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CCDC82 and neurodevelopment: a novel genetic variant linked to infantile spasms and hypotonia. CCDC82与神经发育:一种与婴儿痉挛和张力低下相关的新基因变异。
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-20 DOI: 10.1186/s12920-025-02201-9
Zahra Safarian, Shiva Mehrabi, Arghavan Rakhshani Nejad, Sajad Alavimanesh, Pegah Kavousinia, Mohammad Hossein Shushizadeh, Seyedeh Faezeh Hassani, Latifeh Onagh, Abdolazim Sarli, Nahid Rezaie
{"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}
引用次数: 0
CUX1 variant and 9p deletion: expanding the spectrum and resolving variable GDD/ID in a family. CUX1变异体与9p缺失:扩展谱,解析家族GDD/ID变量
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-20 DOI: 10.1186/s12920-025-02203-7
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
{"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}
引用次数: 0
Long read whole genome sequencing-based discovery of structural variants and their role in aetiology of non-syndromic autism spectrum disorder in India. 基于长读全基因组测序的结构变异发现及其在印度非综合征性自闭症谱系障碍病因学中的作用。
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-20 DOI: 10.1186/s12920-025-02204-6
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
{"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}
引用次数: 0
The changes of immune function after neuroblastoma chemotherapy and the prediction of potential immune targets. 神经母细胞瘤化疗后免疫功能的变化及潜在免疫靶点的预测。
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-20 DOI: 10.1186/s12920-025-02185-6
Yunfei Ma, Yan Su, Jing Huang, Wen Zhao, Cheng Huang, Jing Qin, Shengjie You, Yan Hu, Xin Ni
{"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}
引用次数: 0
Correction: LIMA1 inhibits cisplatin resistance and malignant biological behavior of bladder cancer cells by suppressing the Wnt/β-catenin pathway. 更正:LIMA1通过抑制Wnt/β-catenin通路抑制膀胱癌细胞顺铂耐药及恶性生物学行为。
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-14 DOI: 10.1186/s12920-025-02208-2
Zhong Lv, Shuchen Zhao, Haoran Wu
{"title":"Correction: LIMA1 inhibits cisplatin resistance and malignant biological behavior of bladder cancer cells by suppressing the Wnt/β-catenin pathway.","authors":"Zhong Lv, Shuchen Zhao, Haoran Wu","doi":"10.1186/s12920-025-02208-2","DOIUrl":"10.1186/s12920-025-02208-2","url":null,"abstract":"","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"130"},"PeriodicalIF":2.0,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12351793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144854389","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}
引用次数: 0
The mitochondrial hub gene UCHL1 May serve as a potential biomarker for diagnosing diabetic cardiomyopathy: a comprehensive integration of biological pathways. 线粒体中心基因UCHL1可能作为诊断糖尿病性心肌病的潜在生物标志物:生物学途径的全面整合。
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-11 DOI: 10.1186/s12920-025-02199-0
Chengjie Gao, Yijing Tao, Da Qian, Yafeng Zhou
{"title":"The mitochondrial hub gene UCHL1 May serve as a potential biomarker for diagnosing diabetic cardiomyopathy: a comprehensive integration of biological pathways.","authors":"Chengjie Gao, Yijing Tao, Da Qian, Yafeng Zhou","doi":"10.1186/s12920-025-02199-0","DOIUrl":"10.1186/s12920-025-02199-0","url":null,"abstract":"<p><strong>Background: </strong>Diabetic cardiomyopathy (DCM) is a complex clinical syndrome characterized by cardiac systolic and diastolic dysfunction. Research on the underlying mechanism of mitochondrial dysfunction and the involved genes in patients with DCM is limited.</p><p><strong>Objective: </strong>We aimed to explore the hub genes and pathways related to mitochondrial dysfunction that affect the progression of DCM.</p><p><strong>Methods: </strong>DCM patient datasets (GSE161052, GSE210611 (test sets) and GSE26887 (validation set) were downloaded from the Gene Expression Omnibus (GEO) database. The identification of the differentially expressed genes (DEGs) was performed using the \"limma\" R package. Mitochondrial dysfunction-related genes (MDRGs) associated with DCM were obtained from the Molecular Signatures Database (MSigDB). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were carried out to analyse the biological function of mitochondrial dysfunction-related differentially expressed genes (MDRDEGs) via the \"ClusterProfiler\", \"DOSE\", \"org.Hs.eg.db\" and \"circlize\" R packages. The diagnostic value of the hub genes for DCM was confirmed using receiver operating characteristic (ROC) curves in the test and validation groups. Moreover, the functions of the hub genes in the context of DCM were explored via gene set enrichment analysis (GSEA). A protein‒protein interaction (PPI) network of the hub genes was constructed using the GeneMANIA database. Finally, real-time reverse transcription polymerase chain reaction (real-time RT PCR) analysis and western blot analysis were performed to detect the expression levels of UCHL1.</p><p><strong>Results: </strong>A total of 705 DEGs and 122 MDRGs closely related to DCM were identified, and 6 MDRDEGs (AGT, KIT, SLC2A1, SLC2A4, TK2, and UCHL1) were obtained and subjected to GO and KEGG enrichment analyses. ROC curve analysis was performed for the test and validation groups. Only the AUC of UCHL1 reached 1.0 in both the test and validation groups, and UCHL1 was identified as a hub gene in DCM. GSEA revealed that multiple biological pathways were activated or inhibited along with alterations in the expression of UCHL1. PPI network analysis revealed that the hub genes interacted with mainly the ASPSCR1, PTPRU, STXBP3, SOCS6 and UCHL5 proteins. There was a reciprocal regulatory relationship between UCHL1 expression and hsa-miR-181a-5p, hsa-miR-193b-3p, hsa-miR-877-5p and hsa-miR-218-5p levels. Finally, real-time RT PCR and western blot analysis revealed that UCHL1 may be used as a potential diagnostic biomarker of DCM.</p><p><strong>Conclusions: </strong>In this study, 6 mitochondrial dysfunction-related hub genes related to DCM were identified. The mitochondrial hub gene UCHL1 was demonstrated to be a potential diagnostic biomarker for DCM.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"129"},"PeriodicalIF":2.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12337458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820387","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}
引用次数: 0
Arsenic sulfide alleviates the progression of liver cancer malignancy by inhibiting the expression of TLCD1 in mice. 硫化砷通过抑制TLCD1在小鼠体内的表达来缓解肝癌的恶性进展。
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-09 DOI: 10.1186/s12920-025-02195-4
Xianglu Li, Xuehua Xing, Lin Wang, Shizong Li
{"title":"Arsenic sulfide alleviates the progression of liver cancer malignancy by inhibiting the expression of TLCD1 in mice.","authors":"Xianglu Li, Xuehua Xing, Lin Wang, Shizong Li","doi":"10.1186/s12920-025-02195-4","DOIUrl":"10.1186/s12920-025-02195-4","url":null,"abstract":"<p><p>Liver cancer is the leading cause of cancer deaths worldwide and is the only cancer type among the five deadliest cancers with an increasing incidence each year. The prognosis of liver cancer is poor and no effective treatment for this cancer to date. Arsenic sulfide has been found to be effective in the treatment of hematological malignancies but its therapeutic outcomes and associated mechanisms in liver cancer remain unknown. In this study, we found that arsenic sulfide treatment could effectively inhibit the proliferation, migration and promotion of apoptosis of hepatoma cell lines, and remarkably alleviated the progression of hepatocellular carcinoma in mouse models. Transcriptomic analysis of the HepG2 cell line treated with arsenic sulfide showed that arsenic sulfide inhibited the proliferation of hepatoma cells by inhibiting the expression of Triacylglycerol and Lipid Catabolism Deficient 1 (TLCD1), thereby alleviating the malignant progression of hepatocellular carcinoma. This study provides a molecular basis for arsenic sulfide in the treatment of liver cancer.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"128"},"PeriodicalIF":2.0,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811673","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}
引用次数: 0
Blood cell perturbation responses mediate the causal relationship between the gut microbiota and asthma: a bidirectional Mendelian randomization study. 血细胞扰动反应介导肠道微生物群和哮喘之间的因果关系:一项双向孟德尔随机研究。
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-06 DOI: 10.1186/s12920-025-02196-3
Junjie Bi, Liqun Zhao, Xue Liu, Jingjing Zhang, Wei Zhang
{"title":"Blood cell perturbation responses mediate the causal relationship between the gut microbiota and asthma: a bidirectional Mendelian randomization study.","authors":"Junjie Bi, Liqun Zhao, Xue Liu, Jingjing Zhang, Wei Zhang","doi":"10.1186/s12920-025-02196-3","DOIUrl":"10.1186/s12920-025-02196-3","url":null,"abstract":"<p><strong>Background: </strong>Asthma is a complex and heterogeneous disease presenting with a wide range of phenotypes. While prior studies have highlighted the importance of gut microbiota in asthma development, the extent of their influence varies. The exact causal links between gut microbiota and asthma remain to be fully understood, and the role of blood cell perturbation responses as potential mediators in this relationship remains unclear.</p><p><strong>Methods: </strong>To elucidate the connections between gut microbiota, blood cell perturbation responses, and asthma, we utilized data from comprehensive genome-wide association studies (GWAS). Our investigation covered six distinct asthma phenotypes: unspecified asthma, eosinophilic asthma, allergic asthma, childhood asthma, non-allergic asthma, and obesity-related asthma. Employing Mendelian randomization (MR) techniques, we evaluated the causal associations among gut microbiota, blood cell perturbation responses, and these asthma phenotypes, primarily using inverse variance weighting (IVW) for statistical analysis. Furthermore, we examined the potential mediating effects of blood cell perturbation responses on the relationship between gut microbiota and asthma.</p><p><strong>Results: </strong>Our comprehensive analysis uncovered significant interactions among gut microbiota, blood cell perturbation responses, and asthma. We pinpointed five specific blood cell perturbation responses that play a crucial role in modulating the progression of three distinct asthma phenotypes.</p><p><strong>Conclusion: </strong>Our investigation yields compelling evidence of causal connections between gut microbiota and asthma, with blood cell perturbation responses serving as pivotal mediators in this pathway.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"127"},"PeriodicalIF":2.0,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793386","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}
引用次数: 0
Molecular landscape of non-driver genes in myeloproliferative neoplasms through 333 cancer genes panel: Insights to reveal in Pakistan. 通过333个癌症基因小组研究骨髓增生性肿瘤非驱动基因的分子景观:在巴基斯坦揭示的见解。
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-04 DOI: 10.1186/s12920-025-02159-8
Munazza Rashid, Rifat Zubair Ahmed, Muhammad Asad Usmani, Samina Naz Mukry, Uzma Zaidi, Muhammad Nadeem Asghar
{"title":"Molecular landscape of non-driver genes in myeloproliferative neoplasms through 333 cancer genes panel: Insights to reveal in Pakistan.","authors":"Munazza Rashid, Rifat Zubair Ahmed, Muhammad Asad Usmani, Samina Naz Mukry, Uzma Zaidi, Muhammad Nadeem Asghar","doi":"10.1186/s12920-025-02159-8","DOIUrl":"10.1186/s12920-025-02159-8","url":null,"abstract":"<p><strong>Background: </strong>Discoveries of driver mutations in myeloproliferative neoplasms (MPNs) have filled the diagnostic gap however there are non-driver genes which play an important role in the phenotype of the disease. This study is the first to evaluate the molecular landscape of non-driver genes in MPNs patients from Pakistan.</p><p><strong>Methods: </strong>A sample of fourteen MPNs patients (eight essential thrombocythemia, five primary myelofibrosis and one polycythemia vera) was investigated by the next generation sequencing, using 333 cancer genes panel. Chi square test was run in SPSS 22.0 to check association of non-driver genes with sub categories of MPNs.</p><p><strong>Result: </strong>Among 333 oncology related genes, possible pathogenic variations were identified in 2.1% of analyzed genes (7/333). TP53 and KIT were the only known frequent non-driver genes in MPNs which were found mutated in this study. The highest frequency (85.7%) was found of UGT1 A1 gene variant *28 with 71.4% heterozygous (*1/*28) and 14.2% homozygous genotype (*28/*28). Second most common (64.2%) detected gene variants were of MTHFR with WT/c.1298A > C, c.1298A > C/c.1298A > C and c.677C > T/c.1298A > C genotypes 28.5%, 28.5% and 7.1%, respectively. Frequency of TP53 substitution c.215C > G was 57.1% and XRCC1 c.1196 A > G was 42.8%. KIT CNV was 42.8% whereas KIT substitution c.1924A > G was 7.1%. The frequency of DPYD *9A/c.496A > G/ IVS1 0-15 T > C and *2A/*9A/c.496A > G was 21.4%. The lowest frequency (7.1%) was observed of CYP2D6 *4/*41. KIT was significantly (P = 0.026) frequently mutated in primary myelofibrosis patients (4/5).</p><p><strong>Conclusion: </strong>A distinct molecular landscape of non-driver genes was observed in MPNs from Pakistan and most of the genes detected belonged to drug metabolizing pathways.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"125"},"PeriodicalIF":2.0,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12323069/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783410","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}
引用次数: 0
Correction: Clinical characterizations and molecular genetic study of two co-segregating variants in PDZD7 and PDE6C genes leading simultaneously to non-syndromic hearing loss and achromatopsia. 更正:PDZD7和PDE6C基因两种共分离变异同时导致非综合征性听力损失和色盲的临床特征和分子遗传学研究。
IF 2 4区 医学
BMC Medical Genomics Pub Date : 2025-08-04 DOI: 10.1186/s12920-025-02197-2
Zahra Nouri, Akram Sarmadi, Sina Narrei, Hamidreza Kianersi, Farzan Kianersi, Mohammad Amin Tabatabaiefar
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