BMC Medical Genomics最新文献

{"title":"Identification and validation of the cellular senescence-associated molecular pattern and diagnostic markers for osteoporosis.","authors":"Tengyan Liu, Jiashuang Fan, Jianyun Fang, Zhuan Qu, Yaxin He, Kai Yang, Jianlin Yang, Juye Zhang, Dan Yang, Lifen Dai","doi":"10.1186/s12920-025-02205-5","DOIUrl":"10.1186/s12920-025-02205-5","url":null,"abstract":"","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"140"},"PeriodicalIF":2.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12403493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inherited retinal diseases in Kentucky: diagnostic yield, gene variants, and novel mutations in a U.S. population.","authors":"Nicholas Demas, Cesar Estrada, Paula Morales, Mitchell Jacobs, John Kitchens, Andrew Pearson, Ramiro Maldonado","doi":"10.1186/s12920-025-02186-5","DOIUrl":"https://doi.org/10.1186/s12920-025-02186-5","url":null,"abstract":"","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"139"},"PeriodicalIF":2.0,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12392666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tracking of multidrug-resistant pathogen clones in Ghana: a systematic review and meta-analysis.","authors":"Alex Odoom, Eric S Donkor","doi":"10.1186/s12920-025-02161-0","DOIUrl":"https://doi.org/10.1186/s12920-025-02161-0","url":null,"abstract":"","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"137"},"PeriodicalIF":2.0,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12382024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of an F8 complex recombination in Chinese hemophilia a patient using long-read sequencing and optical genome mapping.","authors":"Yuxin Zhang, Mingjie Yang, Lulu Yan, Chunxiao Han, Jiangyang Xue, Juan Geng, Changshui Chen, Lijun Bao, Bingqin Xu, Shanshan Wu, Haibo Li","doi":"10.1186/s12920-025-02202-8","DOIUrl":"https://doi.org/10.1186/s12920-025-02202-8","url":null,"abstract":"","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"138"},"PeriodicalIF":2.0,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12382273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association of IL-10, IL-6, and TNF-α polymorphisms with acute coronary syndrome risk: a systematic review, meta-analysis, and trial sequential analysis.","authors":"Yang Luo, Shiqi Li, Yan Ding, Shasha Shi","doi":"10.1186/s12920-025-02167-8","DOIUrl":"https://doi.org/10.1186/s12920-025-02167-8","url":null,"abstract":"<p><p>Inflammatory cytokines are pivotal in the pathophysiology of acute coronary syndrome (ACS) and have been associated with major adverse cardiovascular events. In this study, we aimed to assess the association of eight polymorphisms in IL-10, IL-6, and TNF-α with the risk of ACS through a systematic review, meta-analysis, and trial sequential analysis. A comprehensive literature review was conducted across multiple databases, including PubMed/Medline, Web of Science, Scopus, and Cochrane Library, up until August 8, 2024. The Review Manager 5.3 software was utilized to compute the effect sizes such as the odds ratio accompanied by a 95% confidence interval. Out of 1499 records identified from databases, sources, or electronic searches, 51 articles were included in qualitative and quantitative syntheses (meta-analysis). For IL-6 -174G > C, the allelic and homozygous models showed significant associations with ACS risk. IL-6 -572G > C showed no significant association across all genetic models. IL-10 polymorphisms (-592C > A, -819C > T, and -1082A > G) generally showed no significant associations. TNF-α -308G > A polymorphism showed significant associations in all models. TNF-α -1031T > C and -238G > A showed no significant associations, with varying degrees of heterogeneity. Results suggest that certain cytokine polymorphisms, notably IL-6 -174G > C and TNF-α -308G > A, may play a crucial role in increasing susceptibility to ACS. These associations are especially pronounced in certain ethnic groups, such as Asians and Arabs, highlighting the importance of considering genetic diversity in clinical assessments.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"136"},"PeriodicalIF":2.0,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12374326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144940995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First report of Leishmania RNA virus 2 and its high genetic diversity in cutaneous leishmaniasis cases from Ilam Province, Iran.","authors":"Reza Saberi, Amirmohammad Fallahi Lima, Homa Hajjaran, Mahdi Fakhar","doi":"10.1186/s12920-025-02198-1","DOIUrl":"https://doi.org/10.1186/s12920-025-02198-1","url":null,"abstract":"<p><strong>Introduction: </strong>Cutaneous Leishmaniasis (CL) is a vector-borne disease caused by a protozoan parasite and considered a public health challenge in many countries, including Iran. Recent research has focused on the role of Leishmania RNA virus (LRV) in the pathogenesis of cutaneous and mucosal forms of leishmaniasis. This study assessed the presence of LRV2 and its genotype diversity among isolates in Ilam province, western Iran, an old focus of Zoonotic CL.</p><p><strong>Material and method: </strong>Thirty-two lesion specimens were collected from CL patients and subjected to PCR analysis using species-specific primers for Leishmania identification and detection of LRV2. The amplified products were sequenced, and phylogenetic analysis was performed.</p><p><strong>Result: </strong>All samples were identified as L. major. The PCR showed that 4 of 32 (12.5%) clinical cultures were LRV2 positive. Phylogenetic analysis revealed high nucleotide sequence identity (96-99%) with LRV2 isolated from L. major strains from Iran, Turkey, and Uzbekistan. The four sequences analyzed revealed four distinct haplotypes, with high genetic variability among the isolates.</p><p><strong>Conclusion: </strong>This study provides the first identification and phylogenetic analysis of LRV2 in CL patients from western Iran and highlights the extensive genetic diversity among LRV2 isolates across different regions, which may have significant implications for disease pathogenesis, transmission patterns, and clinical manifestations.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"135"},"PeriodicalIF":2.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CCDC82 and neurodevelopment: a novel genetic variant linked to infantile spasms and hypotonia.","authors":"Zahra Safarian, Shiva Mehrabi, Arghavan Rakhshani Nejad, Sajad Alavimanesh, Pegah Kavousinia, Mohammad Hossein Shushizadeh, Seyedeh Faezeh Hassani, Latifeh Onagh, Abdolazim Sarli, Nahid Rezaie","doi":"10.1186/s12920-025-02201-9","DOIUrl":"https://doi.org/10.1186/s12920-025-02201-9","url":null,"abstract":"<p><strong>Background: </strong>Neurodevelopmental disorders (NDDs) are a heterogeneous group of conditions characterized by impairments in motor, cognitive, and behavioral functions. Despite advances in genomic sequencing, the genetic basis of many NDDs remains unexplored. CCDC82 encodes a coiled-coil domain-containing protein with an unknown function in the nervous system. This study aims to further delineate the clinical spectrum of CCDC82-related disorders by identifying a novel homozygous nonsense variant in an Iranian family with early-onset hypotonia, infantile spasms, and developmental delay.</p><p><strong>Methods: </strong>An 8-month-old male proband of Turkmen descent, born to consanguineous parents, presented with severe hypotonia, spasticity, infantile spasms, and developmental delay. Electroencephalography (EEG) revealed a hypsarrhythmic pattern, and brain MRI showed no significant structural abnormalities. Whole-exome sequencing (WES) was performed on the proband, followed by in silico pathogenicity analysis and segregation studies in the family. Sanger sequencing confirmed the variant, and bioinformatics tools assessed its potential impact.</p><p><strong>Results: </strong>WES identified a novel homozygous nonsense variant in CCDC82 (NM_024725.4: c.709 C > T, p.Arg237Ter), which was classified as pathogenic according to ACMG guidelines. This variant is predicted to result in nonsense-mediated decay. This variant was absent in population databases and segregated with the disease phenotype in the family. In silico analyses supported its deleterious effect, and evolutionary conservation studies indicated a conserved role of CCDC82 in neuronal function.</p><p><strong>Conclusion: </strong>This study reports a novel pathogenic variant in CCDC82 associated with a severe neurodevelopmental disorder. These findings expand the known phenotypic spectrum associated with biallelic CCDC82 variants, reinforcing its role in early-onset hypotonia and infantile spasms. Further investigations are necessary to confirm its functional role and establish CCDC82 as a novel disease-associated gene.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"133"},"PeriodicalIF":2.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144940993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CUX1 variant and 9p deletion: expanding the spectrum and resolving variable GDD/ID in a family.","authors":"Haiting Liu, Xiaoyong Liu, Ximin Chen, Yangmei Pu, Wen Liu, Zemin Luo, Ai Chen, Hui Zhu, Fu Xiong, Lan Zeng, Jin Wang, Xiaocheng Nie, Shuyao Zhu","doi":"10.1186/s12920-025-02203-7","DOIUrl":"https://doi.org/10.1186/s12920-025-02203-7","url":null,"abstract":"","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"134"},"PeriodicalIF":2.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long read whole genome sequencing-based discovery of structural variants and their role in aetiology of non-syndromic autism spectrum disorder in India.","authors":"Jhanvi Shah, Debasrija Mondal, Deepika Jain, Priti Mhatre, Ketan Patel, Anand Iyer, Manoj Pandya, Bhargavi Menghani, Gayatri Dave, Jayesh Sheth, Frenny Sheth, Shweta Ramdas, Harsh Sheth","doi":"10.1186/s12920-025-02204-6","DOIUrl":"https://doi.org/10.1186/s12920-025-02204-6","url":null,"abstract":"<p><strong>Background: </strong>Despite having heritability estimates of 80%, ~ 50% cases of autism spectrum disorders (ASD) remain without a genetic diagnosis. Structural variants (SVs) detected using long-read whole genome sequencing (lrWGS) are a relatively new class of variants implicated in neurodevelopmental disorders. Short read sequencing (SRS) and chromosomal microarray (CMA) are unable to resolve these SVs due to their inherent technological limitations. This study was aimed to detect and delineate the role of SVs in children with non-syndromic ASDs using lrWGS in whom prior traditional genetic tests did not yield a definitive genetic diagnosis.</p><p><strong>Methods: </strong>A total of 23 patients with no prior genetic diagnosis from karyotyping, Fragile-X analysis, CMA and short read whole exome sequencing (srWES) were selected for lrWGS using Oxford Nanopore based sequencing platform. Samples were sequenced at an average coverage of ~ 7x. Contigs generated from high accuracy base calling were aligned against GRCh38/hg38 human reference genome build. SVs were called using five variant callers- Sniffles2, cuteSV, NanoVar, SVIM, and npInv, and annotated using AnnotSV. Calls from cuteSV were used as benchmark to identify concordant calls across at least three variant callers.</p><p><strong>Results: </strong>An average whole genome coverage of ~ 7x and N50 read length of 6.65 ± 3.3 kb was obtained across 46 runs (two runs/ sample). On average, a total of approximately 235,163 calls were made across all callers for each sample. The average number of deletions, duplications, insertions, inversions and translocations were 54,787, 3,335, 62,459, 1,286, and 113,296, respectively, were detected across all callers per sample. Of 23 cases, a candidate SV, an inversion of approximately 2.7 Mb in size encompassing SNAP25-AS1 gene was observed. This gene is likely to be involved in the synaptic pathway and has previously been associated with autism.</p><p><strong>Conclusion: </strong>This is the first study from India to assess the role of SVs in the aetiology of non-syndromic ASDs. Despite the small sample size, low-pass genome coverage, and modest N50 read length, the study indicates a modest contribution of SVs in the aetiology of non-syndromic ASD. Dearth of data supporting the role of SVs in non-syndromic ASDs in other cohorts from around the world further supports our conclusion.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"131"},"PeriodicalIF":2.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The changes of immune function after neuroblastoma chemotherapy and the prediction of potential immune targets.","authors":"Yunfei Ma, Yan Su, Jing Huang, Wen Zhao, Cheng Huang, Jing Qin, Shengjie You, Yan Hu, Xin Ni","doi":"10.1186/s12920-025-02185-6","DOIUrl":"https://doi.org/10.1186/s12920-025-02185-6","url":null,"abstract":"<p><strong>Background: </strong>High-dose chemotherapy for neuroblastoma is often intolerable for children, and its effectiveness is difficult to determine. Immunotherapy has become a popular research focus as a potential treatment. Therefore, identifying effective immune targets and drug synergistic chemotherapy against neuroblastoma is crucial.</p><p><strong>Methods: </strong>We conducted proteomics exploratory analysis of urine from 12 neuroblastoma before and after chemotherapy. The immune-related differential proteins before and after chemotherapy were obtained through differential expression analysis and dynamic expression model analysis. The ESTIMATE and ssGSEA analyses used indirectly infer the characteristics of the immune microenvironment. Gene ontology and the Kyoto Encyclopedia of Genes and Genomes enrichment analysis were conducted to reveal the biological functions of the candidate genes.</p><p><strong>Results: </strong>Immune analysis indicated that the immunosuppressive state in neuroblastoma patients caused by chemotherapy was closely related to CD8 T cells. Chemotherapy-associated differentially expressed proteins were significantly enriched in the mTOR signaling pathway. Neuroblastoma chemotherapy can significantly inhibit the expression of SEMA7A protein, and it is closely related to CD8T cell infiltration. Tetrachlorodibenzodioxin acting on SEMA7A was predicted using CTD databases.</p><p><strong>Conclusions: </strong>This study combines proteomics and bioinformatics to predict and explore potential immune targets for synergistic chemotherapy against neuroblastoma, providing a new direction for clinical treatment that warrant further validation.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"132"},"PeriodicalIF":2.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}