Human Genomics最新文献

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Characterizing MEFV gene variants in Jordanian patients with Familial Mediterranean Fever. 约旦家族性地中海热患者MEFV基因变异特征分析
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-05-08 DOI: 10.1186/s40246-026-00964-5
Wissam A Alwazani, Nisreen A Fuqaha, Zekrayat Medras, Yaqeen A Rjoub, Kholoud Altaany
{"title":"Characterizing MEFV gene variants in Jordanian patients with Familial Mediterranean Fever.","authors":"Wissam A Alwazani, Nisreen A Fuqaha, Zekrayat Medras, Yaqeen A Rjoub, Kholoud Altaany","doi":"10.1186/s40246-026-00964-5","DOIUrl":"https://doi.org/10.1186/s40246-026-00964-5","url":null,"abstract":"<p><strong>Background: </strong>Familial Mediterranean Fever (FMF) is inherited as an autosomal recessive autoinflammatory disorder caused by mutations in the Mediterranean fever (MEFV) gene and predominantly affects populations from the Mediterranean region. Despite its clinical significance, data regarding the genetic profile of FMF in Jordan remain limited. This study aimed to determine the frequency and pattern of commonly screened MEFV gene variants in a cohort of Jordanian patients clinically diagnosed with Familial Mediterranean Fever.</p><p><strong>Methods: </strong>A retrospective study was conducted on 366 patients aged 12-18 years who fulfilled the Turkish clinical diagnostic criteria for FMF and were treated at Prince Hamza Hospital between October 2022 and December 2023. The Diagnosis was supported by laboratory investigations and inflammatory markers, followed by genetic screening for most common mutations for the MEFV gene. Ethical approval was obtained, and informed consent was provided by legal guardians. Genetic and clinical data were analyzed using SPSS version 23 and the R Studio program.</p><p><strong>Results: </strong>Out of 366 individuals tested for MEFV gene mutations, 195 (53.3%) were mutation-positive and met the clinical criteria for FMF. The cohort comprised 75% males and 25% females, with a mean age of 13 ± 3 years and a mean age at symptom onset of 11 ± 4 years. The most frequently identified mutation was E148Q (25.12%), predominantly in the heterozygous state, followed by V726A (21.54%) and M694V (22.05%), which were also mainly heterozygous. M694I demonstrated the highest rate of homozygosity (29.41%), while K695R was detected exclusively in the homozygous form. The I692del mutation was not identified in any patient.</p><p><strong>Conclusion: </strong>This study provides baseline data on the frequency of commonly screened MEFV gene variants in Jordanian adolescents with FMF. E148Q, V726A, and M694V were the most frequent mutations, mainly in the heterozygous state, reflecting genetic heterogeneity in the study cohort. Further large-scale studies are warranted to elucidate genotype-phenotype correlations and refine diagnostic and management strategies for FMF in Jordan.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SLC26A2 as a key regulator and therapeutic target in hepatocellular carcinoma: evidence from pan-cancer and mechanistic studies. SLC26A2作为肝细胞癌的关键调节因子和治疗靶点:来自泛癌和机制研究的证据
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-05-08 DOI: 10.1186/s40246-026-00970-7
Rui Wang, Xijie Zhang, Bo Ren, Wence Zhou
{"title":"SLC26A2 as a key regulator and therapeutic target in hepatocellular carcinoma: evidence from pan-cancer and mechanistic studies.","authors":"Rui Wang, Xijie Zhang, Bo Ren, Wence Zhou","doi":"10.1186/s40246-026-00970-7","DOIUrl":"https://doi.org/10.1186/s40246-026-00970-7","url":null,"abstract":"<p><strong>Background: </strong>Hepatocellular carcinoma (HCC) faces a critical shortage of prognostic biomarkers and therapeutic targets. While solute carrier family 26 member 2 (SLC26A2) is known to be involved in skeletal disorders and even tumors, its specific role in HCC pathogenesis remains undefined.</p><p><strong>Methods: </strong>We utilized public databases to conduct a comprehensive analysis of SLC26A2 across 33 different cancer types. Additionally, we performed in vitro and in vivo experiments to investigate the functional role of SLC26A2 in the biological behavior of HCC and to explore its mechanistic pathways.</p><p><strong>Results: </strong>A pan‑cancer analysis revealed significant variability in SLC26A2 mRNA and protein levels, with prognostic implications across cancers. In HCC, SLC26A2 was identified as an independent risk factor for poor overall survival (HR = 1.539, 95% CI 1.084-2.186, p = 0.016) and correlated with higher pathological grade. Functional assays showed that silencing SLC26A2 inhibited HCC cell proliferation, migration, and invasion, while promoting apoptosis; conversely, overexpression led to opposite outcomes. Notably, silencing SLC26A2 significantly increased intracellular ROS, which was linked to subsequent modulation of the JNK/ERK/p38 MAPK signaling pathway-an effect suggested to be reversible by the antioxidant N‑acetylcysteine. In vivo studies demonstrated that silencing SLC26A2 suppressed subcutaneous tumor growth in an HCC xenograft model. Additionally, bioinformatics analysis predicted a competing endogenous RNA regulatory axis comprising the SNHG3/LINC00662-hsa-miR‑122‑5p-SLC26A2.</p><p><strong>Conclusion: </strong>Our study identifies SLC26A2 as a clinically relevant biomarker and candidate therapeutic target in HCC. Mechanistically, SLC26A2 modulates JNK/ERK/p38 MAPK activity in a manner involving ROS signaling. While its biological roles extend beyond HCC, the clinical implications are most pronounced in this malignancy.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Machine learning-based transcriptomic analysis of differentially expressed genes in the epithelium and stroma of keratoconus. 基于机器学习的圆锥角膜上皮和基质差异表达基因转录组学分析。
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-05-08 DOI: 10.1186/s40246-026-00980-5
Kaiyue Du, Rongmei Peng, Gege Xiao, Yi Qu, Liang Han, Jing Hong
{"title":"Machine learning-based transcriptomic analysis of differentially expressed genes in the epithelium and stroma of keratoconus.","authors":"Kaiyue Du, Rongmei Peng, Gege Xiao, Yi Qu, Liang Han, Jing Hong","doi":"10.1186/s40246-026-00980-5","DOIUrl":"https://doi.org/10.1186/s40246-026-00980-5","url":null,"abstract":"<p><strong>Background: </strong>This study was conducted to delineate layer-specific transcriptomic alterations in the keratoconus (KC) epithelium and stroma and to identify potential biomarkers using machine learning (ML)-based analysis.</p><p><strong>Methods: </strong>Two publicly available microarray datasets were integrated for epithelium analysis. For stroma analysis, RNA sequencing data from 31 KC patients and four normal donors were combined with a public microarray dataset. Differentially expressed genes (DEGs) were identified separately, after which functional enrichment, gene set enrichment, and gene set variation analyses were performed. Four ML algorithms were then applied, and feature importance was ranked using SHapley Additive exPlanations. The top 50% of genes across all the models were intersected, and hub genes were identified on the basis of protein-protein interaction (PPI) networks. The key findings were validated in two independent public datasets and by quantitative real-time polymerase chain reaction.</p><p><strong>Results: </strong>A total of 272 and 5,124 DEGs were identified in the epithelium and stroma, respectively, with 53 DEGs downregulated in both. Enrichment analysis of these shared genes revealed dysregulation of retinoid, steroid hormone, and aldehyde metabolism. Layer-specific analyses revealed the downregulation of immune and inflammatory signalling, stress and redox responses, cellular proliferation, and tissue repair. ML and PPI network analysis were used to identify the epithelial hub genes CXCL10 and SLC1A1, which were both downregulated. In the stroma, 10 immune-related hub genes were identified, with the expression of IL6, IL1B, CXCL8, CXCL10, and ICAM1 being downregulated.</p><p><strong>Conclusions: </strong>In KC, inflammation, stress responses, and tissue repair occur in the epithelium and stroma, and metabolic and neural pathway dysregulation occurs, with more extensive stromal alterations than epithelial changes.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Single-cell and machine learning-integrated bulk RNA-seq analysis reveals TKT as an oxidative stress-associated diagnostic biomarker in acute myocardial infarction. 单细胞和机器学习集成的大量RNA-seq分析显示,TKT是急性心肌梗死中氧化应激相关的诊断生物标志物。
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-05-07 DOI: 10.1186/s40246-026-00978-z
Jiayi Wang, Shouwen Zhang, Fahong Li, Yanjin Wei, Ming Li
{"title":"Single-cell and machine learning-integrated bulk RNA-seq analysis reveals TKT as an oxidative stress-associated diagnostic biomarker in acute myocardial infarction.","authors":"Jiayi Wang, Shouwen Zhang, Fahong Li, Yanjin Wei, Ming Li","doi":"10.1186/s40246-026-00978-z","DOIUrl":"https://doi.org/10.1186/s40246-026-00978-z","url":null,"abstract":"<p><strong>Background: </strong>Acute myocardial infarction (AMI) is a leading cause of death worldwide, with oxidative stress (OS) playing a central role in its pathogenesis. However, the dynamic expression profiles and functional implications of OS-related genes at the single-cell level remain poorly understood.</p><p><strong>Methods: </strong>OS activity first assessed in single-cell RNA sequencing (scRNA-seq) data from myocardial tissue samples. Then, we integrated scRNA-seq data from AMI patients with multi-cohort bulk RNA-seq datasets to comprehensively assess OS activity across peripheral immune cells. A curated list of 807 OS-related genes was used to construct OS activity scores at the single-cell level. Differential analysis, correlation filtering, and univariate logistic regression were applied to identify high-risk OS-related genes. Six machine learning algorithms-including LASSO, Random Forest, Boruta, Bayesian modeling, LVQ, and Treebag were used in consensus to prioritize diagnostic biomarkers. To further characterize the functional implications of TKT, we performed downstream analyses including Western Blot analysis, single-cell expression profiling, pseudotime trajectory inference, and cell-cell communication network construction.</p><p><strong>Results: </strong>TKT emerged as a robust diagnostic marker, consistently selected across all machine learning models and validated in both training and independent cohorts (AUC > 0.73). TKT was predominantly expressed in monocytes and neutrophils theoretically, where it correlated with high OS activity and pro-inflammatory gene signatures. Pseudotime analysis revealed distinct expression dynamics in monocyte and neutrophil lineages. CellChat analysis further suggested that TKT⁺ immune cells act as central hubs within the AMI immune microenvironment, mediating enhanced inflammatory communication.</p><p><strong>Conclusion: </strong>This study identifies TKT as a high-confidence, oxidative stress-associated biomarker for AMI through an integrated multi-omics and machine learning approach. TKT may serve as a bridge between metabolic reprogramming and immune activation, offering insights into potential therapeutic targets in post-infarction inflammation.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147837064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bridging the life-course exposome approach with a life-cycle perspective in safe and sustainable by design (SSbD) for chemical risk. 将生命周期暴露方法与生命周期安全与可持续设计(SSbD)的化学品风险联系起来。
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-05-07 DOI: 10.1186/s40246-026-00976-1
Dimosthenis Sarigiannis, Fotini Nikiforou, Achilleas Karakoltzidis, Nafsika Papaioannou, Spyros Karakitsios
{"title":"Bridging the life-course exposome approach with a life-cycle perspective in safe and sustainable by design (SSbD) for chemical risk.","authors":"Dimosthenis Sarigiannis, Fotini Nikiforou, Achilleas Karakoltzidis, Nafsika Papaioannou, Spyros Karakitsios","doi":"10.1186/s40246-026-00976-1","DOIUrl":"https://doi.org/10.1186/s40246-026-00976-1","url":null,"abstract":"<p><p>Safe and Sustainable by Design (SSbD) and life‑course exposome science share a primary‑prevention goal: reducing harmful exposures by intervening early in the chemical and product life cycle. Here we propose an integrated, replacement‑first decision workflow that links life‑course exposure considerations to SSbD stage‑gates using New Approach Methodologies (NAMs). The framework combines: (i) problem formulation informed by susceptible windows and populations; (ii) AOP‑guided selection and curation of mechanistic in vitro bioactivity evidence (e.g., ToxCast/Tox21, transcriptomics); (iii) physiologically based pharmacokinetic (PBPK) modelling with quantitative in vitro‑to‑in vivo extrapolation to translate in vitro potency into internal dose anchors; and (iv) transparent multi‑criteria synthesis to support early design trade‑offs. We illustrate this approach with an endocrine‑relevant substitution scenario comparing bisphenol A (BPA) with a structurally similar alternative (BPAP) and a bio‑based monomer candidate (isosorbide). Estrogen receptor (ER) bioactivity anchors derived from curated HTS assays are contrasted with PBPK‑predicted internal concentration ranges to generate an internal margin for stage‑gate decisions. The example shows how candidates with weak or absent pathway‑relevant bioactivity can be advanced, while structurally similar alternatives with ER potency approaching predicted internal concentrations can be deprioritised or redesigned pending improved exposure controls. By explicitly mapping NAM outputs to AOP key events and life‑course windows, the workflow operationalises the 3Rs by replacing broad exploratory animal testing with targeted, human‑relevant evidence and reducing unnecessary in vivo studies through early prioritisation.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147837141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrating single-cell multi-omics and machine learning to reveal triaptosis heterogeneity in clear cell renal cell carcinoma. 结合单细胞多组学和机器学习揭示透明细胞肾细胞癌的triaptosis异质性。
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-05-07 DOI: 10.1186/s40246-026-00982-3
Haojie Dai, Renjun Lu, Mingcong Zhang, Zhenyu Hang, Ke Jiang, Chao Qin, You Zhao
{"title":"Integrating single-cell multi-omics and machine learning to reveal triaptosis heterogeneity in clear cell renal cell carcinoma.","authors":"Haojie Dai, Renjun Lu, Mingcong Zhang, Zhenyu Hang, Ke Jiang, Chao Qin, You Zhao","doi":"10.1186/s40246-026-00982-3","DOIUrl":"https://doi.org/10.1186/s40246-026-00982-3","url":null,"abstract":"<p><p>Triaptosis, an emerging form of cell death, remains poorly characterized in terms of its heterogeneity within clear cell renal cell carcinoma (ccRCC). Utilizing single-cell transcriptomics, we delineate a landscape of triaptosis heterogeneity and identify monocytes and macrophages as exhibiting the highest triaptosis activity, which further increases upon terminal differentiation. These high-activity cells also demonstrate enhanced pro-angiogenic signaling toward endothelial cells. Within epithelial cells, subpopulations with the strongest triaptosis activity are located at the late differentiation stage and are closely associated with ccRCC traits. Spatial transcriptomic analysis reveals a decline in triaptosis activity with increasing distance from the tumor epithelial core. The epithelial cluster with the highest triaptosis activity showed reduced metabolic activity. In bulk transcriptome analysis, patients with high epithelial triaptosis activity infiltration exhibited improved prognosis, broader immune activation, and similarly suppressed metabolism. We subsequently developed a robust 4-gene prognostic signature based on module genes derived from high-triaptosis epithelial subpopulations. This model showed strong performance in prognostic stratification, immunotherapy guidance, and chemotherapy response prediction. Finally, we identified SLC25A37 as a core oncogenic gene within the signature and proposed Yohimbic acid among several potential molecularly targeted therapeutics.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147837143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genotype-phenotype correlations and mutation spectrum of GBA1 in Gaucher disease across Asian populations: a systematic review. 亚洲人群戈谢病GBA1基因型-表型相关性和突变谱:一项系统综述
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-05-04 DOI: 10.1186/s40246-026-00975-2
Amina Konarbayeva, Sabina Atavliyeva, Dana Auganova, Salima Baduanova, Pavel Tarlykov
{"title":"Genotype-phenotype correlations and mutation spectrum of GBA1 in Gaucher disease across Asian populations: a systematic review.","authors":"Amina Konarbayeva, Sabina Atavliyeva, Dana Auganova, Salima Baduanova, Pavel Tarlykov","doi":"10.1186/s40246-026-00975-2","DOIUrl":"https://doi.org/10.1186/s40246-026-00975-2","url":null,"abstract":"<p><strong>Background: </strong>Gaucher disease exhibits substantial genetic heterogeneity across populations. Asian populations remain understudied despite representing diverse genetic backgrounds. The systematic review was conducted to identify GBA1 mutations and genotype-phenotype correlations in Asian populations.</p><p><strong>Methods: </strong>Following PRISMA guidelines, three databases were searched (January 2000 to December 2025) for studies reporting GBA1 mutations in Asian populations (World Bank classification). From 58 included studies, 419 patients were analyzed with complete genotype-phenotype data. Meta-analyses with Freeman-Tukey transformation estimated pooled proportions of GBA1 variants among reported Gaucher disease cases. Genotype-phenotype associations were assessed using Fisher's exact or chi-square tests. Logistic regression identified predictors of severe phenotype.</p><p><strong>Results: </strong>162 distinct genotypes across 15 countries were identified, with 94% represented by ≤ 4 patients. The GBA1 variant L444P was the most prevalent (pooled proportion: 0.46), contrasting with Ashkenazi populations where the N370S variant predominates. N370S clustered in West Asia (Iraq 58%, Turkey 30%) but was present at very low frequencies or absent in East Asian countries.</p><p><strong>Conclusion: </strong>Gaucher disease in the Asian population exhibits distinct mutation spectra and geographic patterns requiring population-specific diagnostic strategies. Due to high genetic heterogeneity, broad sequencing approaches are more appropriate than limited targeted panels.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147837056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
AI-driven integration of genomic and exposome data for cancer risk: the combined risk score (CRS). 人工智能驱动的癌症风险基因组和暴露数据整合:综合风险评分(CRS)。
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-05-04 DOI: 10.1186/s40246-026-00969-0
Dimosthenis Sarigiannis, Ioannis Boukovinas, Maria Kaparelou, Athanasios-Meletios Dimopoulos, Theodora Psaltopoulou, Kenneth J Pienta, Ourania Anesti, Spyros Karakitsios
{"title":"AI-driven integration of genomic and exposome data for cancer risk: the combined risk score (CRS).","authors":"Dimosthenis Sarigiannis, Ioannis Boukovinas, Maria Kaparelou, Athanasios-Meletios Dimopoulos, Theodora Psaltopoulou, Kenneth J Pienta, Ourania Anesti, Spyros Karakitsios","doi":"10.1186/s40246-026-00969-0","DOIUrl":"https://doi.org/10.1186/s40246-026-00969-0","url":null,"abstract":"<p><p>Polygenic risk scores (PRS) have emerged as important tools for quantifying inherited susceptibility to cancer, and are increasingly combined with environmental and lifestyle factors into composite risk scores (CRS). In this context, environmental inputs should be understood not as isolated covariates, but as components of the human exposome, encompassing cumulative, time-varying, and interacting exposures across the life course, which fundamentally shape cancer risk alongside inherited susceptibility. These approaches are often discussed as candidates for precision prevention and screening, yet their evidentiary basis spans heterogeneous study designs, outcomes, and methodological assumptions. Here, we provide an integrated review of genetic, environmental, and composite cancer risk models, explicitly distinguishing etiologic association from predictive performance and clinical translation. We synthesize evidence from large genome-wide association studies, cohort and case-control analyses, and recent CRS evaluations using both narrative assessment and structured quantitative summaries. Across cancer sites, PRS and CRS consistently stratify relative risk, with monotonic increases in odds ratios across score percentiles. However, gains in discrimination metrics such as the area under the curve or C-index are generally modest and heterogeneous, and calibration performance varies substantially across populations and settings. External validation and multi-ancestry evaluations remain limited, and methodological challenges, including overfitting, population stratification, and model transportability, are frequently under-reported. We argue that current evidence supports the use of PRS and CRS primarily as tools for risk stratification, prioritization, and risk-enriched research designs, rather than as stand-alone clinical decision systems. The most near-term translational value lies in targeted screening strategies, prevention trials, and population-level risk assessment, provided that calibration, governance, and equity considerations are explicitly addressed. We conclude by outlining key methodological and data requirements needed to advance CRS from exploratory models toward robust, population-appropriate tools in cancer prevention.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Inherited TBX4 frameshifting variants predicted to escape nonsense mediated decay in two families with variable phenotypes, including lethal lung developmental disorders. 遗传性TBX4移框变异体在两个具有可变表型(包括致死性肺发育障碍)的家族中有望逃脱无义介导的衰退。
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-04-30 DOI: 10.1186/s40246-026-00974-3
Shruti A Pande, Hiuling Chan Joiner, Przemyslaw Szafranski, Tomasz Gambin, Michelle Wright, Qian Wang, Maiah Walters, Jan M Friedman, Jessica Saunders, Nicholas Avdimiretz, Cornelius F Boerkoel, Nahir Cortes-Santiago, Gail Deutsch, Pawel Stankiewicz
{"title":"Inherited TBX4 frameshifting variants predicted to escape nonsense mediated decay in two families with variable phenotypes, including lethal lung developmental disorders.","authors":"Shruti A Pande, Hiuling Chan Joiner, Przemyslaw Szafranski, Tomasz Gambin, Michelle Wright, Qian Wang, Maiah Walters, Jan M Friedman, Jessica Saunders, Nicholas Avdimiretz, Cornelius F Boerkoel, Nahir Cortes-Santiago, Gail Deutsch, Pawel Stankiewicz","doi":"10.1186/s40246-026-00974-3","DOIUrl":"https://doi.org/10.1186/s40246-026-00974-3","url":null,"abstract":"<p><strong>Background: </strong>Pathogenic variants involving the transcription factor TBX4 gene have been associated with various skeletal and pulmonary abnormalities, including lethal lung developmental disorders (LLDD).</p><p><strong>Methods: </strong>Whole-genome sequencing (WGS) with AI-powered platform for variant detection and interpretation followed by Sanger sequencing targeted variant segregation analysis were used. Reverse transcription quantitative PCR (RT-qPCR) and immunohistochemistry (IHC) studies were performed to assess gene and protein expression levels, respectively.</p><p><strong>Results: </strong>We describe two unrelated families with intrafamilial variability in the TBX4 phenotypic expressivity, including LLDDs. WGS analyses revealed two frameshift variants, c.1019del; p.(Arg340GlnfsTer40) in the penultimate exon and c.1167dup; p.(Arg390GlnfsTer30) in the last exon of TBX4, both predicted to escape nonsense mediated mRNA decay (NMD) and associated with highly variable phenotypes. RT-qPCR and IHC studies implied incomplete NMD in one family.</p><p><strong>Conclusions: </strong>Our data expand the phenotypic and genotypic landscape of TBX4-associated pulmonary disease to include asthma. We propose incompleteness and variability of NMD escape contributing to the observed wide phenotypic spectrum and increased risk of LLDDs.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147814470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction: Two recurrent pathogenic/likely pathogenic variants in PALB2 account for half of PALB2 positive families in Slovenia. 更正:PALB2中两种复发致病性/可能致病性变异占斯洛文尼亚PALB2阳性家庭的一半。
IF 4.3 3区 医学
Human Genomics Pub Date : 2026-04-29 DOI: 10.1186/s40246-026-00960-9
Vita Andreja Mesarič, Ana Blatnik, Kristina Drusany Starič, Ksenija Strojnik, Vida Stegel, Simona Hotujec, Vita Šetrajčič Dragoš, Petra Škerl, Srdjan Novaković, Mateja Krajc
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