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Technological Advances Around Next-Generation Sequencing Application, 2nd Edition

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: 28 February 2027 | Viewed by 2032

Editor

Dr. Gaurav Tripathi

E-Mail Website
Guest Editor
Kashi Clinical Laboratory, Portland, OR 97219, USA
Interests: next-generation sequencing; single-cell sequencing; metagenomics; epigenomics; precision medicine
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Technological Advances Around Next-Generation Sequencing Application”.

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.

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 (4 papers)

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Research

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21 pages, 10363 KB  
Article
Uncovering Functional Genetic Variation in the Indigenous Greek Eghoria Goat: An Integrative Genome-Wide Discovery and Validation Approach
by Maria-Anna Kyrgiafini, Georgios Stamatellos, Costas Stamatis and Zissis Mamuris
Curr. Issues Mol. Biol. 2026, 48(8), 778; https://doi.org/10.3390/cimb48080778 - 30 Jul 2026
Viewed by 343
Abstract
The Eghoria goat constitutes the major indigenous goat population in Greece and represents an important genetic resource. Despite its significance, genomic information remains scarce. This study aimed to investigate coding variation in the Eghoria goat using whole-genome sequencing (WGS), with particular focus on [...] Read more.
The Eghoria goat constitutes the major indigenous goat population in Greece and represents an important genetic resource. Despite its significance, genomic information remains scarce. This study aimed to investigate coding variation in the Eghoria goat using whole-genome sequencing (WGS), with particular focus on missense single nucleotide polymorphisms (SNPs) and coding insertions/deletions (indels). Whole-genome sequencing was performed on Eghoria goats (n = 6), followed by bioinformatic processing and variant filtering. Functional characterization was conducted through Gene Ontology (GO) and KEGG pathway analyses (FDR < 0.05). Normalized variant density metrics identified highly polymorphic genes. Selected missense SNPs were validated in an independent population (n = 54) using MassARRAY genotyping. Whole-genome analysis identified 10,796,211 SNPs and 1,022,779 indels. After prioritization, 15,949 missense SNPs and 861 indels were retained. Functional enrichment analyses highlighted pathways related to metabolism, ion transport, calcium signaling, immune function, transcriptional regulation, and environmental adaptation. Genes exhibiting elevated polymorphism density included olfactory receptor family members, and loci associated with metabolic regulation. Validation analyses confirmed the presence of selected variants in the Eghoria goat population. The study expands current knowledge of genomic diversity in the indigenous Eghoria goat and provides valuable resources for future genetic improvement, conservation, and breeding programs. Full article
(This article belongs to the Special Issue Technological Advances Around Next-Generation Sequencing Application, 2nd Edition)
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28 pages, 11956 KB  
Article
Comparative Whole Genome Analysis and Targeted Validation of Variants in Three Greek Indigenous Sheep Breeds
by Maria-Anna Kyrgiafini, Georgios Stamatellos, Costas Stamatis and Zissis Mamuris
Curr. Issues Mol. Biol. 2026, 48(5), 480; https://doi.org/10.3390/cimb48050480 - 5 May 2026
Cited by 1 | Viewed by 686
Abstract
Indigenous sheep breeds represent valuable reservoirs of genetic diversity shaped by long-term adaptation to local environments and management systems. Greek autochthonous sheep breeds remain underrepresented in genomic and functional studies. The objective of this study was to characterize and compare coding sequence variation [...] Read more.
Indigenous sheep breeds represent valuable reservoirs of genetic diversity shaped by long-term adaptation to local environments and management systems. Greek autochthonous sheep breeds remain underrepresented in genomic and functional studies. The objective of this study was to characterize and compare coding sequence variation in three indigenous Greek sheep breeds—Lesvos (LES), Serres (SER), and Thrace (THR)—and to identify shared and breed-associated functional patterns. The study was designed using a two-stage approach, comprising a discovery (exploratory) phase and a validation phase. In the discovery phase, whole genome sequencing data (one animal per breed; total n = 3; mean sequencing depth ~36.9×) were analyzed to identify protein-altering exonic variants, focusing on missense single-nucleotide polymorphisms (SNPs) and exonic insertions/deletions (indels). Variants were examined at breed-specific and comparative levels, followed by functional enrichment analyses using Gene Ontology (GO) and KEGG pathways. Normalized variant density metrics identified genes with elevated polymorphism levels. In the validation phase, a subset of prioritized missense SNPs was genotyped in an independent cohort of 54 animals (18 per breed) using MassARRAY genotyping. Genes harboring prioritized missense SNPs showed a conserved enrichment profile across breeds, dominated by genome maintenance, DNA repair, cytoskeletal organization, and core regulatory functions. Distinct breed-associated patterns were also observed. LES showed enrichment in metabolic, biosynthetic, and sensory-related processes, SER in regulatory and signaling functions, and THR in cytoskeletal, extracellular matrix, and organelle-associated pathways. Polymorphism density analyses highlighted highly variable genes across breeds, including olfactory receptor (OR) gene families, keratin-associated protein genes (KRTAPs), and loci involved in immune and regulatory functions (e.g., PRKDC, CDH15). The validation phase confirmed the expected allele frequency patterns for most prioritized SNPs, supporting the robustness of the approach. This study identifies functionally relevant coding variation across Greek indigenous sheep breeds, revealing conserved genomic patterns and breed-associated signatures linked to metabolic, structural, and regulatory processes. Full article
(This article belongs to the Special Issue Technological Advances Around Next-Generation Sequencing Application, 2nd Edition)
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Review

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24 pages, 1832 KB  
Review
Technological Advances in Molecular Diagnostic Methods for Hereditary Diseases in Preconception and Prenatal Settings
by Deyuan Kong, Jianing Zhao, Haichang Diao, Shuyao Qiu, Yuanyuan Peng and Tingting Liu
Curr. Issues Mol. Biol. 2026, 48(8), 756; https://doi.org/10.3390/cimb48080756 - 25 Jul 2026
Viewed by 264
Abstract
Precision prevention and control of genetic diseases represent a major public health challenge. This paper provides a structured narrative review of advances in molecular diagnostic technologies across the preconception, preimplantation, and prenatal stages over the past five years. In the preconception phase, next-generation [...] Read more.
Precision prevention and control of genetic diseases represent a major public health challenge. This paper provides a structured narrative review of advances in molecular diagnostic technologies across the preconception, preimplantation, and prenatal stages over the past five years. In the preconception phase, next-generation sequencing has become central to carrier screening, while long-read sequencing significantly enhances detection capabilities for complex variants. In the preimplantation phase, research has increasingly focused on non-invasive preimplantation genetic testing, leveraging maternal contamination quantification algorithms and deep learning models to address DNA contamination challenges. During the prenatal phase, stratified diagnostic strategies combining chromosomal microarray analysis and whole-exome sequencing have improved the diagnostic evaluation of fetal structural anomalies. Simultaneously, non-invasive prenatal testing is expanding to include microdeletion/duplication and monogenic disease screening, though positive screening results still require invasive diagnostic confirmation. Future trends lie in multi-technology integration, multi-omics data fusion, and artificial intelligence-assisted decision-making, aiming to enhance resolution while balancing health-economic considerations and ethical standards. Full article
(This article belongs to the Special Issue Technological Advances Around Next-Generation Sequencing Application, 2nd Edition)
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22 pages, 3499 KB  
Review
Next-Generation Sequencing in Pulmonary Fibrosis: Translational Promise and Current Clinical Limitations
by Raffaella Pagliaro, Fabio Perrotta, Stefano Sanduzzi Zamparelli, Valerio Maria Carrozzo, Alfredo Cipriano, Michele Mondoni, Giulia Maria Stella, Andrea Bianco and Filippo Scialò
Curr. Issues Mol. Biol. 2026, 48(7), 721; https://doi.org/10.3390/cimb48070721 - 15 Jul 2026
Viewed by 323
Abstract
Pulmonary fibrosis (PF), particularly idiopathic pulmonary fibrosis (IPF), is a progressive and often fatal interstitial lung disease characterised by complex genetic and molecular heterogeneity. Traditional diagnostic approaches, which rely on clinical, radiological and histopathological assessment, are frequently insufficient to capture the underlying biological [...] Read more.
Pulmonary fibrosis (PF), particularly idiopathic pulmonary fibrosis (IPF), is a progressive and often fatal interstitial lung disease characterised by complex genetic and molecular heterogeneity. Traditional diagnostic approaches, which rely on clinical, radiological and histopathological assessment, are frequently insufficient to capture the underlying biological diversity of the disease. The advent of next-generation sequencing (NGS) has substantially advanced the understanding of PF by enabling comprehensive genomic and transcriptomic profiling. NGS technologies, including whole-exome sequencing (WES), whole-genome sequencing (WGS), RNA sequencing (RNA-seq), and targeted gene panels, have uncovered key genetic determinants. These include mutations in telomere-related genes (TERT, TERC, RTEL1) and surfactant-related genes (SFTPC, SFTPA2), as well as common variants like the MUC5B promoter polymorphism. These discoveries have clarified disease pathogenesis, revealed polygenic risk models, and may improve diagnostic accuracy, particularly in distinguishing overlapping interstitial lung disease (ILD) phenotypes. Beyond genetics, transcriptomic analyses have identified dysregulated pathways, including TGF-β, Wnt/β-catenin, and PI3K/Akt signalling, and have enabled the discovery of novel biomarkers for prognosis and therapeutic response. In selected clinical settings, NGS is beginning to support patient stratification and inform management decisions. Emerging applications, including liquid biopsy and integration with artificial intelligence, further expand the potential clinical utility of NGS. Despite challenges related to cost, data interpretation and standardisation, NGS represents a powerful research tool in PF. Full article
(This article belongs to the Special Issue Technological Advances Around Next-Generation Sequencing Application, 2nd Edition)
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