MASQC: Next Generation Sequencing Assists Third Generation Sequencing for Quality Control in N6-Methyladenine DNA Identification

Biotech & Bioengineering

Yang

et al. 2021

DNA modification plays a pivotal role in regulating gene expression in cell development. As prevalent markers on DNA, 5-methylcytosine (5mC), N6-methyladenine (6mA), and N4-methylcytosine (4mC) can be recognized by specific methyltransferases, facilitating cellular defense and the versatile regulation of gene expression in eukaryotes and prokaryotes. Recent advances in DNA sequencing technology have permitted the positions of different modifications to be resolved at the genome-wide scale, which has led to the discovery of several novel insights into the complexity and functions of multiple methylations. In this review, we summarize differences in the various mapping approaches and discuss their pros and cons with respect to their relative read depths, speeds, and costs. We also discuss the development of future sequencing technologies and strategies for improving the detection resolution of current sequencing technologies. Lastly, we speculate on the potentially instrumental role that these sequencing technologies might play in future research.

Section: Discussionmentioning

confidence: 99%

Advances in mapping the epigenetic modifications of 5‐methylcytosine (5mC), N6‐methyladenine (6mA), and N4‐methylcytosine (4mC)

Biotech & Bioengineering

Yang

et al. 2021

“…The potential capability of the FRlncRNA signature to instruct clinical treatment also deserves further study. In addition, it is worth promoting application of analyzing a few gene data to reduce the cost of sequencing [ 71 ]. It would be much better if the outcome, mutated and immune related events can be predicted only by measuring these FRlncRNAs expression.…”

Section: Discussionmentioning

confidence: 99%

A Ferroptosis-Related LncRNA Signature Associated with Prognosis, Tumor Immune Environment, and Genome Instability in Hepatocellular Carcinoma

Lian

Computational and Mathematical Methods in Medicine

2022

Background. Ferroptosis is an iron-dependent form of cell death. In this study, we identified ferroptosis-related long noncoding RNAs (FRlncRNAs) to investigate their association with hepatocellular carcinoma (HCC) in prognosis, tumor immune environment, and genome instability. Methods. Transcriptome profile data of HCC were retrieved from a public database. FRlncRNAs were identified by co-expression analysis. Patients were randomly divided into training and test cohorts. Univariate Cox analysis and Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression were performed to construct a risk model. Patients were divided into high- and low-risk groups based on the risk model. AUC and C index were used to assess the risk model. Survival analysis, immune status, and genome instability were compared between the two groups. Results. Sixteen FRlncRNAs were identified and used to construct an FRlncRNA signature for the risk model. The Kaplan-Meier analysis revealed that patients in the high-risk group had poorer overall survival than patients in the low-risk group. The area under curve of the risk model was 0.879, 0.809, and 0.757 in the training cohort and 0.635, 0.688, and 0.739 in the test cohort at 1, 2, and 3 years, respectively. The risk model was an independent prognostic predictor and showed excellent prediction of prognosis compared with clinicopathological features. For the differentially expressed ferroptosis-related genes, many enriched metabolic pathways were identified in the functional enrichment analysis. Immune cells such as CD8+ T cells, macrophages M1, natural killer cells, and B cells, which may be associated with antitumor immune responses, differed between the high- and low-risk groups. Genome instability based on the risk model was also explored. A total of 61 genes were differently mutated between the two risk groups, and among them, TP53, HECW2, TRIM66, MCTP2, and KIAA1551 had the most significant mutation frequency differences. Conclusion. The FRlncRNA signature is closely related with overall survival, tumor immune environment, and genome instability in HCC.

“…The AC variable can represent the average interaction between residues with a series of lags, which is defined as

where AC j , g ( S ) can indicate the interaction between two spacer g residues. But it can just calculate the residue interaction in the same column [ 48 ]. In order to solve this problem, we calculated total correlations among all the columns by the following formula:

…”

Section: Methodsmentioning

confidence: 99%

Mathematical Modeling and Computational Prediction of High-Risk Types of Human Papillomaviruses

Computational and Mathematical Methods in Medicine

Wang

2022

Cervical cancer is one of the main causes of cancer death all over the world. Most diseases such as cervical epithelial atypical hyperplasia and invasive cervical cancer are closely related to the continuous infection of high-risk types of human papillomavirus. Therefore, the high-risk types of human papillomavirus are the key to the prevention and treatment of cervical cancer. With the accumulation of high-throughput and clinical data, the use of systematic and quantitative methods for mathematical modeling and computational prediction has become more and more important. This paper summarizes the mathematical models and prediction methods of the risk types of human papillomavirus, especially around the key steps such as feature extraction, feature selection, and prediction algorithms. We summarized and discussed the advantages and disadvantages of existing algorithms, which provides a theoretical basis for follow-up research.