Knowledge Base ◽  
General Information ◽  
Pharmacy Students ◽  
Personal Genome ◽  
Genetic Privacy ◽  
Drug Dosing ◽  
First Semester ◽  
Incoming Freshmen ◽  
And Personalized Medicine

Objectives: To evaluate a weblog (blog)-based course introducing pharmacogenetics (PGt) and personalized medicine (PM) relative to freshmen pharmacy students' knowledge base. Methods: Incoming freshmen pharmacy students were invited by email to enroll in a one semester-hour, elective, on-line blog-based course entitled "Personal Genome Evaluation". The course was offered during the students' first semester in college. A topic list related to PGt and PM was developed by a group of faculty with topics being presented via the blog once or twice weekly through week 14 of the 15 week semester. A pre-course and post-course survey was sent to the students to compare their knowledge base relative to general information, drug response related to PGt, and PM. Results: Fifty-one freshmen pharmacy students enrolled in the course and completed the pre-course survey and 49 of the 51 students completed the post-course survey. There was an increase in the students' general, PGt and PM knowledge base as evidenced by a statistically significant higher number of correct responses for 17 of 21 questions on the post-course survey as compared to the pre-course survey. Notably, following the course, students had an increased knowledge base relative to "genetic privacy", drug dosing based on metabolizer phenotype, and the breadth of PM, among other specific points. Conclusions: The study indicated that introducing PGt and PM via a blog format was feasible, increasing the students' knowledge of these emerging areas. The blog format is easily transferable and can be adopted by colleges/schools to introduce PGt and PM.   Type: Case Study

scholarly journals TYPES OF PUBLIC INFORMATION IN THE FORM OF OPEN DATA AND THEIR CLASSIFICATION

2020 ◽  
pp. 33-37
Author(s):  
D. Nesterova
Keyword(s):  
Public Sector ◽  
Public Awareness ◽  
Open Data ◽  
Public Information ◽  
Economic Benefits ◽  
Full Potential ◽  
Data Discovery ◽  
The Public ◽  
Public Data

The concept of public information in the form of open data and its main features are studied. It is determined that due to the possible wide application of open data, the definition of the main grounds for the classification of open data is an insufficiently covered issue. The purpose of this study is to determine the types and criteria for the classification of public information in the form of open data. This is necessary for their widespread use in order to solve socially important tasks and to use their full potential in unusual directions. The author has analyzed international reports on open data and identified the problems of the quality of such data and the possibility of using them to solve socially important tasks. The classification of open data is formed on the following grounds: 1. by data type; 2. by data format; 3. by subject. The article determines the value of open data to society and the possibility of its wide use in the example of other countries. The problems that complicate the implementation of the government data discovery initiative in Ukraine include the underdeveloped culture of open government; insufficient level of training of public authorities to work with open data; insufficient funding for the public data discovery initiative; low level of public awareness and interest in public data and the benefits of using it. Unfortunately, most citizens are still satisfying their curiosity by using open data. The author notes that using data that describes the patterns we live in can help us solve problems in ways we may not have anticipated. As a rule, public sector systems do not respond too quickly on changes. With open data, they could track, predict and respond to real-time changes. This would allow the public sector to streamline its processes and services and it would be possible to clearly identify areas for improving and increasing productivity, to develop specialized solutions based on various demographic indicators and other factors. This would be a huge transformational leap in attracting open data to the public sector, as it opens up a number of areas for innovation. The author substantiates the importance of open data for public sector transformation, economic benefits and their use as an instrument for creating an information society.

scholarly journals A citizen science initiative for open data and visualization of COVID-19 outbreak in Kerala, India

2020 ◽  
Author(s):  
Jijo Pulickiyil Ulahannan ◽  
Nikhil Narayanan ◽  
Nishad Thalhath ◽  
Prem Prabhakaran ◽  
Sreekanth Chaliyeduth ◽  
...  
Keyword(s):  
Citizen Science ◽  
Web Application ◽  
Public Awareness ◽  
Open Data ◽  
Epidemiological Data ◽  
Demographic Characteristics ◽  
Real Time Analysis ◽  
Department Of Health ◽  
The Government ◽  
Science Initiative

ABSTRACTObjectiveIndia reported its first COVID-19 case in the state of Kerala and an outbreak initiated subsequently. The Department of Health Services, Government of Kerala, initially released daily updates through daily textual bulletins for public awareness to control the spread of the disease. However, this unstructured data limits upstream applications, such as visualization, and analysis, thus demanding refinement to generate open and reusable datasets.Materials and MethodsThrough a citizen science initiative, we leveraged publicly available and crowd-verified data on COVID-19 outbreak in Kerala from the government bulletins and media outlets to generate reusable datasets. This was further visualized as a dashboard through a frontend web application and a JSON repository, which serves as an API for the frontend.ResultsFrom the sourced data, we provided real-time analysis, and daily updates of COVID-19 cases in Kerala, through a user-friendly bilingual dashboard (https://covid19kerala.info/) for non-specialists. To ensure longevity and reusability, the dataset was deposited in an open-access public repository for future analysis. Finally, we provide outbreak trends and demographic characteristics of the individuals affected with COVID-19 in Kerala during the first 138 days of the outbreak.DiscussionWe anticipate that our dataset can form the basis for future studies, supplemented with clinical and epidemiological data from the individuals affected with COVID-19 in Kerala.ConclusionWe reported a citizen science initiative on the COVID-19 outbreak in Kerala to collect and deposit data in a structured format, which was utilized for visualizing the outbreak trend and describing demographic characteristics of affected individuals.

scholarly journals Reproducible integration of multiple sequencing datasets to form high-confidence SNP, indel, and reference calls for five human genome reference materials

2018 ◽  
Author(s):  
Justin M. Zook ◽  
Jennifer McDaniel ◽  
Hemang Parikh ◽  
Haynes Heaton ◽  
Sean A. Irvine ◽  
...  
Keyword(s):  
Reference Materials ◽  
Performance Metrics ◽  
Genome Project ◽  
Personal Genome ◽  
High Confidence ◽  
Global Alliance ◽  
Human Genomes ◽  
Open Consent ◽  
Genome Context ◽  
Human Genome Reference

AbstractBenchmark small variant calls from the Genome in a Bottle Consortium (GIAB) for the CEPH/HapMap genome NA12878 (HG001) have been used extensively for developing, optimizing, and demonstrating performance of sequencing and bioinformatics methods. Here, we develop a reproducible, cloud-based pipeline to integrate multiple sequencing datasets and form benchmark calls, enabling application to arbitrary human genomes. We use these reproducible methods to form high-confidence calls with respect to GRCh37 and GRCh38 for HG001 and 4 additional broadly-consented genomes from the Personal Genome Project that are available as NIST Reference Materials. These new genomes’ broad, open consent with few restrictions on availability of samples and data is enabling a uniquely diverse array of applications. Our new methods produce 17% more high-confidence SNPs, 176% more indels, and 12% larger regions than our previously published calls. To demonstrate that these calls can be used for accurate benchmarking, we compare other high-quality callsets to ours (e.g., Illumina Platinum Genomes), and we demonstrate that the majority of discordant calls are errors in the other callsets, We also highlight challenges in interpreting performance metrics when benchmarking against imperfect high-confidence calls. We show that benchmarking tools from the Global Alliance for Genomics and Health can be used with our calls to stratify performance metrics by variant type and genome context and elucidate strengths and weaknesses of a method.

Genomics and Personalized Medicine

2016 ◽  
Author(s):  
Michael Snyder
Keyword(s):  
Health Care ◽  
Personalized Medicine ◽  
Genome Project ◽  
Cancer Treatments ◽  
Essential Information ◽  
Data Elements ◽  
The Human Genome Project ◽  
Biomedical Interventions ◽  
Integrated Study ◽  
And Personalized Medicine

In 2001 the Human Genome Project succeeded in mapping the DNA of humans. This landmark accomplishment launched the field of genomics, the integrated study of all the genes in the human body and the related biomedical interventions that can be tailored to benefit a person's health. Today genomics, part of a larger movement toward personalized medicine, is poised to revolutionize health care. By cross-referencing an individual's genetic sequence -- their genome -- against known elements of "Big Data," elements of genomics are already being incorporated on a widespread basis, including prenatal disease screening and targeted cancer treatments. With more innovations soon to arrive at the bedside, the promise of the genomics revolution is limitless. This entry in the What Everyone Needs to Know series offers an authoritative resource on the prospects and realities of genomics and personalized medicine. As this science continues to alter traditional medical paradigms, consumers are faced with additional options and more complicated decisions regarding their health care. This book provides the essential information everyone needs.

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