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Technological Advances around Next-Generation Sequencing Application

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Bioinformatics and Systems Biology".

Deadline for manuscript submissions: closed (20 November 2024) | Viewed by 2113

Special Issue Editor


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Guest Editor
Immunogenetics Laboratory, Pathology and Laboratory Medicine, Temple University and Hospital, Lewis Katz School of Medicine, 3401 N. Broad St., Office B242, Philadelphia, PA 19140, USA
Interests: next-generation sequencing; single-cell sequencing; metagenomics; epigenomics; precision medicine

Special Issue Information

Dear Colleagues,

Next-generation sequencing (NGS) has revolutionized genomics and molecular biology since its inception, enabling rapid and cost-effective sequencing of DNA and RNA to investigate genetic variations linked to diseases or other biological events. The common steps of the NGS experiment are library preparation, clonal amplification, sequencing, and data analysis, regardless of the instrument technology employed. The NGS technology is transforming many life science fields all over the world, suggesting that it can be a valuable tool in the field and may undergo a significant change in the years to come. Technological advances surrounding NGS applications denote the ongoing enhancements and innovations in the methodologies, instruments, and computational tools utilized for the efficient and high-throughput sequencing of DNA and RNA molecules. Key developments include the emergence of single-cell sequencing techniques, which enable the characterization of cellular heterogeneity within complex tissues and populations, and long-read sequencing technologies that facilitate the assembly of genomes, detection of structural variants, and analysis of repetitive regions with unprecedented accuracy. Metagenomics, which is another area of rapid progress, leverages NGS to explore microbial communities in diverse environments, revealing their composition, dynamics, and functional potential. Furthermore, advances in epigenomic sequencing methods allow clinicians and scientists to map DNA methylation patterns, histone modifications, and chromatin accessibility, thereby providing insights into gene regulation and cellular differentiation. In the realm of clinical applications, NGS has revolutionized molecular diagnostics, enabling the identification of genetic variants underlying inherited diseases, cancer susceptibility, and pharmacogenetic traits. Other notable advancements include the use of NGS-based liquid biopsies for the non-invasive detection of tumor-derived nucleic acids in bodily fluids and the integration of NGS with CRISPR-based technologies for functional genomics studies and genome editing applications.

This Special Issue is supervised by Dr. Gaurav Tripathi and assisted by Dr. Minal B Tripathi (University of Calgary, AB, Canada and BioAro.com).

Dr. Gaurav Tripathi
Guest Editor

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Keywords

  • next-generation sequencing
  • single-cell sequencing
  • long-read sequencing
  • metagenomics
  • epigenomics
  • cancer genomics
  • clinical applications
  • liquid biopsy
  • CRISPR-Cas9
  • precision medicine
  • personalized healthcare

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Published Papers (2 papers)

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Research

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16 pages, 2842 KiB  
Article
Using NGS to Uncover the Corruption of a Peptide Phage Display Selection
by Danna Kamstrup Sell, Babak Bakhshinejad, Anders Wilgaard Sinkjaer, Ida Melissa Dawoodi, Mette Neiegaard Wiinholt, Ane Beth Sloth, Camilla Stavnsbjerg and Andreas Kjaer
Curr. Issues Mol. Biol. 2024, 46(9), 10590-10605; https://doi.org/10.3390/cimb46090627 - 21 Sep 2024
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Abstract
Phage display has been widely used to identify peptides binding to a variety of biological targets. In the current work, we planned to select novel peptides targeting CD4 through screening of a commercial phage display library (New England Biolabs Ph.D.TM-7). After [...] Read more.
Phage display has been widely used to identify peptides binding to a variety of biological targets. In the current work, we planned to select novel peptides targeting CD4 through screening of a commercial phage display library (New England Biolabs Ph.D.TM-7). After three rounds of biopanning, 57 phage clones were Sanger-sequenced. These clones represented 30 unique peptide sequences, which were subjected to phage ELISA, resulting in the identification of two potential target binders. Following peptide synthesis, downstream characterization was conducted using fluorescence plate-based assay, flow cytometry, SPR, and confocal microscopy. The results revealed that neither of the peptides identified in the Sanger-based phage display selection exhibited specific binding toward CD4. The naïve library and the phage pool recovered from the third round of biopanning were then subjected to next-generation sequencing (NGS). The results of NGS indicated corruption of the selection output by a phage already known as a fast-propagating clone whose target-unrelated enrichment can shed light on the misidentification of target-binding peptides through phage display. This work provides an in-depth insight into some of the challenges encountered in peptide phage display selection. Furthermore, our data highlight that NGS, by exploring a broader sequence space and providing a more precise picture of the composition of biopanning output, can be used to refine the selection protocol and avoid misleading the process of ligand identification. We hope that these findings can describe some of the complexities of phage display selection and offer help to fellow researchers who have faced similar situations. Full article
(This article belongs to the Special Issue Technological Advances around Next-Generation Sequencing Application)
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Review

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23 pages, 790 KiB  
Review
From Genomic Exploration to Personalized Treatment: Next-Generation Sequencing in Oncology
by Vishakha Vashisht, Ashutosh Vashisht, Ashis K. Mondal, Jana Woodall and Ravindra Kolhe
Curr. Issues Mol. Biol. 2024, 46(11), 12527-12549; https://doi.org/10.3390/cimb46110744 - 6 Nov 2024
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Abstract
Next-generation sequencing (NGS) has revolutionized personalized oncology care by providing exceptional insights into the complex genomic landscape. NGS offers comprehensive cancer profiling, which enables clinicians and researchers to better understand the molecular basis of cancer and to tailor treatment strategies accordingly. Targeted therapies [...] Read more.
Next-generation sequencing (NGS) has revolutionized personalized oncology care by providing exceptional insights into the complex genomic landscape. NGS offers comprehensive cancer profiling, which enables clinicians and researchers to better understand the molecular basis of cancer and to tailor treatment strategies accordingly. Targeted therapies based on genomic alterations identified through NGS have shown promise in improving patient outcomes across various cancer types, circumventing resistance mechanisms and enhancing treatment efficacy. Moreover, NGS facilitates the identification of predictive biomarkers and prognostic indicators, aiding in patient stratification and personalized treatment approaches. By uncovering driver mutations and actionable alterations, NGS empowers clinicians to make informed decisions regarding treatment selection and patient management. However, the full potential of NGS in personalized oncology can only be realized through bioinformatics analyses. Bioinformatics plays a crucial role in processing raw sequencing data, identifying clinically relevant variants, and interpreting complex genomic landscapes. This comprehensive review investigates the diverse NGS techniques, including whole-genome sequencing (WGS), whole-exome sequencing (WES), and single-cell RNA sequencing (sc-RNA-Seq), elucidating their roles in understanding the complex genomic/transcriptomic landscape of cancer. Furthermore, the review explores the integration of NGS data with bioinformatics tools to facilitate personalized oncology approaches, from understanding tumor heterogeneity to identifying driver mutations and predicting therapeutic responses. Challenges and future directions in NGS-based cancer research are also discussed, underscoring the transformative impact of these technologies on cancer diagnosis, management, and treatment strategies. Full article
(This article belongs to the Special Issue Technological Advances around Next-Generation Sequencing Application)
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