Enhanced phenylpropanoid metabolism underlies resistance to Fusarium oxysporum f. sp. vasinfectum race 4 infection in the cotton cultivar Pima-S6 (Gossypium barbadense L.)
Discussion: Our results highlight an essential role for the phenylpropanoid synthesis pathway in FOV4 resistance in Pima-S6 cotton. These genes represent attractive research prospects for FOV4-disease resistance and breeding approaches of other cotton cultivars of economic relevance. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 8, 2024 Category: Genetics & Stem Cells Source Type: research
Natural and artificial selection of multiple alleles revealed through genomic analyses
Genome-to-phenome research in agriculture aims to improve crops through in silico predictions. Genome-wide association study (GWAS) is potent in identifying genomic loci that underlie important traits. As a statistical method, increasing the sample quantity, data quality, or diversity of the GWAS dataset positively impacts GWAS power. For more precise breeding, concrete candidate genes with exact functional variants must be discovered. Many post-GWAS methods have been developed to narrow down the associated genomic regions and, ideally, to predict candidate genes and causative mutations (CMs). Historical natural selection ...
Source: Frontiers in Genetics - January 8, 2024 Category: Genetics & Stem Cells Source Type: research
Erratum: Integration of multiple-omics data to reveal the shared genetic architecture of educational attainment, intelligence, cognitive performance, and Alzheimer ’s disease
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 5, 2024 Category: Genetics & Stem Cells Source Type: research
Erratum: Community dynamics and co-occurrence relationships of pelagic ciliates and their potential prey at a coastal and an offshore station in the ultra-oligotrophic Eastern Mediterranean Sea
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 5, 2024 Category: Genetics & Stem Cells Source Type: research
Phylogenetic conservation of Trop-2 across species —rodent and primate genomics model anti-Trop-2 therapy for pre-clinical benchmarks
A phylogenetic conservation analysis of Trop-2 across vertebrate species showed a high degree of sequence conservation, permitting to explore multiple models as pre-clinical benchmarks. Sequence divergence and incomplete conservation of expression patterns were observed in mouse and rat. Primate Trop-2 sequences were found to be 95%–100% identical to the human sequence. Comparative three-dimension primate Trop-2 structures were obtained with AlphaFold and homology modeling. This revealed high structure conservation of Trop-2 (0.66 ProMod3 GMQE, 0.80–0.86 ± 0.05 QMEANDisCo scores), with conservative amino acid changes ...
Source: Frontiers in Genetics - January 5, 2024 Category: Genetics & Stem Cells Source Type: research
Variable clinical presentation of split hand/foot malformation syndrome in a family with microduplication of 10q24.32: a case report
SHFM (Split Hand/Foot Malformation) is a heterogeneous group of disorders characterized by the presence of clefts in the hands and feet, along with syndactyly of the digits. In this article, we describe a family in which two members exhibit characteristic developmental abnormalities associated with SHFM, presenting with variable clinical features. Using whole-genome sequencing, we identified a microduplication of a chromosomal segment on locus 10q24.32, specifically spanning positions 102934495 to 103496555, encompassing genes BTRC, POLL, FBXW4 and LBX1 in the proband. Genomic duplications, including these genes, were prev...
Source: Frontiers in Genetics - January 5, 2024 Category: Genetics & Stem Cells Source Type: research
Next-generation sequencing testing in children with epilepsy reveals novel clinical, diagnostic and therapeutic implications
Conclusion: This study demonstrates the high diagnostic and therapeutic utility of large panel testing in childhood epilepsies irrespective of seizure types. Copy number variations and somatic mosaic variants are important disease-causing factors, pointing the need for comprehensive genetic testing in all unexplained cases. Pleiotropy is a common phenomenon contributing to the growing phenotypic complexity of single-gene epilepsies. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 5, 2024 Category: Genetics & Stem Cells Source Type: research
Causal association between colorectal cancer and Alzheimer ’s disease: a bidirectional two-sample mendelian randomization study
Conclusion: According to the findings of this Mendelian randomization study, there appears to be a causal association between colorectal cancer and Alzheimer’s disease. These results could have important implications for clinical practice in terms of how colorectal cancer and Alzheimer’s disease are treated. To better understand the relationship between these two diseases, more research and screening are needed in clinical settings. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 5, 2024 Category: Genetics & Stem Cells Source Type: research
Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells
In this study, we evaluated the gene expression profiles of the RUNX3- and the ZBTB46-instructed murine ESCs with RNA-seq testing two next-generation sequencing technologies.Methods: We compared the DNA nanoball-based DNBSEQ G400 sequencer (MGI) with the bridge-PCR-based NextSeq 500 instrument (Illumina) for RNA sequencing. Moreover, we also compared two types of MGI sequencing reagents (Standard versus Hot-massive parallel sequencing (MPS)) with the DNBSEQ G400.Results: We observed that both sequencing platforms showed comparable levels of quality, sequencing uniformity, and gene expression profiles. For example, highly o...
Source: Frontiers in Genetics - January 5, 2024 Category: Genetics & Stem Cells Source Type: research
Exploiting in silico structural analysis to introduce emerging genotype –phenotype correlations in DHCR24-related sterol biosynthesis disorder: a case study
This report expands the clinical and molecular spectra of the DHCR24-related disorder, reports on a novel DHCR24 deleterious variant associated with desmosterolosis, and gives new insights into genotype–phenotype correlations. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 4, 2024 Category: Genetics & Stem Cells Source Type: research
Systematic comparison of variant calling pipelines of target genome sequencing cross multiple next-generation sequencers
In this study, we performed a TS of Reference OncoSpan FFPE (HD832) sample enriched by TSO500 panel using four commercially available sequencers, and analyzed the output 50 datasets using five commonly-used bioinformatics pipelines. We systematically investigated the sequencing quality and variant detection sensitivity, expecting to provide optimal recommendations for future research. Four sequencing platforms returned highly concordant results in terms of base quality (Q20 > 94%), sequencing coverage (>97%) and depth (>2000×). Benchmarking revealed good concordance of variant calling across different platforms a...
Source: Frontiers in Genetics - January 4, 2024 Category: Genetics & Stem Cells Source Type: research
Dissecting cellular heterogeneity and intercellular communication in cholangiocarcinoma: implications for individualized therapeutic strategies
Conclusion: Our findings reveal the intricate cellular heterogeneity and dynamic intercellular communication in cholangiocarcinoma, providing valuable insights into disease progression and potential therapeutic strategies. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 4, 2024 Category: Genetics & Stem Cells Source Type: research
Association between gut microbiota and glioblastoma: a Mendelian randomization study
Conclusion: This groundbreaking study is the first to demonstrate that family.Ruminococcaceae is significantly associated with a reduced risk of GBM. The modulation of family_Ruminococcaceae for the treatment of GBM holds considerable potential clinical significance. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 4, 2024 Category: Genetics & Stem Cells Source Type: research
Integration of multi-omics technologies for molecular diagnosis in ataxia patients
Conclusion: Despite failure to identify pathogenic variants through clinical genetic testing, the multi-omics approach enabled the molecular diagnosis in 50% of patients, also giving valuable insights for variant prioritization in remaining cases. The findings demonstrate the value of long-read sequencing for the validation of candidate variants in various scenarios. Our study demonstrates the effectiveness of leveraging complementary omics technologies to unravel the underlying genetics in patients with unresolved rare diseases such as ataxia. Molecular diagnoses not only hold significant promise in improving patient care...
Source: Frontiers in Genetics - January 4, 2024 Category: Genetics & Stem Cells Source Type: research
“A very big challenge”: a qualitative study to explore the early barriers and enablers to implementing a national genomic medicine service in England
Conclusion: Our findings highlight the challenges of implementing system-wide change within a complex healthcare system. Local as well as national solutions can undoubtedly address many of these barriers over time. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 4, 2024 Category: Genetics & Stem Cells Source Type: research
