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Bioinformatic Analysis of NGS Data
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Bioinformatic Analysis of NGS Data

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: closed (20 June 2022) | Viewed by 21267

Special Issue Editors

Dr. Qiongyi Zhao

E-Mail Website
Guest Editor
Queensland Brain Institute, The University of Queensland, Brisbane 4072, Australia
Interests: next generation sequencing; RNA-Seq; circular RNA; extrachromosomal circular DNA; epigenomics; whole-exome sequencing; whole-genome sequencing; neuroscience
Dr. Pei Hao

E-Mail Website
Guest Editor
Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
Interests: next generation sequencing; RNA Editing; big data, pathogen; evolution

Special Issue Information

Dear Colleagues,

With the fast advances in next generation sequencing (NGS) technologies, NGS and its associated bioinformatic analysis techniques have revolutionised omics disciplines over the past 15 years.  There are two major paradigms in NGS technologies: short-read sequencing and long-read sequencing. Short-read sequencing, such as Illumina, offers cost-effective and high-accuracy data that have wide applications for research in genomics, transcriptomics, and epigenomics. By contrast, long-read sequencing, such as Oxford Nanopore and PacBio, is well-tailored for applications like de novo assembly and/or full-length sequencing for RNA, circular RNAs, extrachromosomal circular DNA elements, etc. Analysis of NGS data utilizes bioinformatic approaches to convert signals from sequencing platforms to biologically meaningful information. Unsurprisingly, an array of bioinformatic analysis strategies and tools is emerging to cope with a wide range of NGS applications.

This Special Issue in Genes will focus on the bioinformatic analysis of NGS data and the applications of NGS in various research areas. We welcome original articles, new methods and reviews covering any aspect of NGS data analysis.

We look forward to receiving your contributions.

Dr. Qiongyi Zhao
Dr. Pei Hao
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. Genes is an international peer-reviewed open access monthly 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

  • next generation sequencing
  • bioinformatic analysis
  • genomics
  • transcriptomics
  • epigenomics
  • NGS applications

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Published Papers (6 papers)

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Research

14 pages, 2021 KiB  
Communication
Optimization of Oxford Nanopore Technology Sequencing Workflow for Detection of Amplicons in Real Time Using ONT-DART Tool
by Robert Player, Kathleen Verratti, Andrea Staab, Ellen Forsyth, Amanda Ernlund, Mihir S. Joshi, Rebecca Dunning, David Rozak, Sarah Grady, Bruce Goodwin and Shanmuga Sozhamannan
Genes 2022, 13(10), 1785; https://doi.org/10.3390/genes13101785 - 3 Oct 2022
Cited by 3 | Viewed by 3900
Abstract
An optimized, well-tested and validated targeted genomic sequencing-based high-throughput assay is currently not available ready for routine biodefense and biosurveillance applications. Earlier, we addressed this gap by developing and establishing baseline comparisons of a multiplex end-point Polymerase Chain Reaction (PCR) assay followed by [...] Read more.
An optimized, well-tested and validated targeted genomic sequencing-based high-throughput assay is currently not available ready for routine biodefense and biosurveillance applications. Earlier, we addressed this gap by developing and establishing baseline comparisons of a multiplex end-point Polymerase Chain Reaction (PCR) assay followed by Oxford Nanopore Technology (ONT) based amplicon sequencing to real time PCR and customized data processing. Here, we expand upon this effort by identifying the optimal ONT library preparation method for integration into a novel software platform ONT-DART (ONT-Detection of Amplicons in Real-Time). ONT-DART is a dockerized, real-time, amplicon-sequence analysis workflow that is used to reproducibly process and filter read data to support actionable amplicon detection calls based on alignment metrics, within sample statistics, and no-template control data. This analysis pipeline was used to compare four ONT library preparation protocols using R9 and Flongle (FL) flow cells. The two 4-Primer methods tested required the shortest preparation times (5.5 and 6.5 h) for 48 libraries but provided lower fidelity data. The Native Barcoding and Ligation methods required longer preparation times of 8 and 12 h, respectively, and resulted in higher overall data quality. On average, data derived from R9 flow cells produced true positive calls for target organisms more than twice as fast as the lower throughput FL flow cells. These results suggest that utilizing the R9 flowcell with an ONT Native Barcoding amplicon library method in combination with ONT-DART platform analytics provides the best sequencing-based alternative to current PCR-based biodetection methods. Full article
(This article belongs to the Special Issue Bioinformatic Analysis of NGS Data)
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16 pages, 7504 KiB  
Article
Comprehensive Analysis of HMCN1 Somatic Mutation in Clear Cell Renal Cell Carcinoma
by Ziqi Gong, Xiaowen Wu, Qian Guo, Haizhen Du, Fenghao Zhang and Yan Kong
Genes 2022, 13(7), 1282; https://doi.org/10.3390/genes13071282 - 20 Jul 2022
Cited by 5 | Viewed by 2564
Abstract
Background: Renal cell carcinoma (RCC) is a common malignancy of the genitourinary system and clear cell renal cell carcinoma (ccRCC) is the most representative subtype. The morbidity and mortality of ccRCC have gradually risen during recent years; however, the pathogenesis and potential biomarkers [...] Read more.
Background: Renal cell carcinoma (RCC) is a common malignancy of the genitourinary system and clear cell renal cell carcinoma (ccRCC) is the most representative subtype. The morbidity and mortality of ccRCC have gradually risen during recent years; however, the pathogenesis and potential biomarkers remain unclear. The purpose of our study was to find out prognostic genes correlated with somatic mutation and the underlying mechanisms of HMCN1 mutation in ccRCC. Methods: Somatic mutation data of two ccRCC cohorts were acquired from TCGA and cBioPortal. Genes frequently mutated in both datasets were extracted, from which tumor mutation burden and survival analysis revealed three prognostic genes. Further comprehensive analysis of HMCN1 mutation was carried out to identify differentially expressed genes and apply functional annotations. The correlation of HMCN1 mutation and tumor immunity was also evaluated. Results: HMCN1, SYNE1, and BAP1 mutations were associated with both tumor mutation burden and clinical prognosis in ccRCC. Gene enrichment analysis suggested the effects of HMCN1 mutation on biological processes and pathways linked to energy metabolism. HMCN1 mutation was also correlated with anti-tumor immunity. There were several limitations in the sample size and cohort availability of the present computational study. Conclusions: The present results inferred that HMCN1 mutation might have an important clinical significance for ccRCC patients by regulating metabolism and the immune microenvironment. Full article
(This article belongs to the Special Issue Bioinformatic Analysis of NGS Data)
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13 pages, 2004 KiB  
Article
Dynamics of the Gut Microbiome and Transcriptome in Korea Native Ricefish (Oryzias latipes) during Chronic Antibiotic Exposure
by Ju Bin Yoon, Sungmin Hwang, Jun Hyeok Yang, Seungki Lee, Woo Young Bang and Ki Hwan Moon
Genes 2022, 13(7), 1243; https://doi.org/10.3390/genes13071243 - 14 Jul 2022
Cited by 6 | Viewed by 2428
Abstract
Antibiotics have been widely used to inhibit microbial growth and to control bacterial infection; however, they can trigger an imbalance in the gut flora of the host and dysregulate the host gene regulatory system when discharged into the aquatic environment. We investigated the [...] Read more.
Antibiotics have been widely used to inhibit microbial growth and to control bacterial infection; however, they can trigger an imbalance in the gut flora of the host and dysregulate the host gene regulatory system when discharged into the aquatic environment. We investigated the effects of chronic exposure to a low concentration of erythromycin and ampicillin, focusing on gut microbiome and global gene expression profiles from Korea native ricefish (Oryzias latipes). The proportion of Proteobacteria (especially the opportunistic pathogen Aeromonas veronii) was significantly increased in the ricefish under the chronic exposure to erythromycin and ampicillin, whereas that of other bacterial phyla (i.e., Fusobacteria) decreased. In addition, the expression of genes involved in immune responses such as chemokines and immunocyte chemotaxis was significantly influenced in ricefish in the aquatic environment with antibiotics present. These results show that the internal microbial flora and the host gene expression are susceptible even at a low concentration of chronic antibiotics in the environment, supporting the importance of the appropriate use of antibiotic dose to maintain the sustainable and healthy aquaculture industry and water ecosystem. Full article
(This article belongs to the Special Issue Bioinformatic Analysis of NGS Data)
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Graphical abstract

50 pages, 14553 KiB  
Article
Altered Transcriptional Regulation of Glycolysis in Circulating CD8+ T Cells of Rheumatoid Arthritis Patients
by Shilpa Harshan, Poulami Dey and Srivatsan Raghunathan
Genes 2022, 13(7), 1216; https://doi.org/10.3390/genes13071216 - 7 Jul 2022
Cited by 9 | Viewed by 3658
Abstract
Peripheral T lymphocytes of rheumatoid arthritis (RA) patients show pathological changes in their metabolic pathways, especially glycolysis. These changes may drive the increased proliferation and tissue invasiveness of RA T cells. In order to study the transcriptional regulation underlying these alterations, we analysed [...] Read more.
Peripheral T lymphocytes of rheumatoid arthritis (RA) patients show pathological changes in their metabolic pathways, especially glycolysis. These changes may drive the increased proliferation and tissue invasiveness of RA T cells. In order to study the transcriptional regulation underlying these alterations, we analysed publicly available RNA sequencing data from circulating T lymphocyte subsets of healthy individuals, untreated RA patients, and patients undergoing treatment for RA. Differential co-expression networks were created using sample-wise edge weights from an analysis called “linear interpolation to obtain network estimates for single sample” (lionessR), and annotated using the Gene Transcription Regulation Database (GTRD). Genes with high centrality scores were identified. CD8+ effector memory cells (Tem) and CD8+CD45RA+ effector memory cells (Temra) showed large changes in the transcriptional regulation of glycolysis in untreated RA. PFKFB3 and GAPDH were differentially regulated and had high centrality scores in CD8+ Tem cells. PFKFB3 downregulation may be due to HIF1A post transcriptional inhibition. Tocilizumab treatment partially reversed the RA-associated differential expression of several metabolic and regulatory genes. MYC was upregulated and had high centrality scores in RA CD8+ Temra cells; however, its glycolysis targets were unaltered. The upregulation of the PI3K-AKT and mTOR pathways may explain MYC upregulation. Full article
(This article belongs to the Special Issue Bioinformatic Analysis of NGS Data)
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22 pages, 4551 KiB  
Article
Dietary Restriction and Rapamycin Affect Brain Aging in Mice by Attenuating Age-Related DNA Methylation Changes
by Zhilei Yin, Xinpeng Guo, Yang Qi, Pu Li, Shujun Liang, Xiangru Xu and Xuequn Shang
Genes 2022, 13(4), 699; https://doi.org/10.3390/genes13040699 - 15 Apr 2022
Cited by 10 | Viewed by 4415
Abstract
The fact that dietary restriction (DR) and long-term rapamycin treatment (RALL) can ameliorate the aging process has been reported by many researchers. As the interface between external and genetic factors, epigenetic modification such as DNA methylation may have latent effects on the aging [...] Read more.
The fact that dietary restriction (DR) and long-term rapamycin treatment (RALL) can ameliorate the aging process has been reported by many researchers. As the interface between external and genetic factors, epigenetic modification such as DNA methylation may have latent effects on the aging rate at the molecular level. To understand the mechanism behind the impacts of dietary restriction and rapamycin on aging, DNA methylation and gene expression changes were measured in the hippocampi of different-aged mice. Examining the single-base resolution of DNA methylation, we discovered that both dietary restriction and rapamycin treatment can maintain DNA methylation in a younger state compared to normal-aged mice. Through functional enrichment analysis of genes in which DNA methylation or gene expression can be affected by DR/RALL, we found that DR/RALL may retard aging through a relationship in which DNA methylation and gene expression work together not only in the same gene but also in the same biological process. This study is instructive for understanding the maintenance of DNA methylation by DR/RALL in the aging process, as well as the role of DR and RALL in the amelioration of aging. Full article
(This article belongs to the Special Issue Bioinformatic Analysis of NGS Data)
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15 pages, 3638 KiB  
Article
Multi-Level Analysis and Identification of Tumor Mutational Burden Genes across Cancer Types
by Shuangkuai Wang, Yuantao Tong, Hui Zong, Xuewen Xu, M. James C. Crabbe, Ying Wang and Xiaoyan Zhang
Genes 2022, 13(2), 365; https://doi.org/10.3390/genes13020365 - 17 Feb 2022
Cited by 4 | Viewed by 2882
Abstract
Tumor mutational burden (TMB) is considered a potential biomarker for predicting the response and effect of immune checkpoint inhibitors (ICIs). However, there are still inconsistent standards of gene panels using next-generation sequencing and poor correlation between the TMB genes, immune cell infiltrating, and [...] Read more.
Tumor mutational burden (TMB) is considered a potential biomarker for predicting the response and effect of immune checkpoint inhibitors (ICIs). However, there are still inconsistent standards of gene panels using next-generation sequencing and poor correlation between the TMB genes, immune cell infiltrating, and prognosis. We applied text-mining technology to construct specific TMB-associated gene panels cross various cancer types. As a case exploration, Pearson’s correlation between TMB genes and immune cell infiltrating was further analyzed in colorectal cancer. We then performed LASSO Cox regression to construct a prognosis predictive model and calculated the risk score of each sample for receiver operating characteristic (ROC) analysis. The results showed that the assessment of TMB gene panels performed well with fewer than 500 genes, highly mutated genes, and the inclusion of synonymous mutations and immune regulatory and drug-target genes. Moreover, the analysis of TMB differentially expressed genes (DEGs) suggested that JAKMIP1 was strongly correlated with the gene expression level of CD8+ T cell markers in colorectal cancer. Additionally, the prognosis predictive model based on 19 TMB DEGs reached AUCs of 0.836, 0.818, and 0.787 in 1-, 3-, and 5-year OS models, respectively (C-index: 0.810). In summary, the gene panel performed well and TMB DEGs showed great potential value in immune cell infiltration and in predicting survival. Full article
(This article belongs to the Special Issue Bioinformatic Analysis of NGS Data)
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