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Next-Generation Sequencing and Whole-Genome Sequencing in Molecular Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 20 September 2024 | Viewed by 1157

Special Issue Editor


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Guest Editor
1. Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL 60501, USA
2. Food Science and Nutrition Department, Illinois Institute of Technology, Chicago, IL 60616, USA
Interests: gene and genome evolution; gene transfers (HGT & EGT); organelle genome, transcriptome, proteome; organelle metabolism; evolution of biochemical pathways; endosymbiosis; reductive evolution; evolutionary history of eukaryotes; evolution of pathogenicity; food safety and microorganisms

Special Issue Information

Dear Colleagues,

Since its emergence approximately two decades ago, High-Throughput or Next-Generation Sequencing (HTS/NGS) has continuously advanced, significantly influencing a wide array of scientific disciplines, including biology, genetics, genomics, physiology, ecology, chemistry, and biochemistry. Researchers and practitioners worldwide, working in governmental, academic, and industrial sectors, have adopted this technology as an essential tool for unraveling profound scientific inquiries, as well as in response to the serious challenges of our times that have tremendous implications for human health and the well-being of plants, animals, and even our planet.

HTS is a fast-moving technology characterized by ongoing improvements in quality, length, depth, and the number of sequences, complemented by innovative breakthroughs in biochemistry, design, and engineering. These developments have led to the introduction of more powerful instruments with increasing throughput power year by year. The numerous applications of HTS, such as Whole-Genome Sequencing (WGS), RNA-Seq, and Amplicon or Shotgun Mass Sequencing, have greatly contributed to the advancement of metagenomics, transcriptomics, proteomics, metabolomics, and phylogenomics, fostering the rapid development of novel investigative, diagnostic, and analytical methods, thus harnessing the full potential of this transformative technology.

Finally, HTS has become one of the main contributors to ‘big data’, a valuable resource for predictive modeling through the application of machine learning and artificial intelligence (AI). In this Special Issue, we cordially invite you to share your HTS-based research and review papers, emphasizing your latest discoveries and the transformative power and influence of this technology, as well as its numerous applications within varied domains of study and organizations.

Dr. Behzad Imanian
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • high-throughput sequencing
  • whole-genome sequencing
  • big data
  • machine learning
  • artificial intelligence
  • predictive modeling
  • transformative technology
  • investigative and diagnostic tools

Published Papers (1 paper)

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Research

15 pages, 602 KiB  
Article
Comparative Analyses of Targeted Myeloid Cancer Next-Generation Sequencing Panel in Fresh Blood, Bone Marrow and FFPE Material
by Andrea Daniela Hobeck, Sophia Wendt, Saskia Krohn, Gudrun Knuebel, Stephan Bartels, Elisa Schipper, Christian Junghanss and Hugo Murua Escobar
Int. J. Mol. Sci. 2024, 25(6), 3534; https://doi.org/10.3390/ijms25063534 - 21 Mar 2024
Viewed by 648
Abstract
Next-generation sequencing is a vital tool for personalized diagnostics and therapies in cancer. Despite numerous advantages, the method depends on multiple parameters regarding the sample material, e.g., sample fixation. A panel’s ability to ensure balanced pre-amplification of the regions of interest is challenging, [...] Read more.
Next-generation sequencing is a vital tool for personalized diagnostics and therapies in cancer. Despite numerous advantages, the method depends on multiple parameters regarding the sample material, e.g., sample fixation. A panel’s ability to ensure balanced pre-amplification of the regions of interest is challenging, especially in targeted sequencing approaches, but of significant importance to its applicability across hematological malignancies and solid tumors. This study comparatively evaluated the technical performance of the commercially available OncomineTM Myeloid Panel in fresh and Formalin-fixed paraffin-embedded (FFPE) material by using an Ion Torrent™ Personal Genome Machine™ System and Ion GeneStudio S5 System platform. In total, 114 samples were analyzed, including 55 fresh materials and 59 FFPE samples. Samples were sequenced with a minimum of one million reads. Amplicons with coverage below 400 reads were classified as underperforming. In fresh material, 49/526 amplicons were identified as performing insufficiently, corresponding with 18 genes. Using FFPE material, 103/526 amplicons underperformed. Independent of input material, regions in 27 genes, including ASXL1, BCOR and BRAF, did not match quality parameters. Subsequently, exemplary mutations were extracted from the Catalogue of Somatic Mutations in Cancer database. This technical evaluation of the OncomineTM Myeloid Panel identified amplicons that do not achieve adequate coverage levels and which need to be considered when interpreting sequencing. Full article
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