Frontiers in Genetics最新文献

{"title":"Blood toxicogenomics reveals potential biomarkers for management of idiosyncratic drug-induced liver injury.","authors":"Rachel J Church, Benedict Anchang, Brian D Bennett, Pierre R Bushel, Paul B Watkins","doi":"10.3389/fgene.2025.1524433","DOIUrl":"https://doi.org/10.3389/fgene.2025.1524433","url":null,"abstract":"<p><p><b>Introduction:</b> Accurate diagnosis, assessment, and prognosis of idiosyncratic drug-induced liver injury (IDILI) is problematic, in part due to the shortcomings of traditional blood biomarkers. Studies in rodents and healthy volunteers have supported that RNA transcript changes in whole blood may address some of these shortcomings. <b>Methods:</b> In this study, we conducted RNA-Seq analysis on peripheral blood samples collected from 55 patients with acute IDILI and 17 patients with liver injuries not attributed to IDILI. <b>Results and discussion:</b> Three differentially expressed genes (DEGs; <i>CFD</i>, <i>SQLE</i>, and <i>INKA1</i>) were identified as significantly associated with IDILI vs. other liver injuries. No DEGs were identified comparing IDILI patients to the 5 patients with autoimmune hepatitis, suggesting possible common underlying mechanisms. Two genes (<i>VMO1</i> and <i>EFNA1</i>) were significantly associated with hepatocellular injury compared to mixed/cholestatic injury. When patients with severe vs. milder IDILI were compared, we identified over 500 DEGs. The top pathways identified from these DEGs had in common down regulation of multiple T-cell specific genes. Further analyses confirmed that these changes could largely be accounted for by a fall in the concentration of circulating T-cells during severe DILI, perhaps due to exhaustion or sequestration of these cells in the liver. Exploration of DEGs specific for the individual causal agents was largely unsuccessful, but isoniazid-induced IDILI demonstrated 25 DEGs compared to other non-isoniazid IDILI cases. Finally, among the 14 IDILI patients that had hepatocellular jaundice (i.e., Hy's Law cases), we identified 39 DEGs between the 4 patients with fatal or liver transplantation outcomes compared to those that recovered. These findings suggest the potential for blood-based transcriptomic biomarkers to aid in the diagnosis and prognostic stratification of IDILI.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1524433"},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11975945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811022","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":"Karyotype and genome size analyses for two spiders of the lycosidae family.","authors":"Yuxuan Zhang, Mengying Zhang, Liang Leng, Ya Wu, Hanting Yang, Liangting Wang, Baimei Liu, Shuai Yang, Zizhong Yang, Shilin Chen, Chi Song","doi":"10.3389/fgene.2025.1544087","DOIUrl":"https://doi.org/10.3389/fgene.2025.1544087","url":null,"abstract":"<p><strong>Background: </strong>Karyotype and genome size are critical genetic characteristics with significant value for cytogenetics, taxonomy, phylogenetics, evolution, and molecular biology. The Lycosidae family, known for its diverse spiders with varying ecological habits and behavioral traits, has seen limited exploration of its karyotype and genome size.</p><p><strong>Methods: </strong>We utilized an improved tissue drop technique to prepare chromosome slides and compare the features of male and female karyotypes for two wolf spiders with different habits of Lycosidae. Furthermore, we predicted their genome sizes using flow cytometry (FCM) and K-mer analysis.</p><p><strong>Results: </strong>The karyotypes of female and male <i>Hippasa lycosina</i> were 2n♀ = 26 = 14 m + 12 sm and 2n♂ = 24 = 10 m + 14 sm, respectively, and were composed of metacentric (m) and submetacentric (sm) chromosomes. In contrast, the karyotypes of <i>Lycosa grahami</i> consisted of telocentric (t) and subtelocentric (st) chromosomes (2n♀ = 20 = 20th and 2n♂ = 18 = 12th + 6t, for females and males). The sex chromosomes were both X₁X₂O. The estimated sizes of the <i>H. lycosina</i> and <i>L. grahami</i> genomes were 1966.54-2099.89 Mb and 3692.81-4012.56 Mb, respectively. Flow cytometry yielded slightly smaller estimates for genome size compared to k-mer analysis. K-mer analysis revealed a genome heterozygosity of 0.42% for <i>H. lycosina</i> and 0.80% for <i>L. grahami</i>, along with duplication ratios of 21.39% and 54.91%, respectively.</p><p><strong>Conclusion: </strong>This study describes the first analysis of the genome sizes and karyotypes of two spiders from the Lycosidae that exhibit differential habits and provides essential data for future phylogenetic, cytogenetic, and genomic studies.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1544087"},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11975668/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811036","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":"Genetic analysis reveals the shared genetic architecture between breast cancer and atrial fibrillation.","authors":"Yang Yang, Jiayi Chen, XiaoHua Zhao, Fuhong Gong, Ruimin Liu, Jingge Miao, Mengping Lin, Fei Ge, Wenlin Chen","doi":"10.3389/fgene.2025.1450259","DOIUrl":"https://doi.org/10.3389/fgene.2025.1450259","url":null,"abstract":"<p><strong>Background: </strong>Epidemiological studies have observed an association between atrial fibrillation (AF) and breast cancer (BC). However, the underlying mechanisms linking these two conditions remain unclear. This study aims to systematically explore the genetic association between AF and BC.</p><p><strong>Methods: </strong>We utilized the largest available genome-wide association study (GWAS) datasets for European individuals, including summary data for AF (N = 1,030,836) and BC (N = 247,173). Multiple approaches were employed to systematically investigate the genetic relationship between AF and BC from the perspectives of pleiotropy and causality.</p><p><strong>Results: </strong>Global genetic analysis using LDSC and HDL revealed a genetic correlation between AF and BC (rg = 0.0435, P = 0.039). Mixer predicted genetic overlap between non-MHC regions of the two conditions (n = 125, rg = 0.05). Local genetic analyses using LAVA and GWAS-PW identified 22 regions with potential genetic sharing. Cross-trait meta-analysis by CPASSOC identified one novel pleiotropic SNP and 14 pleiotropic SNPs, which were subsequently annotated. Eight of these SNPs passed Bayesian colocalization tests, including one novel pleiotropic SNP. Further fine-mapping analysis identified a set of causal SNPs for each significant SNP. TWAS analyses using JTI and FOCUS models jointly identified 10 pleiotropic genes. Phenome-wide association study (PheWAS) of novel pleiotropic SNPs identified two eQTLs (PELO, ITGA1). Gene-based PheWAS results showed strong associations with BMI, height, and educational attainment. PCGA methods combining GTEx V8 tissue data and single-cell RNA data identified 16 co-enriched tissue types (including cardiovascular, reproductive, and digestive systems) and 5 cell types (including macrophages and smooth muscle cells). Finally, univariable and multivariable bidirectional Mendelian randomization analyses excluded a causal relationship between AF and BC.</p><p><strong>Conclusion: </strong>This study systematically investigated the shared genetic overlap between AF and BC. Several pleiotropic SNPs and genes were identified, and co-enriched tissue and cell types were revealed. The findings highlight common mechanisms from a genetic perspective rather than a causal relationship. This study provides new insights into the AF-BC association and suggests potential experimental targets and directions for future research. Additionally, the results underscore the importance of monitoring the potential risk of one disease in patients diagnosed with the other.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1450259"},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11975938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811034","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":"Novel variations in the PLOD1, COL1A1, COL5A2 and COL4A1 genes related to keratoconus.","authors":"Qinghong Lin, Xuejun Wang, Xiaoliao Peng, Tian Han, Ling Sun, Xiaoyu Zhang, Xingtao Zhou","doi":"10.3389/fgene.2025.1497915","DOIUrl":"https://doi.org/10.3389/fgene.2025.1497915","url":null,"abstract":"<p><strong>Purpose: </strong>To investigate the genetic characteristics of four Chinese families affected by keratoconus (KC).</p><p><strong>Methods: </strong>In the four families affected by KC, medical records, clinical observations, and blood samples were collected from all individuals. One hundred subjects without KC served as healthy controls. All controls and subjects in the four families underwent whole exome sequencing of their genomic DNA and polymerase chain reaction to confirm the variants. All variants were analyzed using online software; and <i>in silico</i> predictions of three-dimensional protein structures were performed.</p><p><strong>Results: </strong>The clinical manifestations in those first-degree family members of the probands were atypical. The following four variants were identified in the four probands and other family members with KC: heterozygous missense variation c.109G>A (p.Glu37Lys, rs369263247) in the procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (<i>PLOD1</i>) gene; heterozygous missense variation c.3766G>A (p.Ala1256Thr, rs148216434) in the collagen type I alpha 1 (<i>COL1A1</i>) gene; heterozygous missense variant c.4364G>A (p.Gly1455Glu) in the collagen type V alpha 2 (<i>COL5A2</i>) gene; and missense variation c.976G>A (p.Glu326Ser) in the collagen type IV alpha 1 (<i>COL4A1</i>) gene. The above genotypes were co-segregated with corresponding phenotypes. All variations in these families appeared to be pathogenic.</p><p><strong>Conclusion: </strong>Four variants in the <i>PLOD1</i>, <i>COL1A1</i>, <i>COL5A2</i>, and <i>COL4A1</i> genes were identified in this study, which are collagen-coding genes and collagen crosslink regulatory genes and may be associated with the origin and development of KC. This study updates the knowledge of genes related to KC and the biomedical implications.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1497915"},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11975878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811038","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":"Genetic diversity, reproductive performance, and genetic enhancement strategies in Huang-Huai goats.","authors":"Kai Quan, Huibin Shi, Caihong Wei, Jun Li, Kun Liu, Huihua Wang, Wei Sun, Haoyuan Han","doi":"10.3389/fgene.2025.1549051","DOIUrl":"10.3389/fgene.2025.1549051","url":null,"abstract":"<p><p>The Huang-huai goat, indigenous to China's Huang-Huai Plain, is celebrated for its exceptional reproductive capacity, succulent meat, and superior leather qualities. The Huang-huai goat's reproductive characteristics, genetic diversity, and the genetic underpinnings of intersexuality, aiming to inform conservation efforts and genetic resource management. Our study at <i>the Huang-huai Goat Science and Technology R&D Center</i> monitored 600-800 female goats and 16-24 male goats from June 2020 to May 2022, adhering to NIH guidelines and with ethical approval from <i>Henan University of Animal Husbandry and Economics</i>. Our findings indicate that these goats exhibit a year-round estrus cycle averaging 19-23 days, a gestation period of 146-150 days, and an average litter size of 2.74, with an annual reproduction rate of 418.96% and a weaning survival rate of 94.75%. Transcriptome sequencing identified eleven candidate genes associated with multiple offspring, including <i>PTX3</i>, <i>MMP13</i>, and <i>NR4A1</i>, which play roles in organ development and hormonal regulation. SNP analysis revealed specific genotypes in <i>GJB6</i> and <i>PRKAA1</i> linked to higher lambing numbers, offering molecular markers for selective breeding. The study also highlighted the role of the Polled Intersex Syndrome (PIS) locus in causing both hornless and intersexual traits, emphasizing the importance of genetic screening for maintaining breed health and productivity. The genetic resources of the Huang-huai goat, recognized as a national geographical indication product, are vital for the livestock industry and require strategic conservation for sustainable development. This review highlights the importance of preserving and utilizing the genetic resources of the Huang-huai goat to enhance its contribution to agriculture.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1549051"},"PeriodicalIF":2.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803114","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":"Multi-trait phenotypic modeling through factor analysis and bayesian network learning to develop latent reproductive, body conformational, and carcass-associated traits in admixed beef heifers.","authors":"Muhammad Anas, Bin Zhao, Haipeng Yu, Carl R Dahlen, Kendall C Swanson, Kris A Ringwall, Lauren L Hulsman Hanna","doi":"10.3389/fgene.2025.1551967","DOIUrl":"10.3389/fgene.2025.1551967","url":null,"abstract":"<p><p>Despite high-throughput and large-scale phenotyping becoming easier, interpretation of such data in cattle production remains challenging due to the complex and highly correlated nature of many traits. Underlying biological traits (UBT) of economic importance are defined by a subset of easy-to-measure traits, leading to challenges in making appropriate selection decisions on them. Research on UBT in beef cattle is limited. In this study, the phenotypic data of admixed beef heifers (n = 336) for reproductive, body conformation, and carcass-related traits (traits, t = 35) were used to identify latent variables from factor analysis (FA) that can be characterized as UBT. Given sample size constraints for carcass (n = 161) and other body size-related traits (n = 336), two models were explored. In Model 1, all individual traits were considered (n = 161), while in Model 2, the dataset was split into body size (n = 336) and carcass (n = 161) traits to maximize available heifers per dataset. A combination of FA and Bayesian network (BN) learning was adopted to develop UBT and infer BN structure for subsequent analyses. All heifers (n = 336) were genotyped using GeneSeek Genomic Profiler 150K for Beef Cattle. Following quality checks, 117,373 autosomal SNP markers were retained and used for genomic estimated breeding values (gEBV) in BN learning steps. Using exploratory and confirmatory FA, Body Size (BS) and Body Composition (BC) were identified as UBT for Model 1, explaining 14 phenotypic traits (t = 14). For Model 2, BS, Ovary Size, and Yield Grade (YG) were identified as UBT, explaining 12 phenotypic traits (t = 12). When using gEBV, the causal network structure inferred showed BS contributed to BC in Model 1 and to Ovary Size in Model 2. Therefore, a structure equation-based approach should be used in subsequent modeling for these traits. From Model 2, YG should be modeled univariately. This study is the first to identify UBT in growing admixed heifers using body size, conformation, and carcass traits. We also identified that BC and YG did not explain intra-muscular fat and body density, indicating these two traits should also be modeled univariately.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1551967"},"PeriodicalIF":2.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803121","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":"Construction of a risk model associated with tryptophan metabolism and identification of related molecular subtypes in laryngeal squamous cell carcinoma.","authors":"Feng Liu, Yanchao Qin, Wei Luo, XianHui Ruan, Lifang Lu, Bowei Feng, Jianfei Yu","doi":"10.3389/fgene.2025.1530334","DOIUrl":"10.3389/fgene.2025.1530334","url":null,"abstract":"<p><p>Catabolic metabolites of tryptophan (Trp) are considered to be important microenvironmental factors by suppressing anti-tumor immune responses in cancers. Nevertheless, the effect of Trp metabolism (Trp metabolism)-related genes Trp metabolism-related genes on laryngeal squamous cell carcinoma (LSCC) progression is not yet clear. So, in this study, the TCGA-LSCC, GSE27020, and 40 TMRGs were extracted <i>via</i> public databases to explore the effects of TMRGs on laryngeal squamous cell carcinoma. Firstly, Weighted Gene Co-expression Network Analysis (WGCNA) was adopted with LSCC samples in TCGA-LSCC to acquire key module, and differentially expressed genes between LSCC and normal samples from TCGA-LSCC were yielded <i>via</i> differential expression analysis. Next, differentially expressed TMRGs (DE-TMRGs) was obtained in key model and DEGs, and prognostic genes were identifde through multiple algorithms. Five prognostic genes, namely <i>SERPINA1</i>, <i>TMC8</i>, <i>RENBP</i>, <i>SDS</i> and <i>FAM107A</i> were finally identified. A risk model was established based on the expressions of prognostic genes and survival information of LSCC samples while that were divided into high and low risk groups. Obviously, the LSCC immune dysfunction and exclusion score of high-risk patients was dramatically higher than that in low-risk patients, indicating that patients in the high-risk subgroup exhibited reduced responsiveness to immunotherapy. Besides, the drug sensitivity analysis showed that the low -risk subgroup was notably sensitive to Salubrinal, Lenalidomide, Metformin, while high -risk subgroup was more responsive to Docetaxel, AUY922, Embelin. Eventually, two clusters of LSCC samples had notable correlations with LSCC prognosis. The above results indicated that the risk model consisted of TMRGs (<i>SERPINA1</i>, <i>TMC8</i>, <i>RENBP</i>, <i>SDS</i> and <i>FAM107A</i>) was constructed in LSCC, contributing to studies related to the prognosis and treatment of LSCC.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1530334"},"PeriodicalIF":2.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803110","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":"Genetic genealogy of Y-chromosome in the Zhetiru tribe of the Kazakh population from Kazakhstan.","authors":"Aigul Zhunussova, Saltanat Tayshanova, Alizhan Bukayev, Ayagoz Bukayeva, Baglan Aidarov, Radik Temirgaliev, Zhaxylyk Sabitov, Maxat Zhabagin","doi":"10.3389/fgene.2025.1516130","DOIUrl":"10.3389/fgene.2025.1516130","url":null,"abstract":"<p><strong>Introduction: </strong>The Y chromosome, transmitted exclusively through the paternal line, is a well-established tool for verifying genealogical data. The Kazakh tribe Zhetiru in Kazakhstan, comprising seven clans, has conflicting historical and genealogical narratives regarding its origin-either as a union of seven independent clans or as descendants of a single common ancestor. A detailed genetic investigation has not yet addressed this question.</p><p><strong>Methods: </strong>350 male volunteers from the Zhetiru tribe were analyzed using 23 Y-STR loci and 17 Y-SNPs. We calculated genetic distances using Arlequin and STRAF, and explored genetic structure with median-joining networks using a comparative dataset of over 3,000 Kazakh individuals.</p><p><strong>Results: </strong>At the tribal level, haplotype diversity (0.997) and haplogroup diversity (0.91) are high. However, at the clan level, haplotypic diversity decreases, revealing clear founder effects in the main haplogroups of Kerderi (R1a1a), Kereit (N1a2), Tama (C2a1a3), and Teleu (J2a2). The genetic structures of Zhagalbaily, Ramadan, and Tabyn indicate additional sub-clan founders. The ages of key clusters suggest stable genetic lineages for over 1,000 years. Zhetiru clans do not form a distinct genetic cluster among Kazakh tribes but demonstrate genetic affinities with others.</p><p><strong>Conclusion: </strong>This study demonstrates the effective application of genetic genealogy approaches in verifying historical and genealogical records concerning the Zhetiru tribe and determining its origin from distinct, genetically independent clans.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1516130"},"PeriodicalIF":2.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803118","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":"Cancer classification in high dimensional microarray gene expressions by feature selection using eagle prey optimization.","authors":"Swetha Dhamercherla, Damodar Reddy Edla, Suresh Dara","doi":"10.3389/fgene.2025.1528810","DOIUrl":"10.3389/fgene.2025.1528810","url":null,"abstract":"<p><p>Microarray gene expression data have emerged as powerful tools in cancer classification and diagnosis. However, the high dimensionality of these datasets presents significant challenges for feature selection, leading to the development of various computational methods. In this paper, we utilized the Eagle Prey Optimization (EPO), a novel genetically inspired approach for microarray gene selection in cancer classification. EPO draws inspiration from the remarkable hunting strategies of eagles, which exhibit unparalleled precision and efficiency in capturing prey. Similarly, our algorithm aims to identify a small subset of informative genes that can discriminate between cancer subtypes with high accuracy and minimal redundancy. To achieve this, EPO employs a combination of genetic mutation operator with EPO fitness function, to evolve a population of potential gene subsets over multiple generations. The key innovation of EPO lies in its incorporation of a fitness function specifically designed for cancer classification tasks. This function considers not only the discriminative power of selected genes but also their diversity and redundancy, ensuring the creation of compact and informative gene subsets. Moreover, EPO incorporates a mechanism for adaptive mutation rates, allowing the algorithm to explore the search space efficiently. To validate the effectiveness of EPO, extensive experiments were conducted on several publicly available microarray datasets representing different cancer types. Comparative analysis with state-of-the-art gene selection algorithms demonstrates that EPO consistently outperforms these methods in terms of classification accuracy, dimensionality reduction, and robustness to noise.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1528810"},"PeriodicalIF":2.8,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795141","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":"Assessment of physician preparedness for implementation of pathology-supported genetic testing: solution-driven post-COVID-19 survey.","authors":"Elouise E Kroon, Yolandi Swart, Chantelle J Scott, Denise Scholtz, Daniel W Olivier, Kelebogile E Moremi, Chantelle Venter, Maxine Waters, Sunday O Oladejo, Craig J Kinnear, Etheresia Pretorius, Kanshukan Rajaratnam, Desiree C Petersen, Marlo Möller, Maritha J Kotze","doi":"10.3389/fgene.2025.1543056","DOIUrl":"10.3389/fgene.2025.1543056","url":null,"abstract":"<p><strong>Introduction: </strong>Rapid advances in personalized medicine and direct-to-consumer genomic applications could increase the risk that physicians will apply genomic results inappropriately. To address a persistent lack of understanding of genomics, we implemented a pathology-supported genetic testing (PSGT) approach, guided by insights from a clinician needs assessment conducted in 2010.</p><p><strong>Methods: </strong>Findings from the previous clinician survey were used to develop a new patient screening tool that integrates non-communicable disease (NCD) and post-COVID-19 care pathways. In parallel to the application of this solution for stratification of patients in different treatment groups, an updated version of the original survey questionnaire was used to reassess the knowledge and willingness of healthcare professionals to apply PSGT.</p><p><strong>Results: </strong>Thirty-six respondents completed the revised needs assessment survey in October 2022, while attending a genomics session at the Annual General Practitioner Congress, Stellenbosch University, South Africa. Nearly 89% of the respondents reported having insufficient knowledge to offer genetic testing; 80% were supportive of using PSGT to differentiate inherited from lifestyle- or therapy-associated NCDs and 83.3% supported integrating wellness screening with genetic testing to identify high-risk individuals.</p><p><strong>Discussion: </strong>It appears that while clinicians are interested in learning about genomics, they continue to report significant knowledge deficits in this area, highlighting the need for targeted clinician training and tools like multidisciplinary NCD-COVID pathway analysis to improve clinical decision-making. The co-development of a genomic counseling report for ongoing studies, guided the selection of Long COVID patients for whole-genome sequencing across the illness and wellness domains.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1543056"},"PeriodicalIF":2.8,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795042","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}