Integration of Single-Cell RNA Sequencing and Bulk RNA Sequencing Data to Establish and Validate a Prognostic Model for Patients With Lung Adenocarcinoma
Conclusion: This study constructed and validated a prognostic model for LUAD by integrating 10× scRNA-seq and bulk RNA-seq data. Besides, we observed two distinct subtypes in this population, with different prognosis and immune characteristics. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

Editorial: Finding New Epigenomics and Epigenetics Biomarkers for Complex Diseases and Significant Developmental Events With Machine Learning Methods
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

Machine Learning: A New Prospect in Multi-Omics Data Analysis of Cancer
Cancer is defined as a large group of diseases that is associated with abnormal cell growth, uncontrollable cell division, and may tend to impinge on other tissues of the body by different mechanisms through metastasis. What makes cancer so important is that the cancer incidence rate is growing worldwide which can have major health, economic, and even social impacts on both patients and the governments. Thereby, the early cancer prognosis, diagnosis, and treatment can play a crucial role at the front line of combating cancer. The onset and progression of cancer can occur under the influence of complicated mechanisms and so...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

MIMRDA: A Method Incorporating the miRNA and mRNA Expression Profiles for Predicting miRNA-Disease Associations to Identify Key miRNAs (microRNAs)
Identifying cancer-related miRNAs (or microRNAs) that precisely target mRNAs is important for diagnosis and treatment of cancer. Creating novel methods to identify candidate miRNAs becomes an imminent Frontier of researches in the field. One major obstacle lies in the integration of the state-of-the-art databases. Here, we introduce a novel method, MIMRDA, which incorporates the miRNA and mRNA expression profiles for predicting miRNA-disease associations to identify key miRNAs. As a proof-of-principle study, we use the MIMRDA method to analyze TCGA datasets of 20 types (BLCA, BRCA, CESE, CHOL, COAD, ESCA, HNSC, KICH, KIRC,...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

The Validation of a Single Multiplex Typing System With 45 Y-STR Markers for Familial Searching and Database Construction
This study aims to establish a novel Y-STR amplification system for forensic casework analysis and database construction, which contains 44 slowly and moderately mutating and one rapidly mutating Y-STR. The validation of the assay was conducted following the recommendations of SWGDAM developmental validation guidelines. Different types of casework samples were tested and reliable profiles were obtained. Furthermore, we genotyped and analyzed 141 unrelated Han Chinese male samples. The results showed that this Y45 kit could improve the performance of identifying male individuals, higher haplotype diversity, and discriminati...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

Integration of Transcriptome and Proteome in Lymph Nodes Reveal the Different Immune Responses to PRRSV Between PRRSV-Resistant Tongcheng Pigs and PRRSV-Susceptible Large White Pigs
In conclusion, this study provides important resources on transcriptomic and proteomic levels in lymph nodes for further revealing the interaction between the host immune response and PRRSV, which would give us new insight into molecular mechanisms related to genetic complexity against PRRSV. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

The Peopling and Migration History of the Natives in Peninsular Malaysia and Borneo: A Glimpse on the Studies Over the Past 100 years
Southeast Asia (SEA) has one of the longest records of modern human habitation out-of-Africa. Located at the crossroad of the mainland and islands of SEA, Peninsular Malaysia is an important piece of puzzle to the map of peopling and migration history in Asia, a question that is of interest to many anthropologists, archeologists, and population geneticists. This review aims to revisit our understanding to the population genetics of the natives from Peninsular Malaysia and Borneo over the past century based on the chronology of the technology advancement: 1) Anthropological and Physical Characterization; 2) Blood Group Mark...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

SCClone: Accurate Clustering of Tumor Single-Cell DNA Sequencing Data
Single-cell DNA sequencing (scDNA-seq) enables high-resolution profiling of genetic diversity among single cells and is especially useful for deciphering the intra-tumor heterogeneity and evolutionary history of tumor. Specific technical issues such as allele dropout, false-positive errors, and doublets make scDNA-seq data incomplete and error-prone, giving rise to a severe challenge of accurately inferring clonal architecture of tumor. To effectively address these issues, we introduce a new computational method called SCClone for reasoning subclones from single nucleotide variation (SNV) data of single cells. Specifically...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

Rare Variants and Polymorphisms of FBN1 Gene May Increase the Risk of Non-Syndromic Aortic Dissection
In this study, DNA samples from 90 Chinese individuals with non-syndromic AD (60 Stanford A, 30 Stanford B types) were analyzed to determine the relationship between diverse genotypes of the FBN1 gene and non-syndromic AD. Eleven pathogenic/likely pathogenic variants (1 novel) were identified in 12.2% of patients with non-syndromic AD. Patients with positive variants suffered from AD at a younger age than those in the negative variant group. Among the six positive missense mutations associated with cysteine residue hosts, four (66.7%) were Stanford A AD, whereas two (33.3%) were Stanford B AD. Three (100%) positive splicin...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

RNA-Binding Protein IGF2BP1 Associated With Prognosis and Immunotherapy Response in Lung Adenocarcinoma
N6-methyladenosine (m6A) is the most common modification in eukaryotic RNAs and plays a vital role in the tumorigenesis and metastasis of various cancers. However, a comprehensive study of m6A methylation regulators in lung adenocarcinoma (LUAD) is still lacking. The present study aimed to systematically explore the role of m6A methylation regulators in LUAD. RNA sequencing data of 20 m6A methylation regulators and clinical data of LUAD patients were downloaded from The Cancer Genome Atlas (TCGA) database. The prognosis value of m6A methylation regulators in LUAD was evaluated using the Gene Expression Profiling Interactiv...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

Analysis and Visualization of Spatial Transcriptomic Data
Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of spatial information. Spatial transcriptomics is a recent technological innovation that measures transcriptomic information while preserving spatial information. Spatial transcriptomic data can be generated in several ways. RNA molecules are measured by in situ sequencing, in situ hybridization, or spatial barcoding to recover original spatial coordinates. The inclusion of spatial informati...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

Combined Transcriptome and Metabolome Analysis of Musa nana Laur. Peel Treated With UV-C Reveals the Involvement of Key Metabolic Pathways
This study is a first attempt to understand such changes in banana peel irradiated with UV-C. We treated Musa nana Laur. with 0.02 KJ/m2 UV-C irradiation for 0, 4, 8, 12, 15, and 18 days and studied the physiological and quality indicators. We found that UV-C treatment reduces weight loss and decay rate, while increased the accumulation of total phenols and flavonoids. Similarly, our results demonstrated that UV-C treatment increases the activity of defense and antioxidant system related enzymes. We observed that UV-C treatment for 8 days is beneficial for M. nana peels. The peels of M. nana treated with UV-C for 8 days w...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations
The objective of this study was to identify ROHet in the Duroc pig genome, and investigate the relationships between ROHet and eight important economic traits. Here, we genotyped 3,770 American Duroc (S21) and 2,096 Canadian Duroc (S22) pigs using 50 K single nucleotide polymorphism array to analyze heterozygosity. A total of 145,010 and 84,396 ROHets were characterized for S21 and S22 populations, respectively. ROHet segments were mostly enriched in 1–2 Mb length classification (75.48% in S21 and 72.25% in S22). The average genome length covered by ROHet was 66.53 ± 12.20 Mb in S21 and 73.32 ± 13.77 Mb in S22 pigs...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

Human Immune System Diseasome Networks and Female Oviductal Microenvironment: New Horizons to be Discovered
Human hypofertility and infertility are two worldwide conditions experiencing nowadays an alarming increase due to a complex ensemble of events. The immune system has been suggested as one of the responsible for some of the etiopathogenic mechanisms involved in these conditions. To shed some light into the strong correlation between the reproductive and immune system, as can be inferred by the several and valuable manuscripts published to date, here we built a network using a useful bioinformatic tool (DisGeNET), in which the key genes involved in the sperm-oviduct interaction were linked. This constitutes an important eve...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research

The Scope of Pathogenic ABCA4 Mutations Targetable by CRISPR DNA Base Editing Systems —A Systematic Review
In this report, we screened the known “pathogenic” and “likely pathogenic” mutations in ABCA4 from available data in gnomAD, Leiden Open Variation Database (LOVD), and ClinVar for potential PAM sites of relevant base editors, including Streptococcus pyogenes Cas (SpCas), Staphylococcus aureus Cas (SaCas), and the KKH variant of SaCas (Sa-KKH). Overall, of the mutations screened, 53% (ClinVar), 71% (LOVD), and 71% (gnomAD), were editable, pathogenic transition mutations, of which 35–47% had “ideal” PAM sites. Of these mutations, 16–20% occur within a range of multiple PAM sites, enabling a variety of editing...
Source: Frontiers in Genetics - January 27, 2022 Category: Genetics & Stem Cells Source Type: research