Genomic Diagnosis in Next-Generation Sequencing

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Pathology and Molecular Diagnostics".

Deadline for manuscript submissions: closed (24 March 2023) | Viewed by 1950

Special Issue Editors


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Guest Editor
Department of Non-Communicable Disease Epidemiology (NCDE), London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
Interests: gene discovery; computational genomics; genetic epidemiology; statistical genetics; bioinformatics

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Guest Editor
School of Life Sciences, Earlham Institute, Norwich, UK
Interests: bioinformatics; genomics; computational biology; genetics; next generation sequencing; NGS data analysis; genetic analysis; human genetics; transcriptomics; sequencing

Special Issue Information

Dear Colleagues, 

Next generation sequencing (NGS) has provided wide range of opportunity including the genetic diagnosis of a number of diseases. Thanks to its rapid evolution and widespread use in clinical laboratories. Therefore, the need for simpler, easier to interpret clinical genomic diagnoses has never been so acute. We request manuscripts at the interface of clinical genome interpretation journey, from the evaluation of promising whole genome sequence analyses to communication and implementation of clinical outcomes. As many non-specialist clinicians are now faced with their healthy patients having access to their personal genomic information, greater consistency and clarity of standards are needed in order to translate new clinical genomic insight into preventative healthcare. We look forward to receiving rigorous research on current challenges and recommendations for interpreting patient genomes inside and outside of the traditional clinical genetics field, the specialist or non-specialist setting, and future scenarios for precision health systems with genomics at their core for the coming years.

Dr. Segun Fatumo
Dr. Manuel Corpas
Guest Editors

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. Diagnostics is an international peer-reviewed open access semimonthly 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

  • gene discovery
  • computational genomics
  • genetic epidemiology
  • statistical genetics
  • bioinformatics
  • bioinformatics
  • genomics
  • computational biology
  • genetics
  • next generation sequencing
  • NGS data analysis
  • genetic analysis
  • human genetics
  • transcriptomics
  • sequencing

Published Papers (1 paper)

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Research

12 pages, 9005 KiB  
Article
Simultaneous Analysis of Bacterial and Fungal Communities in Oral Samples from Intubated Patients in Intensive Care Unit
by Yuri Song, Myoung Soo Kim, Jin Chung and Hee Sam Na
Diagnostics 2023, 13(10), 1784; https://doi.org/10.3390/diagnostics13101784 - 18 May 2023
Cited by 1 | Viewed by 1427
Abstract
Intubated patients in intensive care units (ICUs) too frequently contract ventilator-associated pneumonia or Candida infections. Oropharyngeal microbes are believed to play an important etiologic role. This study was undertaken to determine whether next-generation sequencing (NGS) can be used to simultaneously analyze bacterial and [...] Read more.
Intubated patients in intensive care units (ICUs) too frequently contract ventilator-associated pneumonia or Candida infections. Oropharyngeal microbes are believed to play an important etiologic role. This study was undertaken to determine whether next-generation sequencing (NGS) can be used to simultaneously analyze bacterial and fungal communities. Buccal samples were collected from intubated ICU patients. Primers targeting the V1-V2 region of bacterial 16S rRNA and the internal transcribed spacer 2 (ITS2) region of fungal 18S rRNA were used. V1-V2, ITS2, or mixed V1-V2/ITS2 primers were used to prepare an NGS library. Bacterial and fungal relative abundances were comparable for V1-V2, ITS2, or mixed V1-V2/ITS2 primers, respectively. A standard microbial community was used to adjust the relative abundances to theoretical abundance, and NGS and RT-PCR-adjusted relative abundances showed a high correlation. Using mixed V1-V2/ITS2 primers, bacterial and fungal abundances were simultaneously determined. The constructed microbiome network revealed novel interkingdom and intrakingdom interactions, and the simultaneous detection of bacterial and fungal communities using mixed V1-V2/ITS2 primers enabled analysis across two kingdoms. This study provides a novel approach to simultaneously determining bacterial and fungal communities using mixed V1-V2/ITS2 primers. Full article
(This article belongs to the Special Issue Genomic Diagnosis in Next-Generation Sequencing)
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