scholarly journals Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access

2017 ◽  
Vol 8 ◽  
Author(s):  
Eduardo N. Taboada ◽  
Morag R. Graham ◽  
João A. Carriço ◽  
Gary Van Domselaar
Keyword(s):  
Next Generation Sequencing ◽  
Food Safety ◽  
Open Data ◽  
Data Access ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals The use of next generation sequencing for improving food safety: Translation into practice

2019 ◽  
Vol 79 ◽  
pp. 96-115 ◽  
Author(s):  
Balamurugan Jagadeesan ◽  
Peter Gerner-Smidt ◽  
Marc W. Allard ◽  
Sébastien Leuillet ◽  
Anett Winkler ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Food Safety ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Next-generation sequencing: The future of molecular genetics in poultry production and food safety

2013 ◽  
Vol 92 (2) ◽  
pp. 562-572 ◽  
Author(s):  
S. Diaz-Sanchez ◽  
I. Hanning ◽  
Sean Pendleton ◽  
Doris D'Souza
Keyword(s):  
Next Generation Sequencing ◽  
Food Safety ◽  
Molecular Genetics ◽  
Poultry Production ◽  
Next Generation ◽  
The Future ◽  
Generation Sequencing

scholarly journals Towards reproducible, transparent, and systematic benchmarking of omics computational tools

2018 ◽  
Author(s):  
SERGHEI MANGUL ◽  
Lana S. Martin ◽  
Brian Hill ◽  
Angela Ka-Mei Lam ◽  
Margaret Distler ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Technological Innovation ◽  
Open Data ◽  
Genomic Data ◽  
Data Representation ◽  
Omics Data ◽  
Next Generation ◽  
Computational Tools ◽  
Technological Advances ◽  
Generation Sequencing

Rapid technological advances, such as the development of next-generation sequencing, are driving the need for comprehensive computational tools to analyse the wealth of generated genomic data. Systematic benchmarking has been successful in many research disciplines to help non-computational researchers evaluate the accuracy and applicability of new computational tools. Adopting a standardized benchmarking practice and following established principles for the design of new benchmarking studies could help researchers using omics data to better leverage technological innovation. In this Review, we propose step-by-step instructions for increasing reusability, transparency, and reproducibility of benchmarking studies by using containerization, common data representation, open data, and systematic parameter description.

scholarly journals Next generation sequencing applied to food safety. A new professional profile

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
M Recchioni ◽  
S Pompei ◽  
C Cammà ◽  
V Castello ◽  
F Cito ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Food Safety ◽  
Soft Skills ◽  
Field Research ◽  
European Level ◽  
Next Generation ◽  
Continuous Training ◽  
Research Activities ◽  
Professional Profile ◽  
Generation Sequencing

Abstract The advent of “omics” is transforming Biological Sciences. Next Generation Sequencing (NGS) in Food Safety represents a challenge for Clinical Microbiology and Public Health. A new professional profile which combines different domains represents a strategic lever to increase competitiveness in this field. The Erasmus+ project Learning Genomics for Food Safety(LEGO) is aimed at defining an innovative profile, the Food Microbial Bioinformatician (FMB), a professional able to use NGS technologies applied to the analysis of food-borne pathogens. FMB bridges diverse professional areas within processes integrating Genomics, Computer Science, Statistics and Microbiology. It mixes hard/technical and soft skills and competencies to be applied in different sectors. LEGO is carried out by a European consortium (UH, UTP,UNIVAQ, AINIA, UdAnet), led by IZSAM.Desk and in-field research activities have been conducted at European level to define the FMB profile, leveraging on: national/international professional classification; the 4C model, clustering the profile in 4 areas of hard and soft skills(primary - cognitive, individual, social; organisational interpersonal behaviours). The new profile development process is made of three key phaces. First of all, a questionnaire has been delivered to almost 50 experts within the Consortium to set the draft scheme concerning FMB roles, activities and competences. Secondly, a broad range of relevant stakeholders have beeninvolved for deepening relevance, frequency and complexity of each professional dimension. Finally, the collected information guided the Consortium through the validation of the new profile at the European level. The definition of a comprehensive, standard FMB profileallows to: analyse existing curricula and training gaps; ground customised modular training programmes to fill in the gaps; increase Food Safety, promoting continuous training in a sector strongly influenced by the evolution of technology. Key messages Professional excellence bridging different areas (both scientific and technical). Health System innovation for wellbeing and professional development of carrier pathways and mobility.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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