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Applied Genomics: Bridging the Gap between R&D and Practical Implementations...
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Applied Genomics: Bridging the Gap between R&D and Practical Implementations within Clinical and Public Health Settings

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (15 June 2021) | Viewed by 13062

Special Issue Editor

Dr. Kevin Vanneste

E-Mail Website
Guest Editor
Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
Interests: bioinformatics; next-generation sequencing; public health; pathogen typing and characterization

Special Issue Information

Dear Colleagues,

Spurred by the rapid development of different next-generation sequencing technologies, increasing quantities of whole-genome sequencing data can be produced at decreasing costs. Consequently, genomics has become a well-established methodology that has demonstrated its merit in countless research and development programs within the life sciences. Within applied clinical and public health settings, ample case studies have documented its benefit for many microbial pathogens of interest in clinical and public health settings, and public health genomics.

Nevertheless, a gap still exists between the acclaimed success and the everyday practical implementation of this technology. Bridging this gap will require an integrated approach bringing together experts from different fields: bioinformaticians developing tools to analyze genomics data, microbiologists performing routine pathogen typing and characterization, epidemiologists and public health experts integrating applied genomics data, clinicians making informed decisions based on the output of such applications, quality experts monitoring and validating applied genomics implementations, and policy makers translating these applications into guidelines and regulations.

The aim of this Special Issue is therefore to address this gap by demonstrating how applied genomics is currently maturing by welcoming recent work and current review articles that showcase practical implementations of applied genomics within clinical and public health settings.

Dr. Kevin Vanneste
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Next-generation sequencing
  • Bioinformatics
  • Clinical genomics
  • Public health genomics
  • Pathogen typing and characterization
  • Public health and surveillance
  • Validation

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Published Papers (3 papers)

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19 pages, 2576 KiB  
Article
Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS
by Carlus Deneke, Holger Brendebach, Laura Uelze, Maria Borowiak, Burkhard Malorny and Simon H. Tausch
Genes 2021, 12(5), 644; https://doi.org/10.3390/genes12050644 - 26 Apr 2021
Cited by 48 | Viewed by 4701
Abstract
Sequencing of whole microbial genomes has become a standard procedure for cluster detection, source tracking, outbreak investigation and surveillance of many microorganisms. An increasing number of laboratories are currently in a transition phase from classical methods towards next generation sequencing, generating unprecedented amounts [...] Read more.
Sequencing of whole microbial genomes has become a standard procedure for cluster detection, source tracking, outbreak investigation and surveillance of many microorganisms. An increasing number of laboratories are currently in a transition phase from classical methods towards next generation sequencing, generating unprecedented amounts of data. Since the precision of downstream analyses depends significantly on the quality of raw data generated on the sequencing instrument, a comprehensive, meaningful primary quality control is indispensable. Here, we present AQUAMIS, a Snakemake workflow for an extensive quality control and assembly of raw Illumina sequencing data, allowing laboratories to automatize the initial analysis of their microbial whole-genome sequencing data. AQUAMIS performs all steps of primary sequence analysis, consisting of read trimming, read quality control (QC), taxonomic classification, de-novo assembly, reference identification, assembly QC and contamination detection, both on the read and assembly level. The results are visualized in an interactive HTML report including species-specific QC thresholds, allowing non-bioinformaticians to assess the quality of sequencing experiments at a glance. All results are also available as a standard-compliant JSON file, facilitating easy downstream analyses and data exchange. We have applied AQUAMIS to analyze ~13,000 microbial isolates as well as ~1000 in-silico contaminated datasets, proving the workflow’s ability to perform in high throughput routine sequencing environments and reliably predict contaminations. We found that intergenus and intragenus contaminations can be detected most accurately using a combination of different QC metrics available within AQUAMIS. Full article
(This article belongs to the Special Issue Applied Genomics: Bridging the Gap between R&D and Practical Implementations within Clinical and Public Health Settings)
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13 pages, 633 KiB  
Article
Investigating the Adoption of Clinical Genomics in Australia. An Implementation Science Case Study
by Stephanie Best, Janet C. Long, Clara Gaff, Jeffrey Braithwaite and Natalie Taylor
Genes 2021, 12(2), 317; https://doi.org/10.3390/genes12020317 - 23 Feb 2021
Cited by 11 | Viewed by 4144
Abstract
Despite the overwhelming interest in clinical genomics, uptake has been slow. Implementation science offers a systematic approach to reveal pathways to adoption and a theory informed approach to addressing barriers presented. Using case study methodology, we undertook 16 in-depth interviews with nongenetic medical [...] Read more.
Despite the overwhelming interest in clinical genomics, uptake has been slow. Implementation science offers a systematic approach to reveal pathways to adoption and a theory informed approach to addressing barriers presented. Using case study methodology, we undertook 16 in-depth interviews with nongenetic medical specialists to identify barriers and enablers to the uptake of clinical genomics. Data collection and analysis was guided by two evidence-based behaviour change models: the Theoretical Domains Framework (TDF), and the Capability, Opportunity Motivation Behaviour model (COM-B). Our findings revealed the use of implementation science not only provided a theoretical structure to frame the study but also facilitated uncovering of traditionally difficult to access responses from participants, e.g., “safety in feeling vulnerable” (TDF code emotion/COM-B code motivation). The most challenging phase for participants was ensuring appropriate patients were offered genomic testing. There were several consistent TDF codes: professional identity, social influences, and environmental context and resources and COM-B codes opportunity and motivation, with others varying along the patient journey. We conclude that implementation science methods can maximise the value created by the exploration of factors affecting the uptake of clinical genomics to ensure future interventions are designed to meet the needs of novice nongenetic medical specialists. Full article
(This article belongs to the Special Issue Applied Genomics: Bridging the Gap between R&D and Practical Implementations within Clinical and Public Health Settings)
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12 pages, 569 KiB  
Opinion
Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation
by Caroline Barretto, Cristian Rincón, Anne-Catherine Portmann and Catherine Ngom-Bru
Genes 2021, 12(2), 275; https://doi.org/10.3390/genes12020275 - 15 Feb 2021
Cited by 9 | Viewed by 3545
Abstract
Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking in the food industry thanks to several developments in recent years. However, the cost associated to this technology and the degree of expertise required to accurately process and [...] Read more.
Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking in the food industry thanks to several developments in recent years. However, the cost associated to this technology and the degree of expertise required to accurately process and understand the data has limited its adoption at a wider scale. Additionally, the time needed to obtain actionable information is often seen as an impairment for the application and use of the information generated via WGS. Ongoing work towards standardization of wet lab including sequencing protocols, following guidelines from the regulatory authorities and international standardization efforts make the technology more and more accessible. However, data analysis and results interpretation guidelines are still subject to initiatives coming from distinct groups and institutions. There are multiple bioinformatics software and pipelines developed to handle such information. Nevertheless, little consensus exists on a standard way to process the data and interpret the results. Here, we want to present the constraints we face in an industrial setting and the steps we consider necessary to obtain high quality data, reproducible results and a robust interpretation of the obtained information. All of this, in a time frame allowing for data-driven actions supporting factories and their needs. Full article
(This article belongs to the Special Issue Applied Genomics: Bridging the Gap between R&D and Practical Implementations within Clinical and Public Health Settings)
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