scholarly journals Opportunities and Challenges in Interpreting and Sharing Personal Genomes

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 643 ◽  
Author(s):  
Irit R. Rubin ◽  
Gustavo Glusman
Keyword(s):  
New Technologies ◽  
Full Range ◽  
Risk Scores ◽  
Personal Genome ◽  
Tight Control ◽  
Data Types ◽  
Genetic Privacy ◽  
Global Databases ◽  
Genome Data ◽  
Personal Genomes

The 2019 “Personal Genomes: Accessing, Sharing and Interpretation” conference (Hinxton, UK, 11–12 April 2019) brought together geneticists, bioinformaticians, clinicians and ethicists to promote openness and ethical sharing of personal genome data while protecting the privacy of individuals. The talks at the conference focused on two main topic areas: (1) Technologies and Applications, with emphasis on personal genomics in the context of healthcare. The issues discussed ranged from new technologies impacting and enabling the field, to the interpretation of personal genomes and their integration with other data types. There was particular emphasis and wide discussion on the use of polygenic risk scores to inform precision medicine. (2) Ethical, Legal, and Social Implications, with emphasis on genetic privacy: How to maintain it, how much privacy is possible, and how much privacy do people want? Talks covered the full range of genomic data visibility, from open access to tight control, and diverse aspects of balancing benefits and risks, data ownership, working with individuals and with populations, and promoting citizen science. Both topic areas were illustrated and informed by reports from a wide variety of ongoing projects, which highlighted the need to diversify global databases by increasing representation of understudied populations.

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 THE PROBLEMS OF BRINGING RUSSIAN TRADE POLICY IN LINE WITH WTO REQUIREMENTS

2013 ◽  
pp. 146-152
Author(s):  
M. A. Petrova
Keyword(s):  
Trade Policy ◽  
Automotive Industry ◽  
New Technologies ◽  
Full Range ◽  
Economic Security ◽  
The European Union ◽  
Trade Dispute ◽  
National Economic ◽  
The Stability ◽  
Economic Zones

The article analyzes the role of trade policy in ensuring the competitiveness of the automotive industry – one of the most sensitive to the changes of economic conditions and important for providing national economic security – and finding a balance between the need to regulate the internal market and the implementation of the commitments under WTO. The analyze of the current condition of the Russian automotive industry has shown that, despite the low share in the world production and exports, Russia has a great potential for growth, mainly due to the unsaturated domestic market. It is proved, that the development of the automotive industry as one of the innovative industries in the country has all the necessary terms. Moreover, the priority areas for the development of the automotive industry include, first of all, the creation of a full range production with foreign investment. Measures of attracting and regulating FDI received much attention due to their relationship with the instruments of trade policy, as the production of capital goods, particularly automobiles, require imports of components, and FDI, in turn, promote the export of finished products. The commitments taken by Russia in the automotive industry include reduction of duties on imported cars, the renegotiation of investment programs and rules for the functioning of special economic zones. At present, the most acute question is car recycling tax, which has led to a trade dispute with the European Union, and may lead to countervailing measures against Russian goods. Considering WTO rules, recommendations on the use of the most effective instruments of foreign policy, aimed at improving the competitiveness of the Russian automotive industry, were made, including the rationalization of import and the attraction of new technologies due to the diversification of customs duties on certain groups of automotive components, lowering income taxes, a gradual decrease of the fiscal functions of the customs tariff; the stability and transparency of the instruments of trade policy and simplification of customs procedures.

Research Challenges in Big Data Analytics

2017 ◽  
pp. 83-99
Author(s):  
Sivamathi Chokkalingam ◽  
Vijayarani S.
Keyword(s):  
Big Data ◽  
Data Analytics ◽  
Large Scale ◽  
New Technologies ◽  
Big Data Analytics ◽  
Large Data ◽  
Data Sets ◽  
Data Types ◽  
Customer Preferences ◽  
Research Challenges

The term Big Data refers to large-scale information management and analysis technologies that exceed the capability of traditional data processing technologies. Big Data is differentiated from traditional technologies in three ways: volume, velocity and variety of data. Big data analytics is the process of analyzing large data sets which contains a variety of data types to uncover hidden patterns, unknown correlations, market trends, customer preferences and other useful business information. Since Big Data is new emerging field, there is a need for development of new technologies and algorithms for handling big data. The main objective of this paper is to provide knowledge about various research challenges of Big Data analytics. A brief overview of various types of Big Data analytics is discussed in this paper. For each analytics, the paper describes process steps and tools. A banking application is given for each analytics. Some of research challenges and possible solutions for those challenges of big data analytics are also discussed.

scholarly journals Using Genetics to Examine a General Liability to Childhood Psychopathology

2019 ◽  
Vol 50 (4) ◽  
pp. 213-220 ◽  
Author(s):  
Lucy Riglin ◽  
Ajay K. Thapar ◽  
Beate Leppert ◽  
Joanna Martin ◽  
Alexander Richards ◽  
...  
Keyword(s):  
Association Studies ◽  
Full Range ◽  
Population Based ◽  
Autism Spectrum ◽  
Developmental Changes ◽  
Risk Scores ◽  
Genome Wide Association Studies ◽  
Childhood Psychopathology ◽  
Specific Factors ◽  
P Factor

AbstractPsychiatric disorders show phenotypic as well as genetic overlaps. There are however also marked developmental changes throughout childhood. We investigated the extent to which, for a full range of early childhood psychopathology, a general “p” factor was explained by genetic liability, as indexed by multiple different psychiatric polygenic risk scores (PRS) and whether these relationships altered with age. The sample was a UK, prospective, population-based cohort with psychopathology data at age 7 (N = 8161) and age 13 (N = 7017). PRS were generated from large published genome-wide association studies. At both ages, we found evidence for a childhood “p” factor as well as for specific factors. Schizophrenia and attention-deficit/hyperactivity disorder (ADHD) PRS were associated with this general “p” factor at both ages but depression and autism spectrum disorder (ASD) PRS were not. We also found some evidence of associations between schizophrenia, ADHD and depression PRS with specific factors, but these were less robust and there was evidence for developmental changes.

scholarly journals An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Yun Sung Cho ◽  
Hyunho Kim ◽  
Hak-Min Kim ◽  
Sungwoong Jho ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Reference Genome ◽  
Genomic Structure ◽  
Genome Project ◽  
Personal Genome ◽  
Personal Genomic ◽  
Personal Reference ◽  
Scale Population ◽  
Genome Assemblies

Abstract Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

scholarly journals merlin—A unified modeling framework for data analysis and methods development in Stata

2020 ◽  
Vol 20 (4) ◽  
pp. 763-784
Author(s):  
Michael J. Crowther
Keyword(s):  
Data Analysis ◽  
Data Science ◽  
Full Range ◽  
Hierarchical Structures ◽  
Nonlinear Effects ◽  
Recurrent Event ◽  
Data Types ◽  
Modeling Framework ◽  
Logistic Mixed Effects Model ◽  
Complex Settings

The challenges in statistics and data science are rapidly growing because access to a multitude of data types continues to increase, as well as the sheer quantity of data. Analysts are now presented with multivariate data, sometimes measured repeatedly, and often requiring the ability to model nonlinear relationships and hierarchical structures. In this article, I present the merlin command, which attempts to provide an extremely general framework for data analysis. From simple settings such as fitting a linear regression model or a Weibull survival model to more complex settings such as fitting a three-level logistic mixed-effects model or a multivariate joint model of multiple longitudinal outcomes (of different types) and a recurrent event and survival with nonlinear effects, merlin can fit them all. I will take a single dataset and attempt to show you the full range of capabilities of merlin and discuss some future directions for the implementation in Stata.

scholarly journals Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data

2015 ◽  
Vol 32 (4) ◽  
pp. 635-637 ◽  
Author(s):  
Juan J. Diaz-Montana ◽  
Owen J.L. Rackham ◽  
Norberto Diaz-Diaz ◽  
Enrico Petretto
Keyword(s):  
Personal Genome ◽  
Web Based ◽  
Genome Data ◽  
Web Platform

scholarly journals SAT-LB111 Improving Classification of Diabetes Etiology in Electronic Resources Using Phenotype Algorithms and Polygenic Risk Scores

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Lina Sulieman ◽  
Jing He ◽  
Robert Carroll ◽  
Lisa Bastarache ◽  
Andrea Ramirez
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Chart Review ◽  
Risk Scores ◽  
P Value ◽  
Learning Approaches ◽  
Data Types ◽  
Electronic Health

Abstract Electronic Health Records (EHR) contain rich data to identify and study diabetes. Many phenotype algorithms have been developed to identify research subjects with type 2 diabetes (T2D), but very few accurately identify type 1 diabetes (T1D) cases or more rare forms of monogenic and atypical metabolic presentations. Polygenetic risk scores (PRS) quantify risk of a disease using common genomic variants well for both T1D and T2D. In this study, we apply validated phenotyping algorithms to EHRs linked to a genomic biobank to understand the independent contribution of PRS to classification of diabetes etiology and generate additional novel markers to distinguish subtypes of diabetes in EHR data. Using a de-identified mirror of medical center’s electronic health record, we applied published algorithms for T1D and T2D to identify cases, and used natural language processing and chart review strategies to identify cases of maturity onset diabetes of the young (MODY) and other more rare presentations. This novel approach included additional data types such as medication sequencing, ratio and temporality of insulin and non-insulin agents, clinical genetic testing, and ratios of diagnostic codes. Chart review was performed to validate etiology. To calculate PRS, we used genome wide genotyping from our BioBank, the de-identified biobank linking EHR to genomic data using coefficients of 65 published T1D SNPS and 76,996 T2D SNPS using PLINK in Caucasian subjects. In the dataset, we identified 82,238 cases of T2D but only 130 cases of T1D using the most cited published algorithms. Adding novel structured elements and natural language processing identified an additional 138 cases of T1D and distinguished 354 cases as MODY. Among over 90,000 subjects with genotyping data available, we included 72,624 Caucasian subjects since PRS coefficients were generated in Caucasian cohorts. Among those subjects, 248, 6,488, and 21 subjects were identified as T1D, T2D, and MODY subjects respectively in our final PRS cohort. The T1D PRS did significantly discriminate well between cases and controls (Mann-Whitney p-value is 3.4 e-17). The PRS for T2D did not significantly discriminate between cases and controls using published algorithms. The atypical case count was too low to calculate PRS discrimination. Calculation of the PRS score was limited by quality inclusion of variants available, and discrimination may improve in larger data sets. Additionally, blinded physician case review is ongoing to validate the novel classification scheme and provide a gold standard for machine learning approaches that can be applied in validation sets.

scholarly journals Induced polarization of volcanic rocks. 4. Large-scale induced polarization imaging

2021 ◽  
Vol 225 (2) ◽  
pp. 950-967
Author(s):  
L Gross ◽  
A Soueid Ahmed ◽  
A Revil
Keyword(s):  
Electric Field ◽  
Large Scale ◽  
New Technologies ◽  
Induced Polarization ◽  
Hydrothermal Systems ◽  
Capacitive Coupling ◽  
Electrode Spacing ◽  
Data Types ◽  
Dipole Orientation ◽  
Geothermal Resources

SUMMARY Thanks to the emergence of new technologies developed with the goal of performing large-scale galvanometric induced polarization surveys and thanks a better understanding of the underlying physics of induced polarization, this geophysical method can now be applied in the field of volcanology and geothermal resources assessment. A new approach is developed here for directly inverting the primary and secondary electric fields recorded at a set of independent stations when injecting a primary current. The use of independent stations to measure the primary and secondary electrical fields improves the quality of the data by reducing the capacitive coupling effects inherent to systems based on long cables. It avoids issues associated with using the same electrodes for both current injection and voltage measurements and negative apparent resistivity and chargeability values. With such acquisitions, we can perform true 3-D surveys in areas characterized by complex topography such as volcanoes. The numerical scheme we developed returns as output the electrical conductivity and chargeability fields. The implemented methodology presents several advantages. The first is the use of data types at the stations, for example the electric field intensity, that are independent from the local geometrical station parameters such as electrode spacing and dipole orientation. The second advantage lies in the suitability of the proposed approach to perform large-scale applications since we use a matrix-free approach that does not require the assembly of the Jacobian matrices. The third concerns the possibility of performing the inversion on complex geometries through a consistent use of the finite element method on unstructured meshes in combination with algebraic multigrid preconditioning for the regularization and the solution of the forward and adjoint problems. The computation of 3-D sensitivity maps can also be a real asset in survey design. After validating our approach with a benchmark synthetic case study, we test it on a large-scale induced polarization survey that mimic true field conditions on a volcanic environment with rough topography. Our tests demonstrate the high potential of this electric field approach in volcanology especially for deep (3 km) imagining of the internal structure of volcanoes, which in turn could improve our understanding of hydrothermal systems and allow the monitoring of active volcanoes and the potential risk of collapse.

scholarly journals TOOLS AND SERVICES OF CLOUD-ORIENTED OPEN SCIENCE SYSTEMS FOR LYCEUM TEACHERS PROFESSIONAL DEVELOPMENT

2021 ◽  
pp. 225-230
Author(s):  
Svitlana Lytvynova
Keyword(s):  
Professional Development ◽  
Computer Modeling ◽  
Web Application ◽  
New Technologies ◽  
Full Range ◽  
Open Science ◽  
Educational Process ◽  
Cloud Services ◽  
Modeling Systems ◽  
The World

The article is devoted to the urgent problem of using the tools and services of cloud-oriented systems for the professional development teachers of lyceums as a new type of general secondary education institution as well as the effective use of these tools and services to ensure the quality of specialized education. The purpose of the article is to substantiate the choice of tools and services of cloud-oriented open science systems for the professional development of lyceum teachers. The directions of lyceum teacher’s professional development are determined with the help of such research methods as analysis, generalization, systematization of scientific and scientific-methodical sources on the research problem, and analysis of cloud-oriented tools and services. The author proposes to select tools and services by categories that cover the full range of educational activities of teachers and use innovative approaches and technologies such as open science cloud services and computer modeling systems. The teachers' use of the AiiDA cloud-oriented environment provides access to a number of additional services, such as lecture recordings and interviews on specific aspects and results of groundbreaking research; collections of short training courses on selected topics conducted by renowned lecturers from around the world. The author notes that for biology and chemistry teachers, it would be appropriate to familiarize themselves with the 3DBIONOTES-WS web application (online process modeling), designed for adding biochemical and biomedical information to structural models by scientists from around the world. The author focuses the attention of teachers, in particular natural sciences and mathematics teachers, on the use of competency tasks and computer modeling systems in the educational process. The research provides examples of tasks detailing both areas of long-term teacher development and methodological aspects of new technologies application in educational practice.

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