Comparing Genetic and Socioenvironmental Contributions to Ethnic Differences in C-Reactive Protein
The objective of this study was to compare the contributions of genetic ancestry, socioenvironmental factors, and inflammation-related health conditions to ethnic differences in C-reactive protein levels. We used multivariable regression to compare CRP blood serum levels between Black and White ethnic groups from the United Kingdom Biobank (UKBB) prospective cohort study. CRP serum levels are significantly associated with ethnicity in an age and sex adjusted model. Study participants who identify as Black have higher average CRP than those who identify as White, CRP increases with age, and females have higher average CRP t...
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

Research Progress of PPR Proteins in RNA Editing, Stress Response, Plant Growth and Development
RNA editing is a posttranscriptional phenomenon that includes gene processing and modification at specific nucleotide sites. RNA editing mainly occurs in the genomes of mitochondria and chloroplasts in higher plants. In recent years, pentatricopeptide repeat (PPR) proteins, which may act as trans-acting factors of RNA editing have been identified, and the study of PPR proteins has become a research focus in molecular biology. The molecular functions of these proteins and their physiological roles throughout plant growth and development are widely studied. In this minireview, we summarize the current knowledge of the PPR fa...
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

Comprehensive Analysis of LIN28A in Chinese Patients With Early Onset Parkinson ’s Disease
A loss-of-function variant in Lin-28 Homolog A gene (LIN28A p. R192G, rs558060339) has been identified in two East Asian ancestry patients with early-onset PD (EOPD). Functional studies revealed that such a variant could lead to developmental defects and PD-related phenotype, and the phenotypes could be rescued after correction of the variant. The aim of the study was to screen the variants of LIN28A in Chinese patients with EOPD. A total of 682 EOPD patients were sequenced with whole exome sequencing and the coding and flanking region of LIN28A were analyzed. We identified a rare coding variant, p. P182L, of LIN28A in a C...
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

A Comparative Transcriptional Landscape of Two Castor Cultivars Obtained by Single-Molecule Sequencing Comparative Analysis
Conclusion: The results revealed considerable differences and expression diversity between the two cultivars, well beyond what was reported in previous studies and likely reflecting the differences in architecture between these two cultivars. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

Editorial: Gene, Cell and Protein Replacement Therapy for Genetic Muscle, Bone and Skin Disorders
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

Gene4HL: An Integrated Genetic Database for Hearing Loss
Hearing loss (HL) is one of the most common disabilities in the world. In industrialized countries, HL occurs in 1–2/1,000 newborns, and approximately 60% of HL is caused by genetic factors. Next generation sequencing (NGS) has been widely used to identify many candidate genes and variants in patients with HL, but the data are scattered in multitudinous studies. It is a challenge for scientists, clinicians, and biologists to easily obtain and analyze HL genes and variant data from these studies. Thus, we developed a one-stop database of HL-related genes and variants, Gene4HL (http://www.genemed.tech/gene4hl/), making...
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds
Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, ...
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

MiR-320d Inhibits Progression of EGFR-Positive Colorectal Cancer by Targeting TUSC3
Conclusion: Generally, our results demonstrated that miR-320d could inhibit the malignant phenotype of EGFR-positive CRC through targeting TUSC3. The miR-320d might be a potential therapeutic target for EGFR-positive CRC. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

Development of a 3 RNA Binding Protein Signature for Predicting Prognosis and Treatment Response for Glioblastoma Multiforme
Conclusion: The identified 3 hub RBPs-derived risk score is effective in the prediction of GBM prognosis and treatment response, and benefits to the treatment of GBM patients. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of Novel and Recurrent Variants in MYO15A in Ashkenazi Jewish Patients With Autosomal Recessive Nonsyndromic Hearing Loss
Hearing loss is a genetically and phenotypically heterogeneous disorder. The purpose of this study was to determine the genetic cause underlying hearing loss in four Ashkenazi Jewish families. We screened probands from each family using a combination of targeted mutation screening and exome sequencing to identifiy the genetic cause of hearing loss in each family. We identified four variants in MYO15A, two novel variants never previously linked to deafness (c.7212+5G>A and p.Leu2532ArgfsTer37) and two recurrent variants (p.Tyr2684His and p.Gly3287Gly). One family showed locus heterogeneity, segregrating two genetic forms...
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

Mutation Analysis of MYORG in a Chinese Cohort With Primary Familial Brain Calcification
This study aims to elucidate the mutational and clinical spectrum of MYORG mutations in a large cohort of Chinese PFBC patients with possible autosomal recessive or absent family history. Mutational analyses of MYORG were performed by Sanger sequencing in a cohort of 245 PFBC patients including 21 subjects from 10 families compatible with a possibly autosomal-recessive trait and 224 apparently sporadic cases. In-depth phenotyping and neuroimaging features were investigated in all patients with novel MYORG variants. Two nonsense variants (c.442C> T, p. Q148*; c.972C> A, p. Y324*) and two missense variants (c.1969G>...
Source: Frontiers in Genetics - October 18, 2021 Category: Genetics & Stem Cells Source Type: research

Local Ancestry Adjusted Allelic Association Analysis Robustly Captures Tuberculosis Susceptibility Loci
Pulmonary tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease. The risk of developing active TB is in part determined by host genetic factors. Most genetic studies investigating TB susceptibility fail to replicate association signals particularly across diverse populations. South African populations arose because of multi-wave genetic admixture from the indigenous KhoeSan, Bantu-speaking Africans, Europeans, Southeast Asian-and East Asian populations. This has led to complex genetic admixture with heterogenous patterns of linkage disequilibrium and associated traits. As a result, precise estimatio...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

Small Protein Enrichment Improves Proteomics Detection of sORF Encoded Polypeptides
With the rapid growth in the number of sequenced genomes, genome annotation efforts became almost exclusively reliant on automated pipelines. Despite their unquestionable utility, these methods have been shown to underestimate the true complexity of the studied genomes, with small open reading frames (sORFs; ORFs typically considered shorter than 300 nucleotides) and, in consequence, their protein products (sORF encoded polypeptides or SEPs) being the primary example of a poorly annotated and highly underexplored class of genomic elements. With the advent of advanced translatomics such as ribosome profiling, reannotation e...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

A Holling Functional Response Model for Mapping QTLs Governing Interspecific Interactions
Genes play an important role in community ecology and evolution, but how to identify the genes that affect community dynamics at the whole genome level is very challenging. Here, we develop a Holling type II functional response model for mapping quantitative trait loci (QTLs) that govern interspecific interactions. The model, integrated with generalized Lotka-Volterra differential dynamic equations, shows a better capacity to reveal the dynamic complexity of inter-species interactions than classic competition models. By applying the new model to a published mapping data from a competition experiment of two microbial specie...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

N6-Methyladenosine-Related Long Non-coding RNA Signature Associated With Prognosis and Immunotherapeutic Efficacy of Clear-Cell Renal Cell Carcinoma
In this study, we conducted a comprehensive ccRCC RNA-seq analysis using The Cancer Genome Atlas data to establish an m6A-related lncRNA prognostic signature (m6A-RLPS) for ccRCC. Forty-four prognostic m6A-related lncRNAs (m6A-RLs) were screened using Pearson correlation analysis (|R|> 0.7, p
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

The Predictive Role of Immune Related Subgroup Classification in Immune Checkpoint Blockade Therapy for Lung Adenocarcinoma
Conclusion: In summary, immune related subgroup clustering based on distinct immune associated signatures will enable us to screen potentially responsive LUAD patients for ICB therapy before treatment, and the discovery of metabolism associated mechanism is beneficial to comprehensive therapeutic strategies making involving ICB therapy in combination with metabolism intervention for LUAD. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

Editorial: Functional Annotation of Animal Genomes
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

Ancient Mitogenomes Provide New Insights into the Origin and Early Introduction of Chinese Domestic Donkeys
Both molecular data and archaeological evidence strongly support an African origin for the domestic donkey. Recent genetic studies further suggest that there were two distinct maternal lineages involved in its initial domestication. However, the exact introduction time and the dispersal process of domestic donkeys into ancient China are still unresolved. To address these questions, we retrieved three near-complete mitochondrial genomes from donkey specimens excavated from Gaoling County, Shaanxi Province, and Linxia Basin, Gansu Province, China, dated at 2,349-2,301, 469-311, and 2,160-2,004 cal. BP, respectively. Max...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

Evaluating Causal Relationship Between Metabolites and Six Cardiovascular Diseases Based on GWAS Summary Statistics
In this study, we conducted a two-sample Mendelian randomization (MR) analysis to evaluate the causal effect of metabolites on these diseases by making full use of the latest GWAS summary statistics for 486 metabolites and six major CVDs. Extensive sensitivity analyses were implemented to validate our MR results. We also conducted linkage disequilibrium score regression (LDSC) and colocalization analysis to investigate whether MR findings were driven by genetic similarity or hybridization between LD and disease-associated gene loci. We identified a total of 310 suggestive associations across all metabolites and CVDs, and f...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

Hypertension-Related Drug Activity Identification Based on Novel Ensemble Method
Hypertension is a chronic disease and major risk factor for cardiovascular and cerebrovascular diseases that often leads to damage to target organs. The prevention and treatment of hypertension is crucially important for human health. In this paper, a novel ensemble method based on a flexible neural tree (FNT) is proposed to identify hypertension-related active compounds. In the ensemble method, the base classifiers are Multi-Grained Cascade Forest (gcForest), support vector machines (SVM), random forest (RF), AdaBoost, decision tree (DT), Gradient Boosting Decision Tree (GBDT), KNN, logical regression, and naïve Baye...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

Whole-Transcriptome Sequence of Degenerative Meniscus Cells Unveiling Diagnostic Markers and Therapeutic Targets for Osteoarthritis
Meniscus plays an important role in joint homeostasis. Tear or degeneration of meniscus might facilitate the process of knee osteoarthritis (OA). Hence, to investigate the transcriptome change during meniscus degeneration, we reveal the alterations of messenger RNA (mRNA), microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) in meniscus during OA by whole-transcriptome sequence. A total of 375 mRNAs, 15 miRNAs, 56 lncRNAs, and 90 circRNAs were significantly altered in the degenerative meniscus treated with interleukin-1β (IL-1β). More importantly, highly specific co-expression RNA (ceRNA) net...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

Genome-Wide DNA Methylation Profile in Jejunum Reveals the Potential Genes Associated With Paratuberculosis in Dairy Cattle
In this study, we characterized the profiles of DNA methylation of jejunum from nine Holstein cows in clinical, subclinical, and healthy groups using whole-genome bisulfite sequencing (WGBS). The average methylation level in functional regions was 29.95% in the promoter, 29.65% in the 5’ untranslated region (UTR), 68.24% in exons, 71.55% in introns, and 72.81% in the 3’ UTR. A total of 3,911, 4,336, and 4,094 differentially methylated genes (DMGs) were detected in clinical vs. subclinical, clinical vs. healthy, and subclinical vs. healthy comparative group, respectively. Gene ontology (GO) and analysis based on...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

Complex Age- and Cancer-Related Changes in Human Blood Transcriptome —Implications for Pan-Cancer Diagnostics
In this study, we show that whole transcriptome analysis using RNA-seq could indeed serve as a viable biomarker for pan-cancer detection. Furthermore, a class of long non-coding (lnc) RNAs, very long intergenic non-coding (vlinc) RNAs, demonstrated superior performance compared with protein-coding mRNAs. Finally, we show that age and presence of non-blood cancers change transcriptome in similar, yet not identical, directions and explore implications of this observation for pan-cancer diagnostics. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

A Systematic Review of Transcriptional Dysregulation in Huntington ’s Disease Studied by RNA Sequencing
Huntington’s disease (HD) is a chronic neurodegenerative disorder caused by an expansion of polyglutamine repeats in exon 1 of the Huntingtin gene. Transcriptional dysregulation accompanied by epigenetic alterations is an early and central disease mechanism in HD yet, the exact mechanisms and regulators, and their associated gene expression programs remain incompletely understood. This systematic review investigates genome-wide transcriptional studies that were conducted using RNA sequencing (RNA-seq) technology in HD patients and models. The review protocol was registered at the Open Science Framework (OSF). The bio...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

A Novel Homozygous Missense Mutation in the Zinc Finger DNA Binding Domain of GLI1 Causes Recessive Post-Axial Polydactyly
Conclusion: Herein, we report a novel variant in GLI1 gene, causing autosomal recessive post-axial polydactyly type A (PAPA) type 8. This confirms the critical role of GLI1 in digit development and might help in genotype–phenotype correlation in the future. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

dFRAME: A Video Recording-Based Analytical Method for Studying Feeding Rhythm in Drosophila
Animals, from insects to humans, exhibit obvious diurnal rhythmicity of feeding behavior. Serving as a genetic animal model, Drosophila has been reported to display feeding rhythms; however, related investigations are limited due to the lack of suitable and practical methods. Here, we present a video recording-based analytical method, namely, Drosophila Feeding Rhythm Analysis Method (dFRAME). Using our newly developed computer program, FlyFeeding, we extracted the movement track of individual flies and characterized their food-approaching behavior. To distinguish feeding and no-feeding events, we utilized high-magnificati...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers
The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal sh...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

PBX2-Mediated circTLK1 Activates JAK/STAT Signaling to Promote Gliomagenesis via miR-452-5p/SSR1 Axis
Glioma is considered one of the most lethal brain tumors, as the aggressive blood vessel formation leads to high morbidity and mortality rates. However, the mechanisms underlying the initiation and progression of glioma remain unclear. Here, we aimed to reveal the role of circTLK1 in glioma development. Our results revealed that circTLK1 is highly expressed in glioma tumor tissues and glioma cell lines. We then conducted a series of experiments that showed that circTLK1 was involved in the progression of gliomas. Mechanistically, investigation of the factors downstream of circTLK1 revealed that circTLK1 activated JAK/STAT ...
Source: Frontiers in Genetics - October 15, 2021 Category: Genetics & Stem Cells Source Type: research

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata
This study lays the foundation for the follow-up research of molecular biology and provides a reference for studying the more medicinal value of C. antiquata. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population
In this study, we used 50 K SNP arrays to detect CNVs in Duroc purebred pig. A total number of 211 CNVRs were detected with a total length of 118.48 Mb, accounting for 5.23% of the autosomal genome sequence. Of these CNVRs, 32 were gains, 175 losses, and four contained both types (loss and gain within the same region). The CNVRs we detected were non-randomly distributed in the swine genome and were significantly enriched in the segmental duplication and gene density region. Additionally, these CNVRs were overlapping with 1,096 protein-coding genes (CNV-genes), and 39 miRNAs (CNV-miRNAs), respectively. The CNV-gen...
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Pumpkin (Cucurbita moschata) HSP20 Gene Family Identification and Expression Under Heat Stress
Pumpkin (Cucurbita moschata) is an important cucurbit vegetable crop that has strong resistance to abiotic stress. While heat shock protein 20 (HSP20) has been implicated in vegetable response to heat stress, little is known regarding activity of HSP20 family proteins in C. moschata. Here, we performed a comprehensive genome-wide analysis to identify and characterize the functional dynamics of the Cucurbita moschata HSP20 (CmoHSP20) gene family. A total of 33 HSP20 genes distributed across 13 chromosomes were identified from the pumpkin genome. Our phylogenetic analysis determined that the CmoHSP20 proteins fell into nine ...
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Editorial: Conservation Genomic Studies for Threatened Plants
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Regulatory Non-Coding RNAs Modulate Transcriptional Activation During B Cell Development
B cells play a significant role in the adaptive immune response by secreting immunoglobulins that can recognize and neutralize foreign antigens. They develop from hematopoietic stem cells, which also give rise to other types of blood cells, such as monocytes, neutrophils, and T cells, wherein specific transcriptional programs define the commitment and subsequent development of these different cell lineages. A number of transcription factors, such as PU.1, E2A, Pax5, and FOXO1, drive B cell development. Mounting evidence demonstrates that non-coding RNAs, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), modula...
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation
In this study, we performed a thorough comparison, in terms of assembly quality and purity, of 100+ de novo assembled genomes of C. hominis. Remarkably, after quality genome filtering, a comprehensive phylogenomic analysis allowed us to discover that C. hominis encompasses two lineages with continental segregation. These lineages were named based on the observed continental distribution bias as C. hominis Euro-American (EA) and the C. hominis Afro-Asian (AA) lineages. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Agent Repurposing for the Treatment of Advanced Stage Diffuse Large B-Cell Lymphoma Based on Gene Expression and Network Perturbation Analysis
In conclusion, we propose a novel pipeline to utilize perturbed gene-expression signatures during DLBCL progression for identifying agents, and we successfully utilized this approach to generate a list of promising compounds. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

TUBA1C is a Prognostic Marker in Low-grade Glioma and Correlates with Immune Cell Infiltration in the Tumor Microenvironment
In conclusion, TUBA1C expression is increased in LGG and high TUAB1C expression is related to a poor prognosis. TUBA1C may influence tumor development by regulating the tumor-infiltrating cells in the TME. TUBA1C may be a potential target for immunotherapy. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Multi-Similarities Bilinear Matrix Factorization-Based Method for Predicting Human Microbe –Disease Associations
Accumulating studies have shown that microbes are closely related to human diseases. In this paper, a novel method called MSBMFHMDA was designed to predict potential microbe–disease associations by adopting multi-similarities bilinear matrix factorization. In MSBMFHMDA, a microbe multiple similarities matrix was constructed first based on the Gaussian interaction profile kernel similarity and cosine similarity for microbes. Then, we use the Gaussian interaction profile kernel similarity, cosine similarity, and symptom similarity for diseases to compose the disease multiple similarities matrix. Finally, we integrate t...
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

ACE and ACTN3 Gene Polymorphisms and Genetic Traits of Rowing Athletes in the Northern Han Chinese Population
This investigation aimed to explore the effects of ACE I/D and ACTN3 R577X gene polymorphisms on specific quantitative variables, including height, weight, arm span, biacromial breadth, forced vital capacity (FVC), FVC/weight, maximal oxygen uptake (VO2max), prone bench pull (PBP), loaded barbell squat (LBS), and 3,000-m run, in 243 Chinese rowing athletes. The ACE and ACTN3 genotypes were obtained for each athlete via polymerase chain reaction on saliva samples, and the genotype frequency was analyzed. The ACE genotype frequency of rowing athletes were 45.8% II, 42.2% ID, and 12% DD for males and 33.6% II, 48% ID, and 18....
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

SOD1 Mutation Spectrum and Natural History of ALS Patients in a 15-Year Cohort in Southeastern China
Conclusion: Our results expanded the spectrum of SOD1 mutations, highlighted the mutation distribution, and summarized the natural history of SOD1-mutated patients in southeastern China. Male patients were found to have better survival, and FALS patients received an earlier diagnosis. Our findings assist in providing a detailed clinical picture, which is important for ongoing genetic clinical trials. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Signatures Beyond Oncogenic Mutations in Cell-Free DNA Sequencing for Non-Invasive, Early Detection of Cancer
Early detection of cancer saves lives, but an effective detection strategy in public health settings requires a delicate balance - periodic screening should neither miss rapidly progressing disease nor fail to detect rare tumors at unusual locations; on the other hand, even a modest false positive rate carries risks of over-diagnosis and over-treatment of relatively indolent non-malignant disease. Genomic profiling of cell-free DNA from liquid biopsy using massively parallel sequencing is emerging as an attractive, non-invasive screening platform for sensitive detection of multiple types of cancer in a single assay. Genomi...
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

A Comprehensive Comparison of Haplotype-Based Single-Step Genomic Predictions in Livestock Populations With Different Genetic Diversity Levels: A Simulation Study
The level of genetic diversity in a population is inversely proportional to the linkage disequilibrium (LD) between individual single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs), leading to lower predictive ability of genomic breeding values (GEBVs) in high genetically diverse populations. Haplotype-based predictions could outperform individual SNP predictions by better capturing the LD between SNP and QTL. Therefore, we aimed to evaluate the accuracy and bias of individual-SNP- and haplotype-based genomic predictions under the single-step-genomic best linear unbiased prediction (ssGBLUP) approach in...
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Apolipoprotein E Genetic Variation and Its Association With Cognitive Function in Rural-Dwelling Older South Africans
Apolipoprotein E (APOE) 𝜀4 allele carrier status is well known for its association with an increased likelihood of developing Alzheimer’s disease, but its independent role in cognitive function is unclear. APOE genetic variation is understudied in African populations; hence, this cross-sectional study in a rural South African community examined allele and genotype frequencies, and their associations with cognitive function. Cognitive function was assessed using two different screening methods to produce a total cognition score and four domain-specific cognition scores for verbal episodic memory, executive function...
Source: Frontiers in Genetics - October 14, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of IGF2BP3 as an Adverse Prognostic Biomarker of Gliomas
This study aimed to determine the prognostic value of the m6A RNA methylation regulator in gliomas and investigate the underlying mechanisms of the aberrant expression of m6A-related genes.mRNA expression profiles and clinical information of 448 glioma samples were obtained from The Cancer Genome Atlas and cBioportal. The expression of m6A-related genes in normal controls and low-grade glioma and glioblastoma was obtained from Gene Expression Profiling Interactive Analysis. Further, m6A-related gene expression and its relationship with prognosis were obtained through The Chinese Glioma Genome Atlas (CGGA). Multivariate Cox...
Source: Frontiers in Genetics - October 13, 2021 Category: Genetics & Stem Cells Source Type: research

Down-Regulated CLDN10 Predicts Favorable Prognosis and Correlates With Immune Infiltration in Gastric Cancer
Conclusion: Down-regulated CLDN10 was associated with better overall survival (OS) in gastric cancer. And CLDN10 may serve as a potential prognostic biomarker and correlate to immune infiltration levels in gastric cancer. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - October 13, 2021 Category: Genetics & Stem Cells Source Type: research

A Multi-Marker Test for Analyzing Paired Genetic Data in Transplantation
Emerging evidence suggests that donor/recipient matching in non-HLA (human leukocyte antigen) regions of the genome may impact transplant outcomes and recognizing these matching effects may increase the power of transplant genetics studies. Most available matching scores account for either single-nucleotide polymorphism (SNP) matching only or sum these SNP matching scores across multiple gene-coding regions, which makes it challenging to interpret the association findings. We propose a multi-marker Joint Score Test (JST) to jointly test for association between recipient genotype SNP effects and a gene-based matching score ...
Source: Frontiers in Genetics - October 13, 2021 Category: Genetics & Stem Cells Source Type: research

Molecular Cytogenetics in the Era of Chromosomics and Cytogenomic Approaches
Here the role of molecular cytogenetics in the context of yet available all other cytogenomic approaches is discussed. A short introduction how cytogenetics and molecular cytogenetics were established is followed by technical aspects of fluorescence in situ hybridization (FISH). The latter contains the methodology itself, the types of probe- and target-DNA, as well as probe sets. The main part deals with examples of modern FISH-applications, highlighting unique possibilities of the approach, like the possibility to study individual cells and even individual chromosomes. Different variants of FISH can be used to retrieve in...
Source: Frontiers in Genetics - October 13, 2021 Category: Genetics & Stem Cells Source Type: research

A Novel Six Autophagy-Related Genes Signature Associated With Outcomes and Immune Microenvironment in Lower-Grade Glioma
Since autophagy and the immune microenvironment are deeply involved in the tumor development and progression of Lower-grade gliomas (LGG), our study aimed to construct an autophagy-related risk model for prognosis prediction and investigate the relationship between the immune microenvironment and risk signature in LGG. Therefore, we identified six autophagy-related genes (BAG1, PTK6, EEF2, PEA15, ITGA6, and MAP1LC3C) to build in the training cohort (n = 305 patients) and verify the prognostic model in the validation cohort (n = 128) and the whole cohort (n = 433), based on the data from The Cancer Genome Atlas (TCGA). The ...
Source: Frontiers in Genetics - October 13, 2021 Category: Genetics & Stem Cells Source Type: research

Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.)
APETALA2/ethylene response element-binding factor (AP2/ERF) transcription factors (TFs) have been found to regulate plant growth and development and response to various abiotic stresses. However, detailed information of AP2/ERF genes in peanut against drought has not yet been performed. Herein, 185 AP2/ERF TF members were identified from the cultivated peanut (A. hypogaea cv. Tifrunner) genome, clustered into five subfamilies: AP2 (APETALA2), ERF (ethylene-responsive-element-binding), DREB (dehydration-responsive-element-binding), RAV (related to ABI3/VP), and Soloist (few unclassified factors)). Subsequently, the phylogen...
Source: Frontiers in Genetics - October 13, 2021 Category: Genetics & Stem Cells Source Type: research

SS-RNN: A Strengthened Skip Algorithm for Data Classification Based on Recurrent Neural Networks
Recurrent neural networks are widely used in time series prediction and classification. However, they have problems such as insufficient memory ability and difficulty in gradient back propagation. To solve these problems, this paper proposes a new algorithm called SS-RNN, which directly uses multiple historical information to predict the current time information. It can enhance the long-term memory ability. At the same time, for the time direction, it can improve the correlation of states at different moments. To include the historical information, we design two different processing methods for the SS-RNN in continuous and...
Source: Frontiers in Genetics - October 13, 2021 Category: Genetics & Stem Cells Source Type: research

Peripheral Blood-Based Gene Expression Studies in Schizophrenia: A Systematic Review
Schizophrenia is a disorder that is characterized by delusions, hallucinations, disorganized speech or behavior, and socio-occupational impairment. The duration of observation and variability in symptoms can make the accurate diagnosis difficult. Identification of biomarkers for schizophrenia (SCZ) can help in early diagnosis, ascertaining the diagnosis, and development of effective treatment strategies. Here we review peripheral blood-based gene expression studies for identification of gene expression biomarkers for SCZ. A literature search was carried out in PubMed and Web of Science databases for blood-based gene expres...
Source: Frontiers in Genetics - October 13, 2021 Category: Genetics & Stem Cells Source Type: research