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Research Advances in Whole-Genome/Exome Sequencing (WGS/WES) and Next-Generation Sequencing

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

Deadline for manuscript submissions: closed (30 May 2024) | Viewed by 2202

Special Issue Editor

Department of Toxicogenomics (TGX), School for Mental Health and Neuroscience (MHeNs), Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
Interests: next-generation sequencing; third-generation sequencing; variant classification models; inherited disease; single-cell sequencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Most inherited diseases form a clinically and genetically heterogeneous group of disorders, which generally manifests in many tissues or organs, causing irreversible progressing disease, e.g., cancer, systemic disease, and age-related disease. However, the use of next-generation sequencing such as whole-exome and whole-genome sequencing has improved the diagnostic yield in the search for disease-causing variants in inherited diseases. Still, many genetically inherited diseases remain little-understood, and more research needs to be carried out to unravel these pathophysiological mechanisms. In current standard bulk analyses on DNA genomics or RNA whole-transcriptomics technologies, biologically relevant pathophysiology differences are not always picked up on. However, new technologies, such as long-read sequencing, are being developed for complex bioinformatic analyses in organs, tissue, or even cells, offering the possibility of determining the whole transcriptome, or whole genome, and also the complete epigenome sequence in less than a day. This opens up a fast treatment strategy in translational science.

This Special Issue aims to provide a current overview of advanced research on whole-genome/exome sequencing (WGS/WES) and next-generation sequencing. Reviews and research papers are encouraged on relevant topics.

Dr. Rick Kamps
Guest Editor

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Keywords

  • short/long-read sequencing
  • whole-exome sequencing
  • whole-genome sequencing
  • bioinformatics
  • variant classification models
  • translational medicine

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Published Papers (2 papers)

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Research

13 pages, 3113 KiB  
Article
Emergence and Comparative Genome Analysis of Salmonella Ohio Strains from Brown Rats, Poultry, and Swine in Hungary
by Ama Szmolka, Zsuzsanna Sréterné Lancz, Fanni Rapcsák and László Egyed
Int. J. Mol. Sci. 2024, 25(16), 8820; https://doi.org/10.3390/ijms25168820 - 13 Aug 2024
Viewed by 941
Abstract
Rats are particularly important from an epidemiological point of view, because they are regarded as reservoirs for diverse zoonotic pathogens including enteric bacteria. This study is the first to report the emergence of Salmonella serovar Ohio in brown rats (Rattus norvegicus) [...] Read more.
Rats are particularly important from an epidemiological point of view, because they are regarded as reservoirs for diverse zoonotic pathogens including enteric bacteria. This study is the first to report the emergence of Salmonella serovar Ohio in brown rats (Rattus norvegicus) and food-producing animals in Hungary. We first reveal the genomic diversity of the strains and their phylogenomic relationships in the context of the international collection of S. Ohio genomes. This pathogen was detected in 4.3% (4/92) of rats, captured from multiple sites in Hungary. A whole-genome-based genotype comparison of S. Ohio, Infantis, Enteritidis, and Typhimurium strains showed that 76.4% (117/153) of the virulence and antimicrobial resistance genes were conserved among these serovars, and none of the genes were specific to S. Ohio. All S. Ohio strains lacked virulence and resistance plasmids. The cgMLST phylogenomic comparison highlighted a close genetic relationship between rat and poultry strains of S. Ohio from Hungary. These strains clustered together with the international S. Ohio genomes from aquatic environments. Overall, this study contributes to our understanding of the epidemiology of Salmonella spp. in brown rats and highlights the importance of monitoring to minimize the public health risk of rodent populations. However, further research is needed to understand the route of infection and evolution of this serovar. Full article
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14 pages, 810 KiB  
Article
Genomic Landscape of Branchio-Oto-Renal Syndrome through Whole-Genome Sequencing: A Single Rare Disease Center Experience in South Korea
by Sung Ho Cho, Sung Ho Jeong, Won Hoon Choi and Sang-Yeon Lee
Int. J. Mol. Sci. 2024, 25(15), 8149; https://doi.org/10.3390/ijms25158149 - 26 Jul 2024
Viewed by 868
Abstract
Branchio-oto-renal (BOR) and branchio-otic (BO) syndromes are characterized by anomalies affecting the ears, often accompanied by hearing loss, as well as abnormalities in the branchial arches and renal system. These syndromes exhibit a broad spectrum of phenotypes and a complex genomic landscape, with [...] Read more.
Branchio-oto-renal (BOR) and branchio-otic (BO) syndromes are characterized by anomalies affecting the ears, often accompanied by hearing loss, as well as abnormalities in the branchial arches and renal system. These syndromes exhibit a broad spectrum of phenotypes and a complex genomic landscape, with significant contributions from the EYA1 gene and the SIX gene family, including SIX1 and SIX5. Due to their diverse phenotypic presentations, which can overlap with other genetic syndromes, molecular genetic confirmation is essential. As sequencing technologies advance, whole-genome sequencing (WGS) is increasingly used in rare disease diagnostics. We explored the genomic landscape of 23 unrelated Korean families with typical or atypical BOR/BO syndrome using a stepwise approach: targeted panel sequencing and exome sequencing (Step 1), multiplex ligation-dependent probe amplification (MLPA) with copy number variation screening (Step 2), and WGS (Step 3). Integrating WGS into our diagnostic pipeline detected structure variations, including cryptic inversion and complex genomic rearrangement, eventually enhancing the diagnostic yield to 91%. Our findings expand the genomic architecture of BOR/BO syndrome and highlight the need for WGS to address the genetic diagnosis of clinically heterogeneous rare diseases. Full article
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