Transcriptome profiling and analysis of patients with esophageal squamous cell carcinoma from Kazakhstan
This study aimed to unravel ESCC’s genetic basis in Kazakhstani patients and identify potential biomarkers for early diagnosis and targeted therapies. ESCC patients from Kazakhstan were studied. We analyzed histological subtypes and conducted in-depth transcriptome sequencing. Differential gene expression analysis was performed, and significantly dysregulated pathways were identified using KEGG pathway analysis (p-value < 0.05). Protein-protein interaction networks were constructed to elucidate key modules and their functions. Among Kazakhstani patients, ESCC with moderate dysplasia was the most prevalent subtype. We ...
Source: Frontiers in Genetics - March 18, 2024 Category: Genetics & Stem Cells Source Type: research

Single nucleotide variants in nuclear pore complex disassembly pathway associated with poor survival in osteosarcoma
Discussion:Overall survival is significantly worse in patients whose tumors show aberrations in the NPCD pathway. Moreover, this difference in survival is not driven by MYC-overexpression, suggesting a novel mechanism for some aggressive osteosarcomas. These findings add light to the evolving understanding of the drivers of osteosarcoma and may aid in the search for new treatments based on patient-specific genetic data. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 18, 2024 Category: Genetics & Stem Cells Source Type: research

Genomic analysis in Chilean patients with suspected Rett syndrome: keep a broad differential diagnosis
This study allowed to reach a diagnosis in half of the participants. The diagnosis of RTT was confirmed in over a third of them, while others were found to have alternative neurodevelopmental disorders. Further evaluation is needed to identify the cause in those with negative or uncertain results. This information is useful for the patients, families, and clinicians to guide clinical management, even more so since the development of novel therapies for RTT. We also show the feasibility of implementing a step-wide approach to genomic testing in a setting with limited resources. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 18, 2024 Category: Genetics & Stem Cells Source Type: research

Race, ethnicity, ancestry, and aspects that impact HLA data and matching for transplant
This article describes aspects of race, ethnicity and ancestry information that impact the stem-cell or solid organ transplantation field with particular focus on HLA data collected from donors and recipients by donor registries or transplant centers. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 15, 2024 Category: Genetics & Stem Cells Source Type: research

Impact of deep phenotyping: high diagnostic yield in a diverse pediatric population of 172 patients through clinical whole-genome sequencing at a single center
This study investigates the diagnostic yield of whole-genome sequencing (WGS) in a pediatric cohort with diverse phenotypes, particularly focusing on the role of clinical expertise in interpreting WGS results.Methods: A retrospective cohort study was conducted at Acibadem University’s Maslak Hospital in Istanbul, Turkey, involving pediatric patients (0–18 years) who underwent diagnostic WGS testing. Clinical assessments, family histories, and previous laboratory and imaging studies were analyzed. Variants were classified and interpreted in conjunction with clinical findings.Results: The cohort comprised 172 pediatric ...
Source: Frontiers in Genetics - March 15, 2024 Category: Genetics & Stem Cells Source Type: research

Intelligent computation in cancer gene therapy
In recent years, the use of gene therapy for the treatment of disease has gained substantial interest, both in academic research and in the biomedical industry. Initial experimentation in gene therapy has generated positive results, as well as questions regarding safety. However, lessons have been learned from these first investigations, among them a realization that such treatments require a method to fine-tune the expression of therapeutic genes in real-time. A logical solution to this problem arose through the field of synthetic biology in the form of synthetic gene circuits. Thus, the synthetic biology community today ...
Source: Frontiers in Genetics - March 14, 2024 Category: Genetics & Stem Cells Source Type: research

Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific
In this study, a Gram-stain positive and ovoid-rod shaped the actinobacterium strain R16 was isolated from deep-sea sediment (with a depth of 6,310 m) in the Western Pacific. On the basis of 16S rRNA gene sequence analysis, average nucleotide identity and phylogenomic analysis, strain R16 clearly represents a novel species within the genus Prescottella. Genomic analyses indicate Prescottella sp. R16 contains a circular chromosome of 4,531,251 bp with an average GC content of 68.9%, 4,208 protein-coding genes, 51 tRNA genes, and 12 rRNA operons. Additionally, four CRISPRs and 24 genomic islands are also identified. The pre...
Source: Frontiers in Genetics - March 14, 2024 Category: Genetics & Stem Cells Source Type: research

Non-coding RNA and reprogrammed mitochondrial metabolism in genitourinary cancer
Non-coding ribonucleic acids (ncRNAs) have been recently shown to contribute to tumorigenesis by mediating changes in metabolism. ncRNAs act as key molecules in metabolic pathways regulation. The dysregulation of ncRNAs during cancer progression contributes to altered metabolic phenotypes leading to reprogrammed metabolism. Since ncRNAs affect different tumor processes by regulating mitochondrial dynamics and metabolism, in the future ncRNAs can be exploited in disease detection, diagnosis, treatment, and resistance. The purpose of this review is to highlight the role of ncRNAs in mitochondrial metabolic reprogramming and ...
Source: Frontiers in Genetics - March 13, 2024 Category: Genetics & Stem Cells Source Type: research

Editorial: Enriching genomic breeding with environmental covariates, crop models, and high-throughput phenotyping
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 13, 2024 Category: Genetics & Stem Cells Source Type: research

Genetic architecture of body weight, carcass, and internal organs traits of Ghanaian local chickens
Information on the genetic architecture of the production traits of indigenous African chicken is limited. We performed a genome-wide association study using imputed Affymetrix Axiom® 600K SNP-chip genotypes on 1,113 chickens from three agroecological zones of Ghana. After quality control, a total of 382,240 SNPs remained. Variance components and heritabilities for some growth, carcass and internal organ traits were estimated. The genetic and phenotypic correlations among these traits were also estimated. The estimated heritabilities of body weight at week 22 (BW22), average daily gain (ADG), dressed weight, breast weight...
Source: Frontiers in Genetics - March 13, 2024 Category: Genetics & Stem Cells Source Type: research

TCRpred: incorporating T-cell receptor repertoire for clinical outcome prediction
T-cell receptor (TCR) plays critical roles in recognizing antigen peptides and mediating adaptive immune response against disease. High-throughput technologies have enabled the sequencing of TCR repertoire at the single nucleotide level, allowing researchers to characterize TCR sequences with high resolutions. The TCR sequences provide important information about patients’ adaptive immune system, and have the potential to improve clinical outcome prediction. However, it is challenging to incorporate the TCR repertoire data for prediction, because the data is unstructured, highly complex, and TCR sequences vary widely in ...
Source: Frontiers in Genetics - March 13, 2024 Category: Genetics & Stem Cells Source Type: research

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat
This study involved a comprehensive examination of population structure, genomic diversity, and regions of selection in Xiangdong black goats utilizing whole-genome sequencing data from 20 samples of this breed and 139 published samples from six other Chinese goat breeds. Our genomic analysis revealed a total of 19,133,125 biallelic single nucleotide polymorphisms (SNPs) within the Xiangdong black goat genome, primarily located in intergenic and intronic regions. Population structure analysis indicated that, compared with Jintang, Guizhou and Chengdu goats, Xiangdong black goats exhibit a reduced level of genetic different...
Source: Frontiers in Genetics - March 13, 2024 Category: Genetics & Stem Cells Source Type: research

Association of glutamate receptor gene polymorphisms with attention-deficit hyperactivity disorder susceptibility: a systematic review and meta-analysis
Conclusion: The results of the meta-analysis provide strong evidence that the rs2284411 T allele is significantly associated with reduced susceptibility to ADHD, particularly in the Korean population. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 13, 2024 Category: Genetics & Stem Cells Source Type: research

Long-read sequencing reveals chromothripsis in a molecularly unsolved case of Cornelia de Lange syndrome
Thanks to a long-read sequencing (LRS) approach, in this study, we have reported a molecularly solved case of a proband with a clinical diagnosis of Cornelia de Lange syndrome (CDLS), which is a multisystemic disorder whose causative molecular defects involve cohesin complex genes, with NIPBL located at 5p13.2 accounting for approximately 50%–60% of CDLS cases. The first-tier tests revealed an abnormal karyotype 46,XY,t(5;15)(p13;q25)dn and a preserved NIPBL sequencing. Copy number variants (CNVs) at the translocation breakpoints, in disease genes, or in probably pathogenic loci were excluded by a-CGH analysis. Through f...
Source: Frontiers in Genetics - March 13, 2024 Category: Genetics & Stem Cells Source Type: research

PCGIMA: developing the web server for human position-defined CpG islands methylation analysis
This study develops Human position-defined CGI prediction method to locate CpG islets using high performance computing, and then builds up a novel human genome annotation and analysis method to investigate the connections among CGI, gene expression and methylation. Finally, we integrate these functions into PCGIMA to provide relevant online computing and visualization service.Results: The main results include: (1) Human position-defined CGI prediction method is more efficient to predict position-defined CGIs with multiple consecutive (d) values and locate more potential short CGIs than previous CGI prediction methods. (2) ...
Source: Frontiers in Genetics - March 13, 2024 Category: Genetics & Stem Cells Source Type: research