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        <title>Frontiers in Genetics | New and Recent Articles</title>
        <link>https://www.frontiersin.org/journals/genetics</link>
        <description>RSS Feed for Frontiers in Genetics | New and Recent Articles</description>
        <language>en-us</language>
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        <pubDate>2026-11-12T16:47:47.507+00:00</pubDate>
        <ttl>60</ttl>
        <item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1995121</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1995121</link>
        <title><![CDATA[Resolving previously unresolved regions to advance genetic improvement of domesticated animals: technological foundations, breakthroughs, research directions, and current challenges of T2T assemblies]]></title>
        <pubdate>2026-11-12T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Dubala Wu</author><author>Yaxuan Jiao</author><author>Binhong Wen</author><author>Ting Wang</author><author>Tianwei Zhang</author><author>Sile Hu</author><author>Chun Li</author><author>Tiecheng Wu</author><author>Baoli Yu</author><author>Jianghong Wu</author>
        <description><![CDATA[The difficulty of assembling domesticated animals genomes is related to genome size, but it depends more critically on differences in repetitive sequence content, transposon load, and structural variant density. Owing to limitations in read length and to mapping ambiguity in repetitive regions, these regions and the structural variants within them have long been difficult to detect accurately with short-read sequencing, or they have resulted in assembly breaks and misjoins. Telomere to telomere (T2T) assembly, by constructing gapless complete chromosome sequences that run from telomere to telomere, has substantially improved the resolvability of such complex regions, and the coevolution of long-read sequencing and assembly algorithms is its technical prerequisite. This review outlines the core technological foundations of T2T assembly and summarizes the major breakthroughs of T2T: reshaping the resolution of chromosomal structures and the understanding of species evolution in domesticated animals, systematically uncovering structural variations, novel genes, and selection signals missed by traditional genomes, and providing in-depth resolution of population differentiation and gene flow patterns. It also explores the translational pathways, functional validation methods, and future application directions of the previously unresolved regions (PUR) revealed by T2T in breeding. Furthermore, this review objectively evaluates the current challenges and limitations of T2T technology in domesticated animal research and comprehensively outlines the bottlenecks in its practical application. It aims to provide a theoretical reference and technical support for the in-depth application of high-precision complete genome technology in the fields of domesticated animal evolution research, germplasm innovation, and molecular breeding.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1920571</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1920571</link>
        <title><![CDATA[A compound genetic family with a maternal pathogenic Xp22.2-p21.3 deletion and an inherited 5q15 duplication classified as a VUS: prenatal diagnosis, genetic counseling, and retrospective clinical analysis]]></title>
        <pubdate>2026-11-12T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Hongjun Li</author><author>Lin Li</author><author>Xudong Yu</author><author>Qiu Guo</author><author>Min Xia</author>
        <description><![CDATA[BackgroundPrenatal genetic diagnosis using copy number variation sequencing (CNV-seq) frequently identifies variants of uncertain significance (VUS), which complicate genetic counseling. Parental verification studies performed after a fetal copy number variant (CNV) is identified may also reveal incidental parental CNVs unrelated to the indication for testing. We report a family in which parental verification revealed both an inherited 5q15 duplication and a previously undiagnosed maternal Xp22.2-p21.3 deletion.Materials and MethodsA 36-year-old pregnant woman (G3P1), whose second pregnancy (2021) had been terminated after a positive non-invasive prenatal testing (NIPT) result without confirmatory diagnostic testing and who was subsequently diagnosed with premature ovarian insufficiency (POI), underwent amniocentesis at 18 weeks of gestation because of advanced maternal age and an adverse obstetric history. Amniotic fluid was analyzed by karyotyping and CNV-seq; parental peripheral blood was analyzed by CNV-seq after a fetal CNV was identified.ResultsFetal CNV-seq revealed a 480 kb duplication at 5q15 (chr5:g.94580000_95060000dup) encompassing eight protein-coding genes, which was classified as a VUS. Parental verification showed that the duplication was not detected in the father, whereas the mother carried the same 5q15 duplication. Maternal CNV-seq additionally revealed a 16.65 Mb heterozygous deletion at Xp22.2-p21.3 (chrX:g.12210001_28860000del) encompassing 81 protein-coding genes, including 30 OMIM morbid genes (e.g., ARX, CDKL5, PHEX, and RS1); this deletion was classified as pathogenic. The mother had no overt clinical features of the associated X-linked disorders. The couple elected to continue the pregnancy after counseling, and a term male infant was delivered with no abnormalities identified at birth; longitudinal follow-up is planned.ConclusionThis case illustrates two issues in prenatal genomics. First, the 5q15 duplication detected in this family remains a VUS; although its inheritance from an asymptomatic mother is reassuring, it does not establish benignity, and long-term follow-up is required. Second, parental verification performed to trace the origin of a fetal VUS may incidentally identify clinically significant parental CNVs, as occurred in this case with a previously undiagnosed maternal Xp22.2-p21.3 deletion. This incidental finding was relevant to the mother’s own health and reproductive history, provided a plausible explanation for a previous NIPT-positive result, and required separate counseling. We suggest that parental CNV-seq performed after the identification of a fetal VUS be recognized as having the potential to reveal incidental findings and that counseling and consent processes explicitly address this possibility.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1962821</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1962821</link>
        <title><![CDATA[Different phenotypic presentations of congenital insensitivity to pain with anhidrosis in siblings with identical NTRK1 mutations: a case report and literature review]]></title>
        <pubdate>2026-11-12T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Liang Zhao</author><author>Meng Wang</author><author>Xiaoyan Peng</author><author>Jiaoping Wan</author><author>Naming Wu</author><author>Shan Jiang</author>
        <description><![CDATA[Congenital insensitivity to pain with anhidrosis (CIPA) is a rare autosomal recessive disorder mainly caused by mutations in the NTRK1 gene. Its cardinal features include insensitivity to pain, anhidrosis, recurrent fever, and self-mutilating behavior. While CIPA siblings predominantly show similar phenotypes or severity differences positively correlated with age, phenotypic divergences that are age-independent, inversely correlated with age, or affect distinct organ systems have been rarely reported in siblings with identical NTRK1 mutations. We report two Han Chinese males, aged 29 and 16 years, who carried identical compound heterozygous NTRK1 mutations (c.446_447insTCTG, p. P149fs from the father and c.2293C>T, p. R765C from the mother) but exhibited markedly different clinical manifestations: the elder brother presented with chronic elbow ulcer, severe nail damage, and partial preservation of lingual temperature sensation with mild intellectual disability, whereas the younger brother had recurrent painless fractures, severe knee joint destruction, inability to stand independently, and severe intellectual disability with relatively mild skin and soft tissue involvement. A structured literature review identified 27 CIPA sibling families, among which phenotypic differences mostly manifested as age-positive severity or age-independent phenotypes. In contrast, our siblings exhibited a rare age-inverse divergence across distinct organ systems under an identical genotype. The elder brother was predominantly affected by skin and soft tissue, whereas the younger brother suffered from severe skeletal complications. This phenotypic divergence is unlikely to be fully explained by age or cumulative injury alone. These findings highlight this unexpected age-inverse phenotypic divergence among siblings with identical NTRK1 genotype, emphasizing the need for independent, comprehensive multi-organ assessments for each CIPA patient rather than predicting disease patterns in siblings solely based on the proband’s phenotype.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.2051642</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.2051642</link>
        <title><![CDATA[Editorial: RNA viruses: from molecular mechanisms to novel therapeutic targeting strategies]]></title>
        <pubdate>2026-11-12T00:00:00Z</pubdate>
        <category>Editorial</category>
        <author>Elena Criscuolo</author><author>Alfredo Berzal-Herranz</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1955699</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1955699</link>
        <title><![CDATA[Case report and literature review of spastic paraplegia type 5: a patient with two heterozygous CYP7B1 nonsense variants]]></title>
        <pubdate>2026-11-12T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Ling Gao</author><author>Zhenguo Shi</author><author>Yanli Huang</author><author>Miaosen Huang</author><author>Yingnan Mo</author><author>Yong Wang</author><author>Haipeng Jin</author>
        <description><![CDATA[BackgroundHereditary spastic paraplegia type 5 (SPG5) is a rare autosomal recessive neurodegenerative disorder associated with biallelic CYP7B1 variants and altered oxysterol metabolism. The relationship between genotype and clinical severity remains uncertain.Case PresentationWe describe a 55-year-old woman evaluated at age 55 years for progressive spastic paraplegia. Sequencing identified two heterozygous CYP7B1 nonsense variants, c.1162C>T and c.334C>T, but their allelic phase was not established. An exploratory pooled analysis included 131 patients, of whom 80 had classifiable ambulatory status. In univariable mean bias-reduced cumulative logit regression, the presence of at least one truncating variant was associated with lower odds of worse ambulatory status (odds ratio [OR], 0.30; 95% confidence interval [CI], 0.12–0.78; P = 0.013). The univariable Firth binary sensitivity analysis showed a similar association with wheelchair dependence or no functional ambulation (OR, 0.31; 95% CI, 0.09–0.99; P = 0.048). After adjustment for disease duration, the genotype estimate remained in the same direction but was imprecise (OR, 0.35; 95% CI, 0.12–1.04; P = 0.059), while longer duration was associated with worse ambulatory status (OR per 10 years, 2.22; 95% CI, 1.51–3.26; P < 0.001).ConclusionThe clinical findings and two heterozygous CYP7B1 nonsense variants support SPG5 as the leading diagnosis, although their phase and combined functional effect remain unconfirmed. In pooled cross-sectional data, truncating-variant status showed a consistent univariable association with less severe ambulatory impairment, but the adjusted estimate was uncertain. Larger cohorts with standardized outcomes are needed to assess this genotype–phenotype association.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.2031856</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.2031856</link>
        <title><![CDATA[Shared molecular and immune signatures of tic disorders and allergic diseases: a cross-disease transcriptomic analysis]]></title>
        <pubdate>2026-11-12T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yuzhen Shi</author><author>Xiumei Liu</author>
        <description><![CDATA[BackgroundTic disorders (TD) are epidemiologically associated with allergic diseases, but the peripheral molecular features potentially shared by these conditions remain unclear. This study aimed to identify overlapping peripheral blood transcriptomic features across independent TD and allergic disease cohorts and to explore their associations with peripheral immune signatures.MethodsTwo independent Gene Expression Omnibus whole-blood transcriptomic datasets, GSE310998 (28 individuals with TD and 20 controls) and GSE141661 (248 individuals with allergic diseases and 209 controls), were analyzed using differential expression analysis and weighted gene co-expression network analysis for exploratory cross-disease candidate-gene prioritization. Reactome GSEA, ssGSEA, and CIBERSORT were used to characterize associated pathway and immune features. Male BALB/c mice were assigned to control, OVA-sensitized, IDPN-treated, or combined-treatment groups (n = 8 per group). Stereotypy, OVA-specific IgE, whole-blood Gpx7 mRNA, and the percentage of CD63-positive neutrophils were assessed.ResultsExploratory integrative analysis prioritized GPX7 as a candidate gene for further investigation. The GPX7-low groups showed more pronounced neutrophil-related immune features in both datasets. The combined-treatment group exhibited higher stereotypy scores than the IDPN group, alongside lower whole-blood Gpx7 mRNA and a higher percentage of CD63-positive neutrophils than either single-treatment group.ConclusionThese findings identify overlapping peripheral transcriptomic and neutrophil-related immune features across independent TD and allergic disease cohorts. Although the functional relationship between GPX7 expression and neutrophil-related alterations remains to be established, these findings provide clues to potential biological links between the two conditions.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.2011975</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.2011975</link>
        <title><![CDATA[Explainable machine learning identifies a one-carbon–epigenetic axis associated with sperm DNA fragmentation in reproductive-age men with cancer: a retrospective translational cohort study]]></title>
        <pubdate>2026-11-11T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Honglin Zhang</author><author>Lei Zheng</author><author>Letian Wei</author><author>Tao Jiang</author>
        <description><![CDATA[BackgroundCancer can perturb systemic metabolism, redox homeostasis, and germ-cell genomic integrity before gonadotoxic therapy. Homocysteine (Hcy), a central intermediate of one-carbon metabolism, links methyl-donor balance, oxidative stress, and DNA methylation. We investigated whether serum Hcy was associated with sperm DNA fragmentation in reproductive-age men with cancer and whether explainable machine learning could integrate clinical, semen, and molecular features to characterize a candidate one-carbon–redox–epigenetic axis associated with high DNA fragmentation index (DFI).MethodsThis retrospective translational cohort included men referred for fertility preservation before systemic therapy or radiotherapy. The primary outcome was high sperm DFI (≥30%). Multivariable logistic regression and three machine-learning algorithms were evaluated using a 70% development/30% hold-out split. An archived-sample substudy assessed oxidative stress, global sperm DNA 5-methylcytosine, and MTHFR- and DNMT3A-related expression as candidate readouts of one-carbon and epigenetic regulation.ResultsAmong 286 men, high DFI occurred in 26.2%. Serum Hcy correlated with DFI (Spearman ρ = 0.476, P < 0.001). After adjustment for age, BMI, smoking, varicocele, recent fever, and cancer type, each 5-µmol/L increase in Hcy was associated with higher odds of high DFI (adjusted OR 7.10, 95% CI 3.69–13.67). Logistic regression showed the highest hold-out discrimination (AUC 0.792), and permutation importance identified Hcy as the leading predictor. In 72 archived samples, higher Hcy and DFI were associated with greater oxidative stress, lower global 5-methylcytosine, and lower DNMT3A-related expression; MTHFR-related expression was inversely associated with Hcy.ConclusionIn men with cancer before gonadotoxic therapy, higher serum Hcy was independently associated with sperm DNA fragmentation and contributed substantially to explainable prediction models. The molecular substudy supports, but does not establish, a candidate one-carbon–redox–epigenetic regulatory axis linking systemic metabolic state to germ-cell chromatin vulnerability. These findings provide a clinically anchored framework for future validation using high-resolution methylome, chromatin-accessibility, transcriptomic, and regulatory-network analyses.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1859530</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1859530</link>
        <title><![CDATA[Genetic diversity, population structure, and linkage disequilibrium among tropical quality protein maize (QPM) lines assessed with high-density SNP markers]]></title>
        <pubdate>2026-11-11T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Chelang’at Sitonik</author><author>MacDonald Bright Jumbo</author><author>Dan Makumbi</author><author>Manje Gowda</author><author>B. M. Prasanna</author>
        <description><![CDATA[IntroductionThe study of genetic diversity (GD), population structure, and linkage disequilibrium (LD) provides better understanding of the genetic relationships between individuals in a population which can be utilized in crop research and improvement.MethodsGenotyping by sequencing (GBS) was used to generate single nucleotide polymorphisms (SNPs) by genotyping a collection of 74 quality protein maize (QPM) lines and further characterize their genetic diversity, population structure, and linkage disequilibrium. A total of 235,214 high-quality SNPs were used for different genetic analyses except for structure and genetic diversity analyses where 11,950 and 7,841 SNPs, respectively, were used.Results and DiscussionAnalysis of molecular variance (AMOVA) based on these SNPs revealed high genetic heterozygosity among the five populations with 1% of the total genetic variation present among the subpopulations and 99% of the variation was among individuals within the populations. Population structure analysis using Bayesian-based clustering revealed that the 74 lines could be clustered into four groups. Similarly, the neighbor-joining tree indicated the lines are grouped into five major clusters. Further analysis using Principal Component Analysis (PCA) clustered the genotypes into five groups which are concordant with the groups based on pedigree information. Higher genetic diversity was detected in sub population 1 (Mid-Altitude) with a GD value of 0.484 and the lowest in population 5 (0.396) and overall, with mean of 0.434. The LD pattern in the quality protein maize was investigated, and we observed a relatively rapid LD decay of 3.53 kb and 10.66 kb at r2 = 0.2 and r2 = 0.1, respectively. Our findings provide important information for future Linkage mapping studies, genome-wide association analyses, and marker-assisted selective breeding of QPM as well as genomic prediction-based selection in tropical maize germplasm.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1937504</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1937504</link>
        <title><![CDATA[Integrated bulk and single-cell transcriptomics identify heterogeneous NRF2–HO-1–GPX4-related programs in osteoarthritic synovium]]></title>
        <pubdate>2026-11-11T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Xueqi Liu</author><author>Wenpeng Wang</author><author>Tianxiang Yang</author><author>Tao Ma</author><author>Desheng Chen</author>
        <description><![CDATA[BackgroundThe NRF2-HO-1-GPX4 axis is biologically relevant to oxidative-stress defense and ferroptosis regulation, but its transcriptomic behavior in knee osteoarthritis (KOA) synovium may vary across cohorts and local tissue microenvironments.MethodsWe performed a bioinformatics-led integrated analysis of public human KOA synovial transcriptomic datasets, including bulk OA-versus-control comparisons, paired regional synovial analysis, exploratory pain- and stage-related contrasts, and single-cell/single-nucleus localization. NFE2L2, HMOX1 and GPX4 were analyzed as prespecified genes, and compact module scores summarized NRF2-HO-1-GPX4, ferroptosis-related, oxidative-stress/NRF2 and inflammatory programs. Representative HE and immunohistochemical images were included only as exploratory qualitative tissue-level support.ResultsNFE2L2 showed the most recurrent OA-positive direction across bulk datasets, whereas HMOX1 and GPX4 were cohort dependent. GSE89408 showed coherent increases in axis-related, ferroptosis-related, oxidative-stress/NRF2 and inflammatory signatures, but this pattern was not universal. In GSE46750, paired synovial cell cultures derived from macroscopically inflamed sites showed higher ferroptosis-related and inflammatory transcriptomic module scores than cultures derived from normal/reactive sites of the same osteoarthritic joints. Exploratory pain- and disease-stage-related analyses were inconclusive, particularly because the GSE176223 comparisons involved repeated profiles from the same donors without donor-aware statistical inference. Marker-score-based single-cell analyses detected axis-related transcripts across broad inferred stromal, immune, vascular and perivascular compartments, although precise cell identities were not independently validated. Biological-sample-level pseudobulk analysis did not establish a consistent OA-associated shift in the compact axis score. Histologically, KOA synovium showed denser and more disorganized fibrous stroma; representative IHC images showed an apparent tendency toward stronger NRF2 and HO-1 staining and weaker GPX4 staining in KOA, without semiquantitative scoring.ConclusionNRF2-HO-1-GPX4-related remodeling in KOA synovium is heterogeneous and appears more closely associated with local inflammatory tissue state than with global diagnosis, pain status or disease stage. The pathology findings provide preliminary qualitative support rather than mechanistic proof.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1996339</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1996339</link>
        <title><![CDATA[Chromosome-level genome assembly and annotation of female Acrossocheilus kreyenbergii]]></title>
        <pubdate>2026-11-11T00:00:00Z</pubdate>
        <category>Data Report</category>
        <author>Qingxiang Zeng</author><author>Shan Jiang</author><author>Jing Guo</author><author>Shisong Zhang</author><author>Xinmin Lu</author><author>Daiping Jiang</author><author>Yu Zhong</author><author>Zhihuan Cai</author><author>Jiajun Zhou</author><author>Fugui Li</author><author>Jianfeng Ren</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1814203</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1814203</link>
        <title><![CDATA[Identification of hub genes involved in the pathogenesis of ulcerative colitis: a multi-omics study integrating machine learning, Mendelian randomization, and mediation analysis]]></title>
        <pubdate>2026-11-11T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Bo Yang</author><author>Zhiping Chen</author><author>Huiling Yu</author><author>Zhu Liu</author>
        <description><![CDATA[BackgroundUlcerative colitis (UC) is a chronic inflammatory bowel disease with a steadily increasing global prevalence, yet its precise molecular mechanisms remain incompletely understood. This study aimed to identify potential diagnostic biomarkers for UC and explore potential metabolite-mediated pathways linking gene expression to UC.MethodsGene expression datasets were obtained from the Gene Expression Omnibus database and analyzed using differential expression analysis, weighted gene co-expression network analysis (WGCNA), protein–protein interaction (PPI) network analysis, and multiple machine learning (ML) algorithms to identify key UC-associated genes. Mendelian randomization (MR) analysis based on cis-expression quantitative trait loci was performed to assess potential causal associations between candidate gene expression and UC, with the random-effects inverse-variance-weighted method used as the primary analytical approach. Exploratory two-step MR mediation analysis was subsequently conducted to investigate potential metabolite-mediated pathways. In addition, core-gene expression was assessed in a dextran sulfate sodium-induced mouse model of colitis.ResultsBy integrating transcriptomic analysis, WGCNA, PPI network analysis, and 127 ML model combinations, we identified six potential diagnostic biomarkers for UC: CXCL1, CXCL2, CXCR2, ENPP3, MMP1, and PPBP. The primary MR analyses showed inverse associations of CXCR2 and ENPP3 expression with UC risk (CXCR2: OR = 0.5792, 95% CI: 0.4596–0.7299; P = 3.69 × 10−6; ENPP3: OR = 0.3111, 95% CI: 0.1987–0.4871; P = 3.33 × 10−7; both BH-adjusted P < 0.001). Exploratory two-step MR mediation analysis suggested that arachidonoylcholine may partially mediate the association between CXCR2 expression and UC (indirect effect: β = −0.0566, 95% CI: −0.1041 to −0.0092; P = 0.0193), accounting for an estimated 10.37% of the total effect.ConclusionThis study identified six UC-associated candidate biomarkers and suggested that plasma arachidonoylcholine may be a candidate mediator of the inverse association between whole-blood CXCR2 expression and UC risk. These findings require further validation through functional experiments.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1956770</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1956770</link>
        <title><![CDATA[Maternal obesity, fetal fraction, and non-invasive prenatal testing performance: a large retrospective cohort study]]></title>
        <pubdate>2026-11-10T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Abeer Al Tuwaijri</author><author>Yusra Alyafee</author><author>Alaa Zare</author><author>Raniah S. Alotibi</author><author>Alyaa Farouk Abdelfattah Ibrahim</author><author>Salem Alawbathani</author><author>Hamad AlHomidani</author><author>Shouq Alzaaqi</author><author>Madawi Alhassoun</author><author>Yousef Alharbi</author><author>Hadil Alahdal</author>
        <description><![CDATA[IntroductionMaternal obesity is associated with reduced cell‐free DNA fetal fraction (FF) and may affect non-invasive prenatal testing (NIPT) performance. This study evaluated the associations of maternal body mass index (BMI) and gestational age at sampling with FF and NIPT reportability in a population with a high prevalence of overweight and obesity.MethodsThis retrospective cohort study included singleton and twin pregnancies undergoing NIPT at ≥10 weeks of gestation across three hospitals in Saudi Arabia between 2022 and 2024. Maternal and pregnancy characteristics were analyzed in relation to FF, test reportability, and high-risk screening results for trisomies 13, 18, and 21. Multivariable linear and logistic regression analyses were used to identify factors independently associated with FF and high‐risk screening results.ResultsAmong 2,659 eligible pregnancies, 2,615 yielded reportable results (98.3%), while 44 tests were non-reportable (1.7%). Nearly half of the participants were obese (48.8%). FF measurements were available for 2,612 reportable tests, with a mean of 15% ± 6.1%; only two of 2,612 tests with available FF had FF <4%. Each 1 kg/m2 increase in BMI was independently associated with a 0.161 percentage-point reduction in FF (95% CI, –0.198 to –0.125; p < 0.001), whereas each additional week of gestation was associated with a 0.309 percentage-point increase (95% CI, 0.277–0.340; p < 0.001). Maternal BMI was not significantly associated with reportability. High‐risk results were identified in 99 of 2,615 reportable tests (3.8%), most commonly for trisomy 21. Maternal age, gestational age and a previous history of trisomy were independently associated with high‐risk results, whereas BMI and pregnancy type were not.DiscussionNIPT demonstrated a high overall reportability rate in this cohort despite the high prevalence of overweight and obesity. Higher maternal BMI was independently associated with lower FF but was not significantly associated with reportability. Advancing gestational age was associated with higher FF; however, the present data do not establish that delaying sampling reduces the likelihood of a non-reportable result.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1958808</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1958808</link>
        <title><![CDATA[Cross-regional and transcript-level prioritization of alternative-splicing events in autism cortex]]></title>
        <pubdate>2026-11-10T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Xin Zhou</author><author>Yang Liu</author><author>Xia Yi</author><author>Aojie Lian</author>
        <description><![CDATA[IntroductionSelecting splice events for functional studies requires disease-associated RNA measurements to be connected to regulatory context and explicit transcript consequences. We developed an event-level prioritization framework for this task in autism spectrum disorder (ASD).MethodsWe integrated 34,025 published cortical splicing tests with regional direction, donor-aware sensitivity analyses, external cortical datasets, neural RNA-binding-protein data, and reconstructed coding branches.ResultsAn effect-size-informed rule identified 278 exploratory candidates; no cortical event met transcriptome-wide false-discovery-rate (FDR) significance (minimum FDR = 0.1969). Among direction-evaluable events, 183/267 candidates were concordant in cerebellum, compared with 14,405/26,915 background events (68.5% versus 53.5%; odds ratio [OR] = 1.89). Because 46/48 cerebellar donors also contributed cortex, this comparison measures same-cohort coherence, not independent replication. RBFOX2 overlap showed a model-dependent adjusted association (OR = 1.94), without significant within-gene or binding-permutation support. Separate healthy motor-neuron datasets showed adjusted ORs of 2.16 and 2.13 (both q = 0.0059). Coding reconstruction classified 92/148 coding-overlap events as in-frame changes and distinguished transcript-dependent consequences; a PKM exon exchange preserved protein length while substituting 22 amino acids. External ASD analyses did not establish FDR-corrected replication, and baseline-adjusted neural SRRM4 comparisons were nonsignificant. The framework nominated 18 events under the complete-coding-model scope, including 13 retained under the stricter scope; both branches were observed for 12/18 and 11/18 in separate fetal bulk and single-cell catalogs.DiscussionThe resulting resource connects each nomination to a defined regulatory or coding rationale and an identifiable transcript structure, providing a focused basis for isoform-resolved experimental studies.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1965445</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1965445</link>
        <title><![CDATA[RALY regulates alternative splicing through targeting poly-uridine sequences]]></title>
        <pubdate>2026-11-10T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yongchao Liu</author><author>Ha Na Jang</author><author>Davide Pradella</author><author>Jeong-U. Hong</author><author>Heegyum Moon</author><author>Hina Ashraf</author><author>Xuexiu Zheng</author><author>Claudia Ghigna</author><author>Haihong Shen</author>
        <description><![CDATA[RBP associated with lethal yellow mutation (RALY) is a member of the heterogeneous nuclear ribonucleoprotein family (hnRNP). Although the role of RALY in splicing has been studied in a few specific genes, its regulatory mechanisms partially remain unclear. Here, we applied high-throughput RNA sequencing (RNA-seq) to identify global alternative splicing targets of RALY. Our results showed that RALY significantly affected exon skipping, while it had less influence on other events. To investigate the cis-elements controlling RALY-mediated splicing regulation, we generated a reporter based on the Fas minigene and demonstrated that RALY regulates splicing by targeting poly-uridine regions on pre-mRNA molecules. Moreover, analysis of various structural domains present in RALY showed that all of the domains in RALY are required for its splicing functions, whereas only the variable domain and the basic domain are necessary for its nuclear localization. Finally, we investigated RALY expression across different tumor types and characterized alternative splicing alterations associated with RALY depletion in cell culture. Our reporter-based and in vitro results show RALY can mediate splicing regulation via poly-uridine-rich sequences in reconstituted experimental systems, and multiple RALY domains are indispensable for its splicing activity.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1989287</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1989287</link>
        <title><![CDATA[Integrated transcriptomic and functional analysis identifies an SLC7A11-associated lncRNA program in papillary thyroid carcinoma]]></title>
        <pubdate>2026-11-10T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yu Xiang</author><author>Lin Wu</author><author>Piyun Zhang</author>
        <description><![CDATA[BackgroundTumor progression is shaped by coordinated transcriptional programs that support metabolic stress adaptation and remodel interactions with the immune microenvironment. SLC7A11 is a major regulator of cellular cystine metabolism and redox homeostasis and is also closely linked to susceptibility to disulfide stress. However, the long non-coding RNA (lncRNA) programs associated with SLC7A11-dependent stress states in papillary thyroid carcinoma remain poorly characterized.MethodsTranscriptomic, clinicopathological, and somatic mutation data from The Cancer Genome Atlas thyroid carcinoma cohort (TCGA-THCA), comprising primarily papillary thyroid carcinoma, were integrated to identify lncRNAs associated with an SLC7A11-centered stress-related transcriptional network. Penalized regression was used for feature reduction and generation of a seven-lncRNA score, which was subsequently examined in relation to clinical outcome, tumor-associated pathways, immune programs, and genomic features. Expression of candidate lncRNAs was evaluated in clinical specimens. Functional relevance of selected lncRNAs was further assessed by siRNA-mediated silencing in thyroid cancer cells followed by proliferation, migration, and drug-response assays based on cell viability measurements.ResultsWe identified a seven-lncRNA transcriptional program associated with the SLC7A11-centered network. A higher program score was associated with unfavorable clinical outcome and showed stronger discriminatory value in patients with more advanced disease. Transcriptomic analyses linked the high-score state to immune- and cytokine-related pathways, increased expression of multiple immune checkpoint molecules, and altered estimated immune-cell infiltration, collectively revealing features consistent with an immune-recognizable but potentially functionally constrained tumor phenotype. High-score tumors also displayed distinct somatic mutation patterns and lower tumor mutational burden. Among the seven lncRNAs, AC107071.1, AC073957.3, and PRKAR1B-AS1 were consistently overexpressed in tumor tissues and were selected for functional interrogation. Silencing these lncRNAs reduced proliferation and migration of thyroid cancer cells and enhanced the ML210-associated reduction in cell viability, supporting their functional involvement in malignant cellular behavior and stress-associated drug responses.ConclusionThese findings identify an SLC7A11-linked lncRNA program associated with aggressive disease and immune-related transcriptional features suggestive of a functionally constrained tumor state in papillary thyroid carcinoma. Selected components of this program also contribute functionally to malignant cellular behavior and stress sensitivity. Rather than serving solely as a prognostic classifier, this lncRNA program may provide a framework for understanding the interplay between tumor stress adaptation and immune remodeling in thyroid carcinoma.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1940592</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1940592</link>
        <title><![CDATA[Case Report: Whole-exome sequencing revealing a novel PBX1 gene variant in a Chinese family with renal hypoplasia]]></title>
        <pubdate>2026-11-10T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Wen-qi Chen</author><author>Yan-xin Meng</author><author>Ke-na Hu</author><author>Xiao-lin Hou</author><author>Jun Duan</author><author>Zhao-xi Wang</author><author>Kai Yang</author><author>Hua-ying Hu</author><author>Jing Zhang</author>
        <description><![CDATA[Background and AimsCongenital Anomalies of the Kidney and Urinary Tract with or without Hearing Loss, Abnormal Ears, or Developmental Delay (CAKUTHED) is an autosomal dominant syndromic form of congenital anomalies of the kidney and urinary tract associated with heterozygous pathogenic variants in PBX1. The disorder is characterized by marked phenotypic variability. Identification of the underlying genetic variant can facilitate accurate prenatal diagnosis and genetic counselling of affected families.Materials and MethodsWe recruited a Chinese family affected by CAKUTHED and performed chromosomal microarray analysis, whole-exome sequencing, and Sanger validation in available family members. Exploratory conservation, structural, and transcriptomic analyses were subsequently performed to investigate potential consequences associated with the identified variant.ResultsA novel heterozygous PBX1 variant, c.780C > A(p.Y260X), was identified by whole-exome sequencing and co-segregated with the renal phenotype among the available tested family members. The variant introduces a premature termination codon within the PBX1 homeodomain and is consistent with a predicted loss-of-function effect. Exploratory structural and transcriptomic analyses yielded hypothesis-generating observations but did not establish the molecular mechanism of the variant.ConclusionWe identified a novel heterozygous PBX1 variant, NM_002585.4: c.780C > A(p.Y260X), in a Chinese family with familial renal hypoplasia. The variant co-segregated with the renal phenotype among the available tested family members and is consistent with the established loss-of-function spectrum of PBX1-related CAKUTHED. The available evidence is most consistent with a haploinsufficiency mechanism; however, NMD of the mutant allele was not directly demonstrated, and a potential dominant-negative contribution from an NMD-escaped truncated protein cannot be formally excluded. The transcriptomic and molecular dynamics findings should be regarded as exploratory and hypothesis-generating observations. Further allele-specific RNA analyses, NMD-inhibition experiments, direct protein detection, replicated simulations, and functional assays are required to distinguish between these potential mechanisms.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1958697</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1958697</link>
        <title><![CDATA[A forward genetics workflow for EMS mutagenesis, agar-based screening, and genomic analysis of Macrocystis pyrifera gametophytes]]></title>
        <pubdate>2026-11-10T00:00:00Z</pubdate>
        <category>Methods</category>
        <author>Brandon Vong</author><author>Zhihan Hua</author><author>Isabella Langa</author><author>Jack Monney</author><author>Sergey Nuzhdin</author>
        <description><![CDATA[In this study we establish a proof-of-concept workflow for conducting a mutagenesis screen in Macrocystis pyrifera gametophytes. We accomplish this by treating the gametophytes with chemical mutagen ethyl methanesulfonate (EMS), which is known to induce G > A and C > T transitions. We then culture the EMS-treated gametophytes on solid media to immobilize them for streamlined screening and strain isolation. Whole-genome sequencing identified G > A and C > T substitutions consistent with EMS mutagenesis. In this workflow, agar-based culture is used as a practical tool for immobilizing, screening, and recovering mutagenized M. pyrifera gametophytes for downstream analysis.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1834720</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1834720</link>
        <title><![CDATA[Exome analysis of Brazilian patients with intellectual disability born to consanguineous parents highlights candidate genes]]></title>
        <pubdate>2026-11-09T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Laura Machado Lara Carvalho</author><author>Ana Claudia Dantas Machado</author><author>Giovanna Cantini Tolezano</author><author>Davi Mendes Campos Fialho</author><author>Amanda Shinzato</author><author>Priscila de Oliveira Candido</author><author>Beatriz Cristina de Oliveira</author><author>Gustavo Dib Dangoni</author><author>Maisa Ganz Sanchez Sennes</author><author>Jaqueline Yu Ting Wang</author><author>Victor Hugo Calegari de Toledo</author><author>Marilia de Oliveira Scliar</author><author>Sofia de Oliveira Farias</author><author>Bianca Mie Sato Kurashima</author><author>Esther Bordin Lupion</author><author>Gabriel Pires</author><author>Luciana Elena de Souza Fraga Machado</author><author>Silvia Costa</author><author>Sadegheh Haghshenas</author><author>Haley McConkey</author><author>Bekim Sadikovic</author><author>Philip M. Boone</author><author>Paulo Alberto Otto</author><author>Angela M. Vianna-Morgante</author><author>Guilherme Yamamoto</author><author>Débora Romeo Bertola</author><author>Carla Rosenberg</author><author>Ana Cristina Victorino Krepischi</author>
        <description><![CDATA[BackgroundIntellectual disability is a genetically heterogeneous condition in which molecular diagnosis plays a crucial role in guiding clinical management, prognosis, and reproductive planning. Consanguinity increases homozygosity, providing a unique context to uncover genes underlying recessive disorders.MethodsWe investigated 32 unrelated Brazilian individuals with intellectual disability born to consanguineous parents, all negative for copy number variants and fragile X syndrome. Exome sequencing was performed to identify causative variants and runs of homozygosity were analyzed to estimate parental relatedness.ResultsClinically relevant variants—classified as pathogenic, likely pathogenic, or of uncertain significance (VUS)—were detected in 16 patients (50%). Pathogenic or likely pathogenic variants in established disease genes were identified in 12 patients, involving SCAF4, DOCK7, ADK, QRICH1, PUF60, PCNA, KIF7, MYO1H, SNX14, MTFMT, AP4S1, and ARID1B. In addition, a likely pathogenic variant was identified in EHMT2, an emerging candidate gene. Overall, molecular diagnosis was achieved in 13/32 patients, corresponding to a diagnostic yield of 41%; most diagnosed cases were associated with recessive inheritance (69%). Three patients carried VUS: one in an established disease gene (MAN1B1) and two in candidate genes (TRAPPC6A and WAPL).ConclusionThese findings further support the value of including individuals born to consanguineous parents in genomic studies of intellectual disability, as this can broaden the discovery of candidate disease genes for future functional studies and clinical validation and expand the knowledge base for molecular diagnosis, with potential implications for genetic counseling, reproductive planning, and clinical management. As a broader principle, these findings have diagnostic and biological relevance across populations.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1909079</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1909079</link>
        <title><![CDATA[CurvEdgeNet: edge feature integration with Ricci curvature for circRNA-disease association prediction]]></title>
        <pubdate>2026-11-09T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Wenjie Fan</author><author>Hao Liu</author><author>Xiaoyi Lv</author><author>Chen Chen</author><author>Cheng Chen</author><author>Yandan Xu</author>
        <description><![CDATA[IntroductionCircular RNAs (circRNAs) are important regulatory non-coding RNAs involved in diverse pathological processes and have emerged as promising candidates for disease biomarker discovery. Systematic identification of circRNA–disease associations can help elucidate disease mechanisms and prioritize candidates for biological validation. However, existing computational approaches often rely on conventional similarity networks or node-centered feature learning, which may inadequately capture the non-Euclidean geometry and edge-level interactions of biological networks.MethodsWe propose CurvEdgeNet, a geometry-enhanced computational framework for predicting circRNA–disease associations. CurvEdgeNet constructs a heterogeneous circRNA–disease network by integrating multiple circRNA and disease similarity measures with known associations. A discrete Ollivier–Ricci curvature-based edge descriptor is incorporated into a curvature-enhanced graph attention mechanism to characterize local network geometry. In parallel, a bidirectional long short-term memory (BiLSTM) module captures global feature dependencies, while multi-head attention integrates complementary local geometric and global representations for association prediction.ResultsCurvEdgeNet was evaluated on three public benchmark datasets: CircR2Disease V2, CircRNADisease V2, and CircFunBase. Under five-fold cross-validation, the model achieved area under the receiver operating characteristic curve (AUC) values of 0.9854 ± 0.0031, 0.9900 ± 0.0020, and 0.9932 ± 0.0016 on the three datasets, respectively. These results demonstrate the effectiveness of the proposed framework in predicting circRNA–disease associations.DiscussionIncorporating graph-theoretic curvature-based edge representations and edge-enhanced learning enables CurvEdgeNet to better characterize complex circRNA–disease association patterns. The framework provides a computational approach for prioritizing candidate disease-associated circRNAs and may facilitate further investigations into disease mechanisms and biomarker discovery.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1918538</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1918538</link>
        <title><![CDATA[Selective representation learning boosts intrinsically disordered protein prediction from pretrained language models]]></title>
        <pubdate>2026-11-09T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Mang Jing</author><author>Yun Liu</author><author>ShuMei Miao</author><author>Tingyu Xu</author><author>Tiantian Li</author><author>Yining Hu</author>
        <description><![CDATA[BackgroundIntrinsically disordered proteins and intrinsically disordered regions lack stable tertiary structures yet play indispensable roles in cellular signaling, regulation, and disease processes. Predicting disorder from sequence alone remains a fundamental challenge in computational biology. Recent advances in pretrained protein language models have shown great potential in capturing rich contextual representations. However, hierarchical pretrained protein language model features suffer from token-level noise and multi-layer redundancy, which limits their efficacy in downstream tasks.MethodsIn this work, we present SRLIDP, a selective representation learning framework designed to extract disorder-relevant signals from PPLMs. SRLIDP employs a dual-granularity selection strategy: at the token level, a Depth-Adaptive Retention Schedule (DARS) with Gumbel-Sigmoid differentiable relaxation filters uninformative residue noise; at the layer level, a dynamic cross-layer attention mechanism aggregates contextualized representations, followed by a bidirectional GRU module to restore global sequence context. Furthermore, to minimize potential homology-related data leakage, a strict multi-stage homology filtering pipeline (<25% sequence identity) was established across all evaluation benchmarks (Clean MXD494, SL329, DISORDER723, CAID3_NOX, and CAID3_PDB).ResultsExtensive evaluations on these strictly filtered benchmarks indicate that SRLIDP exhibits highly competitive performance compared to several representative baseline predictors, achieving robust cross-dataset generalization while maintaining high computational efficiency.ConclusionOur findings establish SRLIDP as a robust, rigorously homology-filtered, and effective solution for protein disorder prediction, with broad implications for functional analysis and therapeutic discovery.]]></description>
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