Frontiers in Genetics最新文献

{"title":"From genetic data to kinship clarity: employing machine learning for detecting incestuous relations.","authors":"Dejan Šorgić, Aleksandra Stefanović, Mladen Popović, Dušan Keckarević","doi":"10.3389/fgene.2025.1578581","DOIUrl":"10.3389/fgene.2025.1578581","url":null,"abstract":"<p><strong>Introduction: </strong>The aim of the study was to develop a predictive model based on STR profiles of mothers and children for the detection of incestuous conception.</p><p><strong>Methods: </strong>Based on allele frequency data from the USA and Saudi Arabia, STR profiles were generated and used to simulate offspring profiles corresponding to father-child and brother-sister incest scenarios. Model training and evaluation were performed using the STR profiles of the mother and child. In addition to the baseline model, we examined its performance under a one-step mutation model, as well as its ability to detect incestuous relationships based solely on the child's STR profile. Several machine learning algorithms and neural networks were tested for classification accuracy.</p><p><strong>Results: </strong>The CatBoost algorithm performed best in the binary classification of Normal Paternity vs. Incest Kinship. For the USA, we achieved the following results: 96.94% for 29 markers and 95% for 21 markers. The same accuracy was obtained with a single-step mutation, while prediction based on child profiles exclusively yielded an accuracy of 90.37% in the U.S. population. When analysing profiles from Saudi Arabia and modified Saudi frequencies, an accuracy of 94% was achieved.</p><p><strong>Discussion: </strong>It was established that population structure does not affect the model's accuracy and that it can be applied even in isolated populations.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1578581"},"PeriodicalIF":2.8,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12171372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactions.","authors":"João B Silva Neto, Luiz F Brito, Lucio Flavio M Mota, Claudio U Magnabosco, Fernando Baldi","doi":"10.3389/fgene.2025.1539056","DOIUrl":"10.3389/fgene.2025.1539056","url":null,"abstract":"<p><strong>Introduction: </strong>Feed efficiency is a key factor in animal production sustainability, directly affecting production costs, environmental efficiency, and farmer profitability. The inclusion of feeding efficiency traits in cattle breeding programs has occurred later than other species due to longer life cycles and the high costs associated with measuring feed intake. However, genomic selection has facilitated the inclusion of difficult-to-measure traits in selection schemes. Thus, understanding the genetic basis of feed efficiency, particularly under varying environmental conditions, is essential.</p><p><strong>Methods: </strong>This study aimed to identify genomic regions associated with dry matter intake (DMI) and residual feed intake (RFI) in Nellore cattle by performing a genome-wide association study (GWAS) based on single-step genomic reaction norm models that account for genotype-by-environment interactions (G×E). Phenotypic data from 23,170 young bulls and heifers were collected across 301 feed efficiency trials. Genomic windows explaining more than 1% of the total direct additive genetic variance were identified for both the intercept and slope components of the reaction norm for each trait.</p><p><strong>Results: </strong>For RFI, ten and eleven genomic windows explained more than 1% of the genetic variance for the intercept and slope, respectively. For DMI, 12 windows were identified for the intercept and 17 for the slope. Within these regions, Multiple protein-coding genes were annotated (RFI: 66 for intercept and 47 for slope; DMI: 107 for intercept and 109 for slope), which are involved in key biological processes such as insulin, leptin, glucose, protein, and lipid metabolism; energy balance; heat stress response; feeding behavior; digestion; and nutrient absorption.</p><p><strong>Discussion: </strong>The results highlight the functional diversity of genes involved in feed efficiency and their dynamic response to environmental variation. While certain genes remained central across environments, others were specifically important under more challenging conditions, emphasizing the role of G×E in regulating these traits. Furthermore, the magnitude and direction of SNP effects varied across environmental gradients, reinforcing the relevance of G×E. Consequently, genomic estimated breeding values for DMI and RFI also differed between environmental extremes. These findings underscore the adaptability of genetic networks to environmental changes and are essential for refining strategies to improve feed efficiency in Nellore cattle.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1539056"},"PeriodicalIF":2.8,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12171144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autosomal dominant myopathy caused by a novel <i>ISCU</i> variant.","authors":"Joanna M Rusecka, Camilla Ceccatelli Berti, Dominika Szczęśniak, Małgorzata Bednarska-Makaruk, Magdalena Mroczek, Magdalena M Kacprzak, Agnieszka Sobczyńska-Tomaszewska, Paola Goffrini","doi":"10.3389/fgene.2025.1605440","DOIUrl":"10.3389/fgene.2025.1605440","url":null,"abstract":"<p><p>Hereditary myopathy with lactic acidosis due to Iron-Sulfur Cluster Assembly Enzyme (ISCU) deficiency is a rare disorder of energy metabolism characterized clinically by myopathy with exercise intolerance, and biochemically by deficiencies of skeletal muscle mitochondrial respiratory chain enzymes. ISCU protein plays an important role in iron-sulphur clusters (Fe-S) assembly and is therefore essential for the activity of mitochondrial Fe-S proteins such as succinate dehydrogenase and aconitase. Recessive hypomorphic <i>ISCU</i> alleles have been associated with hereditary myopathy with lactic acidosis, also known as Swedish-type myopathy. To date, only one heterozygous dominant variant (c.287G>T, p.Gly96Val) in the ISCU gene has been reported as pathogenic. Functional studies have shown that this variant has a detrimental, dominant effect on activity of Fe-S-dependent enzymes. Whole exome sequencing performed in an adult female patient with progressive muscle weakness led to the identification of a novel heterozygous variant c.399del (p.Val134Ter) in the ISCU gene. This variant is localized in the functional IscU_like domain of the ISCU protein, with bioinformatics prediction of damaging effects on protein function. Moreover, the same variant was also found in a few family members, who present signs of myopathy. This novel variant segregates with the disease and results in a phenotype reminiscent of the recessive disease previously reported. Yeast <i>Saccharomyces cerevisiae</i> is a widely used tool able to assess the impact of the VUS in a quick and efficient way, therefore functional studies were performed on this model system. The results obtained not only confirm the pathogenetic effect of the variant, but also support its dominant inheritance.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1605440"},"PeriodicalIF":2.8,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12171185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and validation of sex-associated markers using whole-genome re-sequencing in frog <i>Quasipaa spinosa</i>.","authors":"Liaoruilin Zhang, Juan Li, Xiang Li, Jinrong He, Jie Zhou, Jinliang Hou, Yulu Liu, Lei Zhang, Yanfei Huang, Hong Li, Xiaolin Liao, Xinhua Liu, Yazhou Hu, Deliang Li, Jianguo Xiang","doi":"10.3389/fgene.2025.1596192","DOIUrl":"10.3389/fgene.2025.1596192","url":null,"abstract":"<p><p>The development of sex markers is crucial for addressing monosexual breeding in aquaculture species and for identifying traits that are sexually inherited, especially for elucidating the mechanisms of sex determination in amphibians. In aquaculture, comprehending sex determination is especially vital because the market value of animal products frequently depends on their sex. <i>Quasipaa spinosa</i> (Anura, Dicroglossidea) is a valuable frog species in the aquaculture industry of China and southeast Asia, yet there exists limited genomic information regarding this organism. Current data indicates that the adoption of all-male breeding techniques in <i>Q. spinosa</i> could substantially benefit the Chinese aquaculture industry, both by augmenting its economic prospects and by ensuring the effectiveness of wildlife reintroduction efforts. The growth rate, adult size, disease resistance, and other traits of male <i>Q. spinosa</i> surpass those of females, making the development of all-male breeding a significant focus in the <i>Q. spinosa</i> aquaculture industry. Therefore, it is imperative to establish a marker specific to males. In this research, we used the male <i>Q. spinosa</i> genome as reference and performed whole-genome resequencing on 30 males and 30 females. Subsequently, we exhibited evident sexual differentiation on chromosome 3 and primers were designed for PCR detection of the identified candidate male INDEL loci. Ultimately, two sex-associated INDELs that could be effectively detected were obtained and validated on the samples collected from the remaining three locations, thereby confirming the robustness of these two INDELs for sex identification in <i>Q. spinosa</i>.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1596192"},"PeriodicalIF":2.8,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12171147/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The mechanism of RNA methylation writing protein-related prognostic genes in lung adenocarcinoma based on bioinformatics.","authors":"Sha Yin, Guangyan Luo, Lei Luo","doi":"10.3389/fgene.2025.1541541","DOIUrl":"10.3389/fgene.2025.1541541","url":null,"abstract":"<p><strong>Objective: </strong>RNA methylation modifications play biological roles in tumorigenicity and immune response, mainly mediated by the \"writer\" enzyme. Lung adenocarcinoma (LUAD) development is closely related to RNA methylation. Here, the prognostic values of the \"writer\" enzymes and the tumor immunosurveillance in LUAD aim to provide new theoretical references for the research of LUAD.</p><p><strong>Methods: </strong>Genes associated with RNA methylation writer protein in LUAD were identified using The Cancer Genome Atlas Program (TCGA) data and weighted gene co-expression network analysis (WGCNA). Independent prognostic factors were screened by Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. A prognostic risk model and a nomogram were established using these genes. Moreover, Gene Set Enrichment Analysis (GSEA) and CIBERSORTx were used to analyze the immune cell infiltration and enrichment pathways in the low- and high-risk groups, respectively. In addition, genes' potential functions and regulatory mechanisms were explored through gene-gene interaction (GGI) networks and competing endogenous RNA (ceRNA) networks.</p><p><strong>Results: </strong>We selected 202 genes associated with RNA methylation writer proteins, from which we identified the three genes (CLEC3B, GRIA1, and ANOS1). A prognostic risk model was constructed based on genes associated with RNA methylation writer proteins and stage, demonstrating reliable predictive performance. GGI analysis revealed GRIA1 as a crucial gene. Enrichment analysis revealed that the high-risk group had upregulated pathways connected to cell division. Additionally, immune infiltration analysis revealed that the significantly higher levels of NK cells, activated mast cells, activated CD4 memory cells, and M0 and M1 macrophages displayed in the high-risk group, while the significantly lower levels of monocytes, dendritic cells, M2 macrophages, and inactive CD4 memory cells were in the low-risk group. Moreover, Spearman correlation analysis demonstrated that the three prognostic genes and risk scores correlated highly with various immune cells.</p><p><strong>Conclusion: </strong>This study identified three prognostic genes related to RNA methylation writer proteins in LUAD. A reliable prognostic model was constructed. The identified prognostic genes also play significant roles in immune cell infiltration in LUAD. This study provides new theoretical references for subsequent in-depth research on LUAD.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1541541"},"PeriodicalIF":2.8,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12171300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A non-invasive method for screening mitochondrial diabetes.","authors":"Hangyu Fang, Xiaoe Li, Shuping Wang, Mei Zhang, Victor Wei Zhang, Chao Xu","doi":"10.3389/fgene.2025.1536331","DOIUrl":"10.3389/fgene.2025.1536331","url":null,"abstract":"<p><strong>Background: </strong>Mitochondrial diabetes mellitus (MDM) is a special type of diabetes resulting from functional defects in mitochondria. Its incidence rate is low, and it can often be misdiagnosed as either type 1 or type 2 diabetes in clinical settings. Due to limited clinical experience in diagnosing and treating MDM, the rate of missed diagnosis is high. Therefore, employing appropriate detection methods for the rapid screening of suspected MDM patients can facilitate early diagnosis of MDM.</p><p><strong>Methods: </strong>We conducted a multicenter observational study by collecting oral exfoliated cells from patients and detecting the m.3243A>G mutation using Polymerase Chain Reaction (PCR). We estimated the positivity rate of MDM and clinically evaluated the detection method through clinical trials. Additionally, we summarized the clinical phenotypes of patients who tested positive and compared the clinical manifestations between MDM and non-MDM patients using statistical analysis, providing a diagnostic foundation for clinicians.</p><p><strong>Results: </strong>We collected data from a total of 478 patients and identified 16 cases of m.3243A>G mutation-positive patients by collecting oral exfoliated cell samples for PCR testing, yielding a positivity rate of 3.35% and an asymptomatic carrier rate of 0.84%. These results are slightly higher than those reported in previous research. The gene mutation detection method demonstrated high credibility and was non-invasive, with a clinical sensitivity of 87.2% and clinical specificity of 96.9%. Additionally, patient satisfaction was high in this study. Statistical analysis revealed a significant difference in clinical manifestations between MDM and non-MDM patients. MDM patients were more likely to experience neurological hearing loss and multiple systemic manifestations, and their condition was consistent with maternal inheritance, in line with previous research findings.</p><p><strong>Conclusion: </strong>The detection of the m.3243A>G mutation through the collection of oral exfoliated cells offers several advantages over other methods, including simplicity, non-invasiveness, and high specificity and sensitivity. However, it is currently underutilized. Therefore, further experiments are needed to study and validate this approach in order to optimize MDM screening methods and improve diagnostic rates for MDM.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1536331"},"PeriodicalIF":2.8,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12162994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of salinity stress on morphological structure, physiology, and mRNA expression in different wheat (<i>Triticum aestivum</i> L.) cultivars.","authors":"Xiaohui Sun, Yuliu Tan, Yumei Zhang, Weiwei Guo, Ximei Li, Nataliia Golub, Lili Zhang, Huifang Wang","doi":"10.3389/fgene.2025.1535610","DOIUrl":"10.3389/fgene.2025.1535610","url":null,"abstract":"<p><p>Salinity is a major abiotic stress that threatens crop yield and food supply in saline soil areas. Wheat (<i>Triticum aestivum</i> L.) is the most important cereal crop in arid and semiarid land areas, which are often adversely affected by soil salinity. Hence, creating salt tolerance wheat is of great value for utilizing saline soils. In this study, two wheat cultivars QingMai 6 (QM6, salt-tolerant) and Chinese Spring (CS, salt-sensitive) were subjected to salinity stress. Morphological analysis showed that the seedlings of QM6 grew better than CS under salt stress conditions, especially in roots. Electron microscopic studies revealed that salinity stress caused significantly more root hairs and less effect on normal chloroplast structure in QM6 than these in CS. Moreover, QM6 showed a higher photosynthetic activity under salt stress conditions compared to CS. Further investigation showed the salt-tolerant phenotypes of QM6 were accompanied by decreases of reactive oxygen species (ROS) content, and lower antioxidant enzyme activities after salt treatment compared with CS. Additionally, qRT-PCR analyses revealed that the expression level of ROS-scavenging genes (<i>TaSOD6</i>, <i>TaCAT1/5/6</i>, <i>TaPOD7, TaP5CS1</i>) and stress-responsive genes (<i>TaDREB3</i>, <i>TaWRKY19</i>, <i>TaERF5a, TaLTP1, TaTIP2</i>) displayed more transcripts in QM6 than CS. These results provide insight into the mechanisms underlying salt tolerance in wheat, and could be potentially used to develop salt tolerant wheat varieties.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1535610"},"PeriodicalIF":2.8,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12162971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights about the effect of sodium-glucose cotransporter 2 inhibitors: a systematic review.","authors":"Pavitraa Saravana Kumar, Yogapriya Chidambaram, G Shree Devi, Vettriselvi Venkatesan, Ramesh Sankaran, Nagendra Boopathy Senguttuvan, Thanikachalam Sadagopan, Dorairaj Prabhakaran","doi":"10.3389/fgene.2025.1571032","DOIUrl":"10.3389/fgene.2025.1571032","url":null,"abstract":"<p><strong>Introduction: </strong>Heart failure (HF) is a complex clinical syndrome with high morbidity and mortality, significantly burdening healthcare systems worldwide. Despite advances in therapy, effective treatment options remain limited. Sodium-glucose cotransporter 2 (SGLT2) inhibitors, initially developed for diabetes management, have demonstrated cardiovascular benefits, including reductions in HF hospitalizations and mortality. This systematic review examines the genomic effects of SGLT2 inhibitors in HF patients, focusing on gene expression, inflammatory biomarkers, and potential personalized treatment pathways.</p><p><strong>Methods: </strong>A systematic literature search of various databases was conducted up to November 2024, following PRISMA guidelines. Studies were included if they explored the genomic or molecular impacts of SGLT2 inhibitors in HF. Data extraction and analysis focused on gene expression changes, circulating biomarkers, and potential genomic mechanisms.</p><p><strong>Results: </strong>Of the 258 identified studies, three met the inclusion criteria. Key findings include: a) SGLT2 inhibitors downregulate pro-inflammatory genes in adipose tissue, reducing immune cell infiltration and ferroptosis; b) Genetic evidence highlights CXCL10 as a mediator of anti-inflammatory effects, with its inhibition linked to reduced HF risk; c) LRRTM2, a protein associated with synaptic formation, emerged as a critical mediator, with genetic links to reduced HF risk via SGLT2 inhibition.</p><p><strong>Discussion: </strong>This review underscores the genomic mechanisms through which SGLT2 inhibitors provide cardiovascular benefits. Key insights into gene expression modulation and protein interactions reveal pathways for personalized HF treatment. While findings are promising, further large-scale studies are needed to validate these mechanisms and their clinical implications.</p><p><strong>Systematic review registration: </strong>https://www.crd.york.ac.uk/prospero/, identifier CRD42024614674.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1571032"},"PeriodicalIF":2.8,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12162637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hapten-labeled DNA probes can be stored and used in fluorescence <i>in situ</i> hybridization for decades.","authors":"Thomas Liehr, Niklas Padutsch, Stefanie Kankel","doi":"10.3389/fgene.2025.1569308","DOIUrl":"10.3389/fgene.2025.1569308","url":null,"abstract":"<p><p>In molecular cytogenetics, fluorescence <i>in situ</i> hybridization (FISH) is the main technique used. In both research and diagnostics, FISH depends on well-defined and mapped DNA probes that produce brilliant signals with minimal background, visible in metaphases and/or interphases. Such probes are either ready-to-use and commercially available or provided as unlabeled DNA. The latter can be obtained by flow sorting, microdissection, or by cloning DNA segments into appropriate bacterial vectors. Labeling can be done with either nonfluorescent or fluorescent haptens. According to international guidelines, such FISH probes must have a minimum shelf life, which is only between 2 and 3 years in human genetic diagnostics. The Molecular Cytogenetics Laboratory reporting here has been purchasing, producing, using, and storing FISH probes since the 1990s. For this study, the available stock of approximately 25,000 labeled probes was screened. A total of 581 FISH probes, labeled and approved 1-30 years before reuse, were selected for this study; of these, 75 were commercially available probes labeled 1-20 years ago. All of these probes, stored in the dark at -20°C, worked perfectly well in the FISH method. Although only slight to no differences in exposure times were observed over the years for self-labeled homemade probes, commercial probes labeled with SpectrumOrange had shorter exposure times and maintained them over the years. DNA probes labeled with SpectrumAqua/diethylaminocoumarin showed bright labeling for the first 3 years and then faded. Accordingly, it can be assumed that self-labeled homemade and commercial FISH probes can be stored stably in the dark and at -20°C for at least 30 years or longer. There is no need to test approved probes on a slide after the official expiry date. In practice, this suggests that a FISH probe tube that has been approved can be used in diagnostics until it is empty; there is no need to dispose of these expensive probes at any point due to their age.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1569308"},"PeriodicalIF":2.8,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12163036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reference-free deconvolution of complex samples based on cross-cell-type differential analysis: Systematic evaluations with various feature selection options.","authors":"Weiwei Zhang, Zhonghe Tian, Ling Peng","doi":"10.3389/fgene.2025.1570781","DOIUrl":"10.3389/fgene.2025.1570781","url":null,"abstract":"<p><strong>Introduction: </strong>Genomic and epigenomic data from complex samples reflect the average level of multiple cell types. However, differences in cell compositions can introduce bias into many relevant analyses. Consequently, the accurate estimation of cell compositions has been regarded as an important initial step in the analysis of complex samples. A large number of computational methods have been developed for estimating cell compositions; however, their applications are limited due to the absence of reference or prior information. As a result, reference-free deconvolution has the potential to be widely applied due to its flexibility. A previous study emphasized the importance of feature selection for improving estimation accuracy in reference-free deconvolution.</p><p><strong>Methods: </strong>In this paper, we systematically evaluated five feature selection options and developed an optimal feature-selection-based reference-free deconvolution method. Our proposal iteratively searches for cell-type-specific (CTS) features by integrating cross-cell-type differential analysis between one cell type and the other cell types, as well as between two cell types and the other cell types, and performs composition estimation.</p><p><strong>Results and discussion: </strong>Comprehensive simulation studies and analyses of seven real datasets show the excellent performance of the proposed method. The proposed method, that is, reference-free deconvolution based on cross-cell-type differential (RFdecd), is implemented as an R package at https://github.com/wwzhang-study/RFdecd.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1570781"},"PeriodicalIF":2.8,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12162504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}