Functional analysis of differently expressed ferroptosis-related genes in patients with mitral valve prolapse
Conclusion: In summary, CDKN2A, SLC1A4, and ATF3 regulate the pathophysiological process of MVP and are potential therapeutic targets. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT
Since the introduction of the first transformer model with a unique self-attention mechanism, natural language processing (NLP) models have attained state-of-the-art (SOTA) performance on various tasks. As DNA is the blueprint of life, it can be viewed as an unusual language, with its characteristic lexicon and grammar. Therefore, NLP models may provide insights into the meaning of the sequential structure of DNA. In the current study, we employed and compared the performance of popular SOTA NLP models (i.e., XLNET, BERT, and a variant DNABERT trained on the human genome) to predict and analyze the promoters in freshwater ...
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Recent advances and current challenges in population genomics of structural variation in animals and plants
The field of population genomics has seen a surge of studies on genomic structural variation over the past two decades. These studies witnessed that structural variation is taxonomically ubiquitous and represent a dominant form of genetic variation within species. Recent advances in technology, especially the development of long-read sequencing platforms, have enabled the discovery of structural variants (SVs) in previously inaccessible genomic regions which unlocked additional structural variation for population studies and revealed that more SVs contribute to evolution than previously perceived. An increasing number of s...
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

miR-17-92 cluster in osteoarthritis: Regulatory roles and clinical utility
Osteoarthritis (OA) is the most prevalent articular disease, especially in aged population. Caused by multi-factors (e.g., trauma, inflammation, and overloading), OA leads to pain and disability in affected joints, which decreases patients’ quality of life and increases social burden. In pathophysiology, OA is mainly characterized by cartilage hypertrophy or defect, subchondral bone sclerosis, and synovitis. The homeostasis of cell–cell communication is disturbed as well in such pro-inflammatory microenvironment, which provides clues for the diagnosis and treatment of OA. MicoRNAs (miRNAs) are endogenous non-coding RNA...
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

A high-efficiency differential expression method for cancer heterogeneity using large-scale single-cell RNA-sequencing data
Colorectal cancer is a highly heterogeneous disease. Tumor heterogeneity limits the efficacy of cancer treatment. Single-cell RNA-sequencing technology (scRNA-seq) is a powerful tool for studying cancer heterogeneity at cellular resolution. The sparsity, heterogeneous diversity, and fast-growing scale of scRNA-seq data pose challenges to the flexibility, accuracy, and computing efficiency of the differential expression (DE) methods. We proposed HEART (high-efficiency and robust test), a statistical combination test that can detect DE genes with various sources of differences beyond mean expression changes. To validate the ...
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Insights on variant analysis in silico tools for pathogenicity prediction
Molecular biology is currently a fast-advancing science. Sequencing techniques are getting cheaper, but the interpretation of genetic variants requires expertise and computational power, therefore is still a challenge. Next-generation sequencing releases thousands of variants and to classify them, researchers propose protocols with several parameters. Here we present a review of several in silico pathogenicity prediction tools involved in the variant prioritization/classification process used by some international protocols for variant analysis and studies evaluating their efficiency. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Heart failure and late-onset Alzheimer ’s disease: A Mendelian randomization study
Some observational studies suggested that heart failure (HF) is associated with increased risk of late-onset Alzheimer’s disease (AD). On the other hand, a recently published Two-Sample Mendelian Randomization (2SMR) study was reported as inconclusive but the estimated odds ratios (ORs) were less than one indicating a potential causal association between genetically predicted HF and lowered risk of AD. Both HF and AD are quite common among elderly persons and frequently occur together resulting in a series of severe medical challenges and increased financial burden on healthcare. It is of great medical and financial inte...
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Screening prognostic genes related to leucovorin, fluorouracil, and irinotecan treatment sensitivity by performing co-expression network analysis for colon cancer
Conclusion: We found that AEBP1, BGN, and TAGLN, as potential predictive biomarkers, may play an important role in the response to FOLFIRI treatment of colon cancer and as a precise molecular target associated with chemotherapy response in colon cancer. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Development and performance evaluation of an artificial intelligence algorithm using cell-free DNA fragment distance for non-invasive prenatal testing (aiD-NIPT)
In conclusion, FD-based aiD-NIPT was successfully developed, and it showed better performance than FC-based NIPT methods. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Case Report: A novel KNCH2 variant-induced fetal heart block and the advantages of fetal genomic sequencing in prenatal long-term dexamethasone exposure
Conclusion: Genetic screening should be recommended in fetuses with autoimmune antibody negative high-degree AVB, especially for 2:1 transduction AVB and in fetuses with changes in fetal heart rhythm following initial DEX treatment. Genetic screening may help identify genetic variant–related channelopathies and avoid unexpected prenatal exposure of DEX and its possible long-term adverse postnatal complications. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Novel targets in renal fibrosis based on bioinformatic analysis
Conclusion: A gene network reflecting the transcriptome signature in CKD was established. The five hub genes identified in this study are potentially useful for the treatment and/or diagnosis CKD as biomarkers. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Editorial: COVID-19 pandemics: Ethical, legal and social issues
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Exploring the causal relationship between gastroesophageal reflux and oral lesions: A mendelian randomization study
Conclusion: Our findings provide the first evidence for a genetic causal effect of GERD on oral lesion pathogenesis. For patients with confirmed GERD, attention should be paid to taking interventions to prevent the occurrence of oral lesions. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

A heterozygous mutation in NOTCH3 in a Chinese family with CADASIL
Conclusion: We identified a known CADASIL-causing mutation NOTCH3 (c.397C>T, p.Arg133Cys) in a Chinese family. The clinical manifestations of mutation carriers in this family are highly heterogeneous, which is likely a common feature for the etiology of different mutations in CADASIL. Molecular genetic analyses are critical for accurate diagnosis, as well as the provision of genetic counselling for CADASIL. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research

Editorial: Machine learning-based methods for RNA data analysis —Volume II
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - November 29, 2022 Category: Genetics & Stem Cells Source Type: research