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A novel intronic TCOF1 pathogenic variant in a Chinese family with Treacher Collins syndrome BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-18 Haojie Sun, Xinda Xu, Binjun Chen, Yanmei Wang, Jihan Lyu, Luo Guo, Yasheng Yuan, Dongdong Ren
Treacher Collins syndrome (TCS; OMIM 154500) is a craniofacial developmental disorder. To investigate the genetic features of a four-generation Chinese family with TCS, clinical examinations, hearing tests, computed tomography, whole-exome sequencing (WES), Sanger sequencing, reverse transcription (RT)-PCR, and the Minigene assay were performed. The probands, an 11-year-old male and his cousin exhibited
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The RNA sequencing results revealed the expression of different genes and signaling pathways during chemotherapy resistance in peripheral T-cell lymphoma BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-11 Yunyi Lan, Wei Tao, Luyao Ma, Xiaoxiong Wang, Hongsheng Li, Yaxi Du, Ruijiao Yang, Shunxian Wu, Yingxin Ou, Xin Liu, Yunchao Huang, Yongchun Zhou
Peripheral T-cell lymphoma (PTCL) is a subtype of non-Hodgkin's lymphoma that occurs primarily at extranodal sites and is commonly treated using chemotherapy and radiotherapy. PTCL is more malignant than other lymphoid tumors, resulting in a poor prognosis.The 5-year recurrence rate remains high, and there is a lack of standard treatment for patients with relapse-resistant disease. However, the molecular
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Correlation between large rearrangements and patient phenotypes in NF1 deletion syndrome: an update and review BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-06 Laurence Pacot, Milind Girish, Samantha Knight, Gill Spurlock, Vinod Varghese, Manuela Ye, Nick Thomas, Eric Pasmant, Meena Upadhyaya
About 5–10% of neurofibromatosis type 1 (NF1) patients exhibit large genomic germline deletions that remove the NF1 gene and its flanking regions. The most frequent NF1 large deletion is 1.4 Mb, resulting from homologous recombination between two low copy repeats. This “type-1” deletion is associated with a severe clinical phenotype in NF1 patients, with several phenotypic manifestations including
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Transcriptomic analysis delineates preterm prelabor rupture of membranes from preterm labor in preterm fetal membranes BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-05 Lori A. Underhill, J. M. Mennella, G. A. Tollefson, A. Uzun, B. E. Lechner
Globally, preterm birth remains the leading cause of death in children younger than 5 years old. Spontaneous preterm birth is comprised of two events that may or may not occur simultaneously: preterm labor and preterm prelabor rupture of membranes (PPROM). To further explore the concept that spontaneous preterm birth can result from the initializing of two separate but overlapping pathological events
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Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-05 Lluis Moragues-Solanas, Thanh Le-Viet, Elinor McSorley, Carl Halford, Daniel S. Lockhart, Alp Aydin, Gemma L. Kay, Ngozi Elumogo, William Mullen, Justin O’Grady, Matthew W. Gilmour
The timely and accurate diagnosis of bloodstream infection (BSI) is critical for patient management. With longstanding challenges for routine blood culture, metagenomics is a promising approach to rapidly provide sequence-based detection and characterisation of bloodborne bacteria. Long-read sequencing technologies have successfully supported the use of clinical metagenomics for syndromes such as respiratory
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Integration analysis of lncRNA and mRNA expression data identifies DOCK4 as a potential biomarker for elderly osteoporosis BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-05 Chengai Wu, Chao Wang, Bin Xiao, Shan Li, Yueyang Sheng, Qianqian Wang, Jianfeng Tao, Yanzhuo Zhang, Xu Jiang
We aimed to identify some potential biomarkers for elderly osteoporosis (OP) by integral analysis of lncRNA and mRNA expression data. A total of 8 OP cases and 5 healthy participants were included in the study. Fasting peripheral venous blood samples were collected from individuals, and total RNA was extracted. RNA-seq library was prepared and sequenced on the Illumina HiSeq platform. Differential
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Pancancer analysis of the prognostic and immunological role of FANCD2: a potential target for carcinogenesis and survival BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-05 Zedan Zhao, Ruyu Wang, Ruixue Wang, Jialing Song, Fengjun Ma, Huafeng Pan, Cuiyun Gao, Deqiang Wang, Xuemei Chen, Xiangzhen Fan
Recent evidence has shed light on the significant role of FANCD2 in cancer initiation, development, and progression. However, a comprehensive pan-cancer analysis of FANCD2 has been lacking. In this study, we have conducted a thorough investigation into the expression profiles and prognostic significance of FANCD2, as well as its correlation with clinicopathological parameters and immune cell infiltration
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Heterozygous truncating variant of TAOK1 in a boy with periventricular nodular heterotopia: a case report and literature review of TAOK1-related neurodevelopmental disorders BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-05 Anna Cavalli, Stefano Giuseppe Caraffi, Susanna Rizzi, Gabriele Trimarchi, Manuela Napoli, Daniele Frattini, Carlotta Spagnoli, Livia Garavelli, Carlo Fusco
Thousand and one amino-acid kinase 1 (TAOK1) encodes the MAP3K protein kinase TAO1, which has recently been displayed to be essential for neuronal maturation and cortical differentiation during early brain development. Heterozygous variants in TAOK1 have been reported in children with neurodevelopmental disorders, with or without macrocephaly, hypotonia and mild dysmorphic traits. Literature reports
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Swimming exercise reverses transcriptomic changes in aging mouse lens BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-04 Lin Ye, Jiayue Yuan, Shijie Zhu, Shunmei Ji, Jinhui Dai
The benefits of physical activity for the overall well-being of elderly individuals are well-established, the precise mechanisms through which exercise improves pathological changes in the aging lens have yet to be fully understood. 3-month-old C57BL/6J mice comprised young sedentary (YS) group, while aging mice (18-month-old) were divided into aging sedentary (AS) group and aging exercising (AE) group
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Novel polymorphisms in CYP4A22 associated with susceptibility to coronary heart disease BMC Med. Genomics (IF 2.7) Pub Date : 2024-03-04 Kang Huang, Tianyi Ma, Qiang Li, Zanrui Zhong, Yilei Zhou, Wei Zhang, Ting Qin, Shilin Tang, Jianghua Zhong, Shijuan Lu
Coronary heart disease (CHD) has become a worldwide public health problem. Genetic factors are considered important risk factors for CHD. The aim of this study was to explore the correlation between CYP4A22 gene polymorphism and CHD susceptibility in the Chinese Han population. We used SNPStats online software to complete the association analysis among 962 volunteers. False-positive report probability
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Contribution of HLA class I (A, B, C) and HLA class II (DRB1, DQA1, DQB1) alleles and haplotypes in exploring ethnic origin of central Tunisians BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-29 Amène Ben Bnina, Amri Yessine, Yasmine El Bahri, Saoussen Chouchene, Nada Ben Lazrek, Mariem Mimouna, Zeineb Mlika, Aziza Messoudi, Dorsaf Zellama, Wissal Sahtout, Amina Bouatay
Estimation of HLA (Human leukocyte Antigen) alleles’ frequencies in populations is essential to explore their ethnic origin. Anthropologic studies of central Tunisian population were rarely reported. Then, in this work, we aimed to explore the origin of central Tunisian population using HLA alleles and haplotypes frequencies. HLA class I (A, B, C) and HLA class II (DRB1, DQA1, DQB1) loci genotyping
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The influence of Nrf2 gene promoter methylation on gene expression and oxidative stress parameters in preeclampsia BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-28 Saba Zakeri, Zohreh Rahimi, Nayebali Rezvani, Asad Vaisi-Raygani, Reza Alibakhshi, Sahel Zakeri, Kheirolah Yari
Preeclampsia (PE) is a serious medical condition that usually causes high blood pressure and affects multiple organs. Considering the adverse effect of oxidative stress on the process of PE in pregnant women and regarding the role of the Nrf2 gene in placental oxidative pathways, this study was conducted to investigate the DNA methylation status of Nrf2 in PE and healthy pregnant women. The present
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Correction to: Association of IL-10-592 C > A /-1082 A > G and the TNFα -308 G > A with susceptibility to COVID-19 and clinical outcomes BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-26 Raghda E. Eldesouki, Rania M. Kishk, Noha M. Abd El-Fadeal, Rama I Mahran, Noha Kamel, Eman Riad, Nader Nemr, Safaa M. Kishk, Eman Abdel-Moemen Mohammed
Correction to: Eldesouki et al. BMC Medical Genomics (2024) 17:40 https://doi.org/10.1186/s12920-023-01793-4 Following the publication of the original article [1], the authors reported errors in the affiliations of some authors due to typesetting errors. Originally, affiliation 4 was listed as Medical Biochemistry Unit, Ibn sina National College for Medical Studies, Jeddah, Kingdom of Saudi Arabia
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Causal effects between circulating immune cells and heart failure: evidence from a bidirectional Mendelian randomization study BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-26 Rutao Bian, Xuegong Xu, Zishuang Li
Heart failure (HF) is a prevalent cardiac condition characterized by high mortality and morbidity rates. Immune cells play a pivotal role as crucial biomarkers in assessing the overall immune status of individuals. However, the causal relationship between circulating immune cells and the pathogenesis of HF remains an area requiring further investigation. The aim of this study was to investigate the
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Identifying functional subtypes of IgA nephropathy based on three machine learning algorithms and WGCNA BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-23 Hongbiao Ren, Wenhua Lv, Zhenwei Shang, Liangshuang Li, Qi Shen, Shuai Li, Zerun Song, Xiangshu Cheng, Xin Meng, Rui Chen, Ruijie Zhang
IgA nephropathy (IgAN) is one of the most common primary glomerulonephritis, which is a significant cause of renal failure. At present, the classification of IgAN is often limited to pathology, and its molecular mechanism has not been established. Therefore we aim to identify subtypes of IgAN at the molecular level and explore the heterogeneity of subtypes in terms of immune cell infiltration, functional
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Prognosis and biological function of SGOL1 in clear cell renal cell carcinoma: a multiomics analysis BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-21 Zezhong Yang, Yunzhong Jiang, Lu Wang, Binghe Yu, Hui Cai, Jinhai Fan, Mengzhao Zhang
Shugoshin-1 (SGOL1) is a mammalian ortholog of Shugoshin in yeast and is essential for precise chromosome segregation during mitosis and meiosis. Aberrant SGOL1 expression was reported to be closely correlated with the malignant progression of various tumors. However, the expression pattern and biological function of SGOL1 in clear cell renal cell carcinoma (ccRCC) are unclear. The Cancer Genome Atlas
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Proteome-wide mendelian randomization investigates potential associations in heart failure and its etiology: emphasis on PCSK9 BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-21 Lichao Lin, Huizhen Yu, Yan Xue, Liman Wang, Pengli Zhu
Heart failure (HF) is a prevalent clinical syndrome with diverse etiologies. It is crucial to identify novel therapeutic targets based on underlying causes. Here, we aimed to use proteome-wide Mendelian randomization (MR) analyses to identify the associations between genetically predicted elevated levels of circulating proteins and distinct HF outcomes, along with specific HF etiologies. Protein quantitative
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lncRNA-MIAT rs9625066 polymorphism could be a potential biomarker for ischemic stroke BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-21 Yin-Hua Weng, Jie Chen, Wen-Tao Yu, Yan-Ping Luo, Chao Liu, Jun Yang, Hong-Bo Liu
Ischemic stroke (IS) is a common and serious neurological condition that is highly fatal but so far no early diagnostic markers are available. Myocardial infarction-associated transcript (MIAT) is a long non-coding RNA (lncRNA) that could lead to IS by inducing autophagy and apoptosis in neuronal cells. However, there has been no report on the link between susceptibility to IS and the single-nucleotide
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Prenatal detection and molecular cytogenetic characterization of Xp deletion and Xq duplication: a case report and literature review BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-21 Qing Lin, Chunya Liang, Bole Du, Lijiao Li, Hong Li, Xiaolan Mai, Sheng Li, Wenyu Xu, Cunzhen Wu, Mi Zeng
Copy number variation (CNV) of X chromosome can lead to a variety of neonatal abnormalities, especially for male fetuses. In recent years, due to the high sensitivity and high specificity of NIPS, its application has gradually expanded from chromosome aneuploidy to CNV. Few prenatal cases involving the detection of Xq duplication and deletion by NIPS have been reported, but it is of great significance
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Identification of functional genes in liver fibrosis based on bioinformatics analysis of a lncRNA-mediated ceRNA network BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-20 Feng Zhang, Siya Pei, Meifang Xiao
Liver fibrosis is a major global healths problem; nevertheless, its molecular mechanism are not completely clear. This study aimed to build a lncRNA-miRNA-mRNA network, identify potentially related lncRNAs, and explore the pathogenesis of liver fibrosis. We used the Gene Expression Omnibus databases and bioinformatics analysis to identify differentially expressed genes (DEGs) between liver fibrosis
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Low frequency of SLC26A4 c.919-2A > G variant among patients with nonsyndromic hearing loss in Yunnan of Southwest China BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-20 Yan-Qiong Li, Heng Ma, Qin-Yao Wang, De-Sheng Liu, Wei Wang, Shi-Xin Li, Rong-Xia Zuo, Tao Shen, Bao-Sheng Zhu, Ya-Lian Sa
Gene variants are responsible for more than half of hearing loss, particularly in nonsyndromic hearing loss (NSHL). The most common pathogenic variant in SLC26A4 gene found in East Asian populations is c.919-2A > G followed by c.2168A > G (p.H723R). This study was to evaluate their variant frequencies in patients with NSHL from special education schools in nine different areas of Southwest China’s
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Genetic analysis of a pedigree with MECP2 duplication syndrome in China BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-19 Lan Zeng, Hui Zhu, Jin Wang, Qiyan Wang, Ying Pang, Zemin Luo, Ai Chen, Shengfang Qin, Shuyao Zhu
MECP2 duplication syndrome (MDS) is a rare X-linked genomic disorder that primarily affects males. It is characterized by delayed or absent speech development, severe motor and cognitive impairment, and recurrent respiratory infections. MDS is caused by the duplication of a chromosomal region located on chromosome Xq28, which contains the methyl CpG binding protein-2 (MECP2) gene. MECP2 functions as
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Molecular subtype identification and prognosis stratification based on golgi apparatus-related genes in head and neck squamous cell carcinoma BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-16 Aichun Zhang, Xiao He, Chen Zhang, Xuxia Tang
Abnormal dynamics of the Golgi apparatus reshape the tumor microenvironment and immune landscape, playing a crucial role in the prognosis and treatment response of cancer. This study aims to investigate the potential role of Golgi apparatus-related genes (GARGs) in the heterogeneity and prognosis of head and neck squamous cell carcinoma (HNSCC). Transcriptional data and corresponding clinical information
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Identification of diagnostic model in heart failure with myocardial fibrosis and conduction block by integrated gene co-expression network analysis BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-14 Yonghua Yuan, Yiwei Niu, Jiajun Ye, Yuejuan Xu, Xuehua He, Sun Chen
Despite the advancements in heart failure(HF) research, the early diagnosis of HF continues to be a challenging issue in clinical practice. This study aims to investigate the genes related to myocardial fibrosis and conduction block, with the goal of developing a diagnostic model for early treatment of HF in patients. The gene expression profiles of GSE57345, GSE16499, and GSE9128 were obtained from
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Broadening the phenotype and genotype spectrum of novel mutations in pontocerebellar hypoplasia with a comprehensive molecular literature review BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-13 Mohammad-Reza Ghasemi, Sahand Tehrani Fateh, Aysan Moeinafshar, Hossein Sadeghi, Parvaneh Karimzadeh, Reza Mirfakhraie, Mitra Rezaei, Farzad Hashemi-Gorji, Morteza Rezvani Kashani, Fatemehsadat Fazeli Bavandpour, Saman Bagheri, Parinaz Moghimi, Masoumeh Rostami, Rasoul Madannejad, Hassan Roudgari, Mohammad Miryounesi
Pontocerebellar hypoplasia is an umbrella term describing a heterogeneous group of prenatal neurodegenerative disorders mostly affecting the pons and cerebellum, with 17 types associated with 25 genes. However, some types of PCH lack sufficient information, which highlights the importance of investigating and introducing more cases to further elucidate the clinical, radiological, and biochemical features
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RNA sequencing reveals differential long noncoding RNA expression profiles in bacterial and viral meningitis in children BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-12 Xin Li, Suzhen Sun, Huifeng Zhang
We aimed to investigate the involvement of long non-coding RNA (lncRNA) in bacterial and viral meningitis in children. The peripheral blood of five bacterial meningitis patients, five viral meningitis samples, and five healthy individuals were collected for RNA sequencing. Then, the differentially expressed lncRNA and mRNA were detected in bacterial meningitis vs. controls, viral meningitis vs. healthy
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Quantified pathway mutations associate epithelial-mesenchymal transition and immune escape with poor prognosis and immunotherapy resistance of head and neck squamous cell carcinoma BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-08 Yuhong Huang, Han Liu, Bo Liu, Xiaoyan Chen, Danya Li, Junyuan Xue, Nan Li, Lei Zhu, Liu Yang, Jing Xiao, Chao Liu
Pathway mutations have been calculated to predict the poor prognosis and immunotherapy resistance in head and neck squamous cell carcinoma (HNSCC). To uncover the unique markers predicting prognosis and immune therapy response, the accurate quantification of pathway mutations are required to evaluate epithelial-mesenchymal transition (EMT) and immune escape. Yet, there is a lack of score to accurately
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A systematic analysis of deep learning in genomics and histopathology for precision oncology BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-05 Michaela Unger, Jakob Nikolas Kather
Digitized histopathological tissue slides and genomics profiling data are available for many patients with solid tumors. In the last 5 years, Deep Learning (DL) has been broadly used to extract clinically actionable information and biological knowledge from pathology slides and genomic data in cancer. In addition, a number of recent studies have introduced multimodal DL models designed to simultaneously
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Identification of two novel large deletions in FBN1 gene by next-generation sequencing and multiplex ligation-dependent probe amplification BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-05 Xinxin Lu, Ren Wang, Mingjie Li, Biao Zhang, Huiying Rao, Xiaoli Huang, Xijun Chen, Yan’an Wu
Mutations in fibrillin-1 (FBN1) are known to be associated with Marfan syndrome (MFS), an autosomal dominant connective tissue disorder. Most FBN1 mutations are missense or nonsense mutations. Traditional molecular genetic testing for the FBN1 gene, like Sanger sequencing, may miss disease-causing mutations in the gene’s regulatory regions or non-coding sequences, as well as partial or complete gene
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A female patient carrying a novel DMD mutation with non-random X-chromosome inactivation from a DMD family BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-01 Ming-Xia Sun, Miao Jing, Ying Hua, Jian-Biao Wang, Sheng-Quan Wang, Li-Lan Chen, Liang Ju, Yan-Shan Liu
To analyze the clinical phenotype and genetic characteristics of a female proband carrying a novel mutation in the DMD gene with non-random X-chromosome inactivation in a large pedigree with pseudohypertrophic muscular dystrophy. Clinical information of the female proband, her monozygotic twin sister, and other family members were collected. Potential pathogenic variants were detected with Multiplex
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BNIPL is a promising biomarker of laryngeal cancer: novel insights from bioinformatics analysis and experimental validation BMC Med. Genomics (IF 2.7) Pub Date : 2024-02-01 Rui Wang, Ying Gao, Shuxin Wen, Xiudong Guo
Laryngeal cancer (LC) is a malignant tumor with high incidence and mortality. We aim to explore key genes as novel biomarkers to find potential target of LC in clinic diagnosis and treatment. We retrieved GSE143224 and GSE84957 datasets from the Gene Expression Omnibus database to screen the differentially expressed genes (DEGs). Hub genes were identified from protein-protein interaction networks and
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Clinical features and molecular genetic investigation of infantile-onset ascending hereditary spastic paralysis (IAHSP) in two Chinese siblings caused by a novel splice site ALS2 variation BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-31 Qiang Zhang, Qi Yang, Jingsi Luo, Xunzhao Zhou, Shang Yi, Shuyin Tan, Zailong Qin
ALS2-related disorder involves retrograde degeneration of the upper motor neurons of the pyramidal tracts, among which autosomal recessive Infantile-onset ascending hereditary spastic paralysis (IAHSP) is a rare phenotype. In this study, we gathered clinical data from two Chinese siblings who were affected by IAHSP. Our aim was to assess the potential pathogenicity of the identified variants and analyze
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Behavioral variant frontotemporal dementia associated with GRN and ErbB4 gene mutations: a case report and literature review BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-30 Youde Cai, Zhongyong Peng, Qiansong He, Ping Sun
To report the clinical manifestation and genetic characteristics of a patient having frontotemporal dementia (FTD) with abnormal behavior and unstable walking. The clinical and imaging features of a patient who was eventually diagnosed with FTD were analyzed. The patient’s neuropsychological, PET-CT, electromyography, and genetic data were collected. Furthermore, the patient’s blood samples were examined
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Identification of a hub gene VCL for atherosclerotic plaques and discovery of potential therapeutic targets by molecular docking BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-29 Chong Wu, Wei Li, Panfeng Li, Xiaoyang Niu
Atherosclerosis (AS) is a pathology factor for cardiovascular diseases and instability of atherosclerotic plaques contributes to acute coronary events. This study identified a hub gene VCL for atherosclerotic plaques and discovered its potential therapeutic targets for atherosclerotic plaques. Differential expressed genes (DEGs) were screened between unstable and stable plaques from GSE120521 dataset
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Integrated analysis identifies GABRB3 as a biomarker in prostate cancer BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-29 Jun-Yan Chen, Chi-Fen Chang, Shu-Pin Huang, Chao-Yuan Huang, Chia-Cheng Yu, Victor C. Lin, Jiun-Hung Geng, Chia-Yang Li, Te-Ling Lu, Bo-Ying Bao
Treatment failure following androgen deprivation therapy (ADT) presents a significant challenge in the management of advanced prostate cancer. Thus, understanding the genetic factors influencing this process could facilitate the development of personalized treatments and innovative therapeutic strategies. The phosphoinositide 3-kinase (PI3K)/AKT signaling pathway plays a pivotal role in controlling
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Association of IL-10–592 C > A /-1082 A > G and the TNFα -308 G > A with susceptibility to COVID-19 and clinical outcomes BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-29 Raghda E. Eldesouki, Rania M. Kishk, Noha M. Abd El-Fadeal, Rama I Mahran, Noha Kamel, Eman Riad, Nader Nemr, Safaa M. Kishk, Eman Abdel-Moemen Mohammed
Variation in host immune responses to SARS-CoV-2 is regulated by multiple genes involved in innate viral response and cytokine storm emergence like IL-10 and TNFa gene polymorphisms. We hypothesize that IL-10; -592 C > A and − 1082 A > G and TNFa-308 G > A are associated with the risk of SARS-COV2 infections and clinical outcome. Genotyping, laboratory and radiological investigations were done to 110
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Whole genome sequencing in clinical practice BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-29 Frederik Otzen Bagger, Line Borgwardt, Andreas Sand Jespersen, Anna Reimer Hansen, Birgitte Bertelsen, Miyako Kodama, Finn Cilius Nielsen
Whole genome sequencing (WGS) is becoming the preferred method for molecular genetic diagnosis of rare and unknown diseases and for identification of actionable cancer drivers. Compared to other molecular genetic methods, WGS captures most genomic variation and eliminates the need for sequential genetic testing. Whereas, the laboratory requirements are similar to conventional molecular genetics, the
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Chronic osteomyelitis risk is associated with NLRP3 gene rs10754558 polymorphism in a Chinese Han Population BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-29 Yu-dun Qu, Nan Jiang, Jia-xuan Li, Wei Zhang, Chang-liang Xia, Shuan-ji Ou, Yang Yang, Yun-fei Ma, Yong Qi, Chang-peng Xu
Single nucleotide polymorphisms (SNPs) in the nucleotide-binding domain leucine-rich repeat protein-3 (NLRP3) gene are reported to be linked to many inflammatory disorders. However, uncertainty persists over the associations between these SNPs and susceptibilities to chronic osteomyelitis (COM). This study aimed to investigate potential relationships between NLRP3 gene SNPs and the risks of developing
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Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-27 Angelina Sverchkova, Scott Burkholz, Reid Rubsamen, Richard Stratford, Trevor Clancy
The HLA complex is the most polymorphic region of the human genome, and its improved characterization can help us understand the genetics of human disease as well as the interplay between cancer and the immune system. The main function of HLA genes is to recognize “non-self” antigens and to present them on the cell surface to T cells, which instigate an immune response toward infected or transformed
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Truncated FRMD7 proteins in congenital Nystagmus: novel frameshift mutations and proteasomal pathway implications BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-26 Yuqing Su, Juntao Zhang, Jiahui Gao, Guoqing Ding, Heng Jiang, Yang Liu, Yulei Li, Guohua Yang
Idiopathic congenital nystagmus (ICN) manifests as involuntary and periodic eye movements. To identify the genetic defect associated with X-linked ICN, Whole Exome Sequencing (WES) was conducted in two affected families. We identified two frameshift mutations in FRMD7, c.1492dupT/p.(Y498Lfs*15) and c.1616delG/p.(R539Kfs*2). Plasmids harboring the mutated genes and qPCR analysis revealed mRNA stability
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Preliminary study of the effect of gut microbiota on the development of prostatitis BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-25 Cheng Shen, Zhan Chen, Wei Zhang, Xinfeng Chen, Bing Zheng, Chunmei Shi
Dysbacteriosis of intestinal tract may cause systemic inflammation, making distant anatomical locations more susceptible to illness. Recent research has demonstrated that the microbiome can affect both prostatitis and the inflammation of the prostate that is linked to prostate cancer. It is still unclear, though, whether this relationship indicates causation. We conducted a Mendelian randomization
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Prenatal diagnosis of dent disease type I with a nonsense pathogenic variant in CLCN5: a case study BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-24 Ruijue Zhu, Mingming Zhu, Boye Wang, Enen Chen, Danlei Cai, Yinghong Yang, Yi Liang, Chuqi Su, Ding Wang, Xiaofang Sun, Linhuan Huang, Yingjun Xie
Dent disease type I is a rare X-linked recessive renal tubular disease resulting from pathogenic variants in the CLCN5 gene. Due to the rarity of Dent disease type I and the diversity of its phenotypes, its clinical diagnosis is complex and poses a challenge to clinicians. A foetus and a child from a 36-year-old pregnant woman with a birth history of abnormal children were enrolled in this study. Pregnant
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Development of preimplantation genetic testing for monogenic reference materials using next-generation sequencing BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-23 Weihua Zhao, Yanyan Song, Chuanfeng Huang, Shan Xu, Qi Luo, Runsi Yao, Nan Sun, Bo Liang, Jia Fei, Fangfang Gao, Jie Huang, Shoufang Qu
Preimplantation genetic testing for monogenic disorders (PGT-M) has been used for over 20 years to detect many serious genetic conditions. However, there is still a lack of reference materials (RMs) to validate the test performance during the development and quality control of PGT-M. Sixteen thalassemia cell lines from four thalassemia families were selected to establish the RMs. Each family consisted
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MPZL2—a common autosomal recessive deafness gene related to moderate sensorineural hearing loss in the Chinese population BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-23 Lang Zhang, Jin-Yuan Yang, Qiu-Quan Wang, Xue Gao, Guo-Jian Wang, Ming-Yu Han, Dong-Yang Kang, Dong-Yi Han, Sha-Sha Huang, Yong-Yi Yuan
Mutations in MPZL2, the characteristic genetic etiology of autosomal recessive deafness loci 111 (DFNB111), cause non-syndromic and moderate sensorineural hearing loss. In this study, we analyzed the phenotype and genotype of eight pedigrees consisting of 10 hearing loss patients with bi-allelic pathogenic or likely pathogenic variants in MPZL2. These patients were identified from a 3272 Chinese patient
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Delineation and authentication of ferroptosis genes in ventilator-induced lung injury BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-23 Enhao Huang, Hanghang Han, Ke Qin, Xueke Du
Mechanical ventilation, a critical support strategy for individuals enduring severe respiratory failure and general anesthesia, paradoxically engenders ventilator-induced lung injury (VILI). Ferrostatin-1 mitigates lung injury via ferroptosis inhibition, yet the specific ferroptosis genes contributing significantly to VILI remain obscure. Leveraging the Gene Expression Omnibus database, we acquired
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Beyond C9orf72: repeat expansions and copy number variations as risk factors of amyotrophic lateral sclerosis across various populations BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-22 Zsófia Flóra Nagy, Margit Pál, József I. Engelhardt, Mária Judit Molnár, Péter Klivényi, Márta Széll
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder which is characterized by the loss of both upper and lower motor neurons in the central nervous system. In a significant fraction of ALS cases - irrespective of family history- a genetic background may be identified. The genetic background of ALS shows a high variability from one ethnicity to another. The most frequent genetic cause
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Targeted long-read sequencing identified a causal structural variant in X-linked nephrogenic diabetes insipidus BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-22 Lukáš Strych, Monika Černá, Markéta Hejnalová, Tomáš Zavoral, Pavla Komrsková, Jitka Tejcová, Ibrahim Bitar, Eva Sládková, Josef Sýkora, Ivan Šubrt
X-linked nephrogenic diabetes insipidus (NDI) is a rare genetic renal disease caused by pathogenic variants in the AVPR2 gene. Single nucleotide variants and small insertions/deletions in AVPR2 are reliably detected by routine clinical sequencing. Nevertheless, structural variants involving AVPR2 are challenging to identify accurately by conventional genetic testing. Here, we report a novel deletion
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A consideration of CYP2D6 genetic variations in the Ghanaian population as a potential ‘culprit’ for the tramadol ‘abuse crisis’ BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-22 Nicholas Ekow Thomford, Susanna Aba Abraham, Samuel Badu Nyarko, Robert Peter Biney
Cytochrome P450 2D6 is involved in the metabolism of several important medicines including opioids. Variations in CYP2D6 have been implicated in drug response and according to the Clinical Pharmacogenetics Implementation Consortium Guideline (CPIC) for CYP2D6, dosing for CYP2D6 substrates should be based on variants carried by individuals. Although CYP2D6 variations in Ghana had been previously recorded
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Assessing the causal associations of sleep apnea with mental health and socioeconomic status: a bidirectional two-sample Mendelian randomization BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-22 Yuan Wu, Zuming Li, Xueru Chen, Siyi Wu, Xuemei Zhong, Aifang Zheng, Li Li, Hai Chen, Jiqiang Li, Yue Lu, Jiankun Chen, Kao Gan
Traditional observational research has suggested a connection between socioeconomic position, mental health, and sleep apnea (SA), but the specifics of this connection are still unclear. Using the Mendelian randomization approach, we intended to evaluate the potential causal link between mental health, socioeconomic status, and SA. Our research employed summary statistics data from large-scale genome-wide
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Expression profile analysis of LncRNAs and mRNAs in pre-receptive endometrium of women with polycystic ovary syndrome undergoing in vitro fertilization-embryo transfer BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-19 Xiuhua Xu, Aimin Yang, Pengxiang Tian, Kun Zhang, Yuanyuan Liu, Yizhuo Wang, Ziwei Wang, Yanjing Wu, Zhiming Zhao, Qian Li, Baojun shi, Xianghua Huang, Gui-min Hao
To compare the expression levels of long non-coding RNA (lncRNA) and messenger RNA (mRNA) in pre-receptive endometrium between patients with Polycystic Ovary Syndrome (PCOS)and normal ovulation undergoing in vitro fertilization-embryo transfer (IVF-ET). Endometrial tissues were collected with endometrial vacuum curette in pre-receptive phase (3 days after oocytes retrieval) from PCOS and control groups
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Based on whole-exome sequencing to explore the rule of Herceptin and TKI resistance in breast cancer patients BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-19 Liantao Guo, Hong Cheng, Jianhua Liu, Weikang Shao, Lan Luo, Weijie Zheng, Shengrong Sun, Deguang Kong, Chuang Chen
Breast cancer is the second leading cause of cancer-related death in women, and drug resistance during treatment is a major challenge. However, the mechanisms underlying drug resistance are not fully understood. Here we applied whole-exome sequencing (WES) to clarify resistant rules to Herceptin and tyrosine kinase inhibitors (TKIs). There are 12 HER2+ breast cancer patients who were done WES. Samples
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The association of RBX1 and BAMBI gene expression with oocyte maturation in PCOS women BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-18 Kimia Monshizadeh, Masoud Tajamolian, Fatemeh Anbari, Mohammad Yahya Vahidi Mehrjardi, Seyed Mehdi Kalantar, Mohammadreza Dehghani
Polycystic ovarian syndrome (PCOS) is a common endocrine disorder that affects 6–20% of women of reproductive age. One of the symptoms of PCOS is hyperandrogenism, which can impair follicular development. This disruption can cause issues with the development of oocytes and the growth of embryos. Although the exact cause of PCOS is not yet fully understood, studying the gene expression pattern of cumulus
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Identification of a novel intronic mutation of MAGED2 gene in a Chinese family with antenatal Bartter syndrome BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-18 Xu Yan, Yueyue Hu, Xin Zhang, Xia Gao, Yang Zhao, Haiying Peng, Liu Ouyang, Changjun Zhang
Antenatal Bartter syndrome is a life-threatening disease caused by a mutation in the MAGED2 gene located on chromosome Xp11. It is characterized by severe polyhydramnios and extreme prematurity. While most reported mutations are located in the exon region, variations in the intron region are rarely reported. In our study, we employed whole exome sequencing and Sanger sequencing to genotype members
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Association of NPC1L1 and HMGCR gene polymorphisms with coronary artery calcification in patients with premature triple-vessel coronary disease BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-17 Yulong Li, Jiawen Li, Xiaofang Tang, Jingjing Xu, Ru Liu, Lin Jiang, Jian Tian, Yin Zhang, Dong Wang, Kai Sun, Bo Xu, Wei Zhao, Rutai Hui, Runlin Gao, Lei Song, Jinqing Yuan, Xueyan Zhao
Coronary artery calcification (CAC) is a highly specific marker of atherosclerosis. Niemann-Pick C1-like 1 (NPC1L1) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) are the therapeutic targets of ezetimibe and statins, respectively, which are important for the progression of atherosclerosis. However, CAC’s genetic susceptibility with above targets is still unknown. We aimed to investigate
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Nine dietary habits and risk of colorectal cancer: a Mendelian randomization study BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-17 Mengyang He, Luyao Huan, Xuan Wang, Yingyi Fan, Jinchang Huang
Epidemiological studies have provided evidence that there is an association between diet and colorectal cancer. However, the causal relationship between dietary habits and colorectal cancer remains unknown. The UK Biobank provided summary-level genome-wide association study data for nine dietary habits, including alcohol consumption (n = 549,703), instant coffee consumption (n = 250,308), fruit consumption
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Comprehensive review and expanding the genetic landscape of Cornelia-de-Lange spectrum: insights from novel mutations and skin biopsy in exome-negative cases BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-12 Sahand Tehrani Fateh, Nadia Mohammad Zadeh, Shadab Salehpour, Farzad Hashemi-Gorji, Ashkan Omidi, Hossein Sadeghi, Reza Mirfakhraie, Parinaz Moghimi, Sepideh Keyvanfar, Sepideh Mohammadi Sarvaleh, Mohammad Miryounesi, Mohammad-Reza Ghasemi
Cornelia de Lange Syndrome (CdLS) is a rare genetic disorder characterized by a range of physical, cognitive, and behavioral abnormalities. This study aimed to perform a comprehensive review of the literature on CdLS and investigate two cases of CdLS with distinct phenotypes that underwent WES to aid in their diagnosis. We conducted a comprehensive review of the literature on CdLS along with performing
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Identifying hub genes of sepsis-associated and hepatic encephalopathies based on bioinformatic analysis—focus on the two common encephalopathies of septic cirrhotic patients in ICU BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-11 Juan Li, Dong Yang, Shengmei Ge, Lixia Liu, Yan Huo, Zhenjie Hu
In the ICU ward, septic cirrhotic patients are susceptible to suffering from sepsis-associated encephalopathy and/or hepatic encephalopathy, which are two common neurological complications in such patients. However, the mutual pathogenesis between sepsis-associated and hepatic encephalopathies remains unclear. We aimed to identify the mutual hub genes, explore effective diagnostic biomarkers and therapeutic
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Interactions of genetic variations in FAS, GJB2 and PTPRN2 are associated with noise-induced hearing loss: a case-control study in China BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-11 Shan Wu, Zhidan Wu, Manlian Chen, Xiangbin Zhong, Haoyan Gu, Wenjing Du, Weidong Liu, Li Lang, Junyi Wang
This study aimed to screen and validate noise-induced hearing loss (NIHL) associated single nucleotide polymorphisms (SNPs), construct genetic risk prediction models, and evaluate higher-order gene-gene, gene-environment interactions for NIHL in Chinese population. First, 83 cases and 83 controls were recruited and 60 candidate SNPs were genotyped. Then SNPs with promising results were validated in
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Identification of breast cancer subgroups and immune characterization based on glutamine metabolism-related genes BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-10 Hongjing Yu, Junchen Liu
Immunotherapy is a promising treatment for breast cancer (BC). However, due to individual differences and tumor heterogeneity, immunotherapy is only applicable to some BC patients. Glutamine metabolism plays a role in inhibiting immunotherapy, but its role in BC is limitedly studied. Therefore, we aimed to identify different BC subgroups based on glutamine metabolism and characterize the features of
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A novel prognostic signature and therapy guidance for hepatocellular carcinoma based on STEAP family BMC Med. Genomics (IF 2.7) Pub Date : 2024-01-08 Dongxue Fu, Xian Zhang, Yi Zhou, Shanshan Hu
The six-transmembrane epithelial antigen of prostate (STEAP) family members are known to be involved in various tumor-related biological processes and showed its huge potential role in tumor immunotherapy. Biological differences were investigated through Gene set enrichment analysis (GSEA) and tumor microenvironment analysis by CIBERSORT. Tumor mutation burden (TMB), immunotherapy response and chemotherapeutic