BMC MEDICAL GENOMICS 是一本开放获取期刊，在功能基因组学、基因组结构、基因组规模人口遗传学、表观基因组学、蛋白质组学、系统分析和与人类健康和疾病相关的药物基因组学等各个方面发表原创的同行评审研究文章。

BMC Medical Genomics is an open-access journal that publishes original peer-reviewed research articles across various aspects of functional genomics, genomic structure, population genetics at a genomic scale, epigenomics, proteomics, systems analysis, and pharmacogenomics related to human health and disease.

BMC Medical Genomics 是一本开放获取的期刊，专注于功能基因组学、基因组结构、基因组规模的人口遗传学、表观基因组学、蛋白质组学、系统分析以及与人类健康和疾病相关的药物基因组学等领域，发表原创的同行评审研究文章。

BMC Medical Genomics

Abstract Background Lung cancer is a high-incidence cancer, and it is also the most common cause of cancer death worldwide. 80–85% of lung cancer cases can be classified as non-small cell lung cancer (NSCLC). Methods NSCLC transcriptome data and clinical information were downloaded from the TCGA database and GEO database. Firstly, we analyzed and identified the differentially expressed genes (DEGs) between non-metastasis group and metastasis group of NSCLC in the TCGA database, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) were consulted to explore the functions of the DEGs. Thereafter, univariate Cox regression and LASSO Cox regression algorithms were applied to identify prognostic metastasis-related signature, followed by the construction of the risk score model and nomogram for predicting the survival of NSCLC patients. GSEA analyzed that differentially expressed gene-related signaling pathways in the high-risk group and the low-risk group. The survival of NSCLC patients was analyzed by the Kaplan–Meier method. ROC curve was plotted to evaluate the accuracy of the model. Finally, the GEO database was further applied to verify the metastasis‑related prognostic signature. Results In total, 2058 DEGs were identified. GO functions and KEGG pathways analysis results showed that the DEGs mainly concentrated in epidermis development, skin development, and the pathway of Neuro active ligand -receptor interaction in cancer. A six-gene metastasis-related risk signature including C1QL2, FLNC, LUZP2, PRSS3, SPIC, and GRAMD1B was constructed to predict the overall survival of NSCLC patients. The reliability of the gene signature was verified in GSE13213. The NSCLC patients were grouped into low-risk and high-risk groups based on the median value of risk scores. And low-risk patients had lower risk scores and longer survival time. Univariate and multivariate Cox regression verified that this signature was an independent risk factor for NSCLC. Conclusion Our study identified 6 metastasis biomarkers in the NSCLC. The biomarkers may contribute to individual risk estimation, survival prognosis.

Huan Ding

Li Shi

Zhuo Chen

Yi Lu

Zhiyu Tian

Hongyu Xiao

Xiaojing Deng

Peiyi Chen

Yue Zhang

Construction and evaluation of a prognostic risk model of tumor metastasis-related genes in patients with non-small cell lung cancer

非小细胞肺癌患者肿瘤转移相关基因预后风险模型的构建与评估

Abstract Background Pancreatic adenocarcinoma (PDAC) is a malignant tumor with high heterogeneity and poor prognosis. In this study, we sought to identify the value of platelet-related genes in prognosis and heterogeneity of PDAC through multiple transcriptomic methods. Methods Based on datasets from Gene Expression Omnibus and The Cancer Genome Atlas (TCGA), platelet-related genes were screened out, and the TCGA cohort (n = 171) was identified into two subtypes by unsupervised clustering. The platelet-related risk score model (PLRScore) was constructed by univariate Cox and LASSO regression, and the predictive ability was evaluated by Kaplan-Meier test and time-dependent receiver operating characteristic (ROC) curves. The results were validated in two other external validation sets, ICGC-CA (n = 140) and GSE62452 (n = 66). Furthermore, predictive nomogram containing clinical characteristics and PLRScore was established. In addition, we determined the possible correlation between PLRScore and immune infiltration and response of immunotherapy. Finally, we analyzed the heterogeneity of our signature in various types of cells using single-cell analysis. Results Platelet-related subtypes that have significant difference of overall survival and immune states ( p &lt; 0.05) were identified. PLRScore model based on four-gene signature (CEP55, LAMA3, CA12, SCN8A) was constructed to predict patient prognosis. The AUCs of training cohort were 0.697, 0.687 and 0.675 for 1-, 3-and 5-year, respectively. Further evaluation of the validation cohorts yielded similar results. In addition, PLRScore was associated with immune cell infiltration and immune checkpoint expression, and had promising ability to predict response to immunotherapy of PDAC. Conclusions In this study, the platelet-related subtypes were identified and the four-gene signature was constructed and validated. It may provide new insights into the therapeutic decision-making and molecular targets of PDAC.

Jian-Gang Zhao

Yu-Jie Li

Yong Wu

Ke Zhang

Lin-Jia Peng

Hao Chen

Revealing platelet-related subtypes and prognostic signature in pancreatic adenocarcinoma

揭示胰腺腺癌中血小板相关亚型及预后特征

Abstract Background Histone lysine lactylation ( Kla ) is a newly identified histone modification, which plays a crucial role in cancer progression. Hence, we determined the prognostic value of Kla in breast cancer (BC). Methods We obtained RNA expression profiles of BC from The Cancer Genome Atlas (TCGA), following screening out Kla-specific genes. Furthermore, we determined the prognostic value of Kla by constructing a cox model based on Kla-specific genes. Subsequently, we identified expression of lactate accumulation-related genes and prognostic Kla-specific genes through Human Protein Atlas ( HPA ), and further performed a correlation analysis based on their expression. Meanwhile, we explored the effects of Kla on BC tumor microenvironment (TME), drug therapy and immunotherapy. Moreover, we predicted the pathways influenced by Kla via gene set enrichment analysis (GSEA). Results A total of 1073 BC samples and 112 normal controls were obtained from TCGA, and 23 tumor samples were removed owing to inadequate clinical information. We identified 257 differentially expressed Kla-specific genes ( DEKlaG s) in BC. A cox model involved with CCR7 , IGFBP6 , NDUFAF6 , OVOL1 and SDC1 was established, and risk score could be visualized as an independent biomarker for BC. Meanwhile, Kla was remarkably associated with BC immune microenvironment, drug therapy and immunotherapy. Kla was identified to be related to activation of various BC-related KEGG pathways. Conclusion In conclusion, Kla contributes to drug resistance and undesirable immune responses, and plays a crucial role in BC prognosis, suggesting that Kla was expected to be a new therapeutic target for BC.

Jian Deng

Xinyi Liao

BMC Med Genomics

Lysine lactylation (Kla) might be a novel therapeutic target for breast cancer

赖氨酸乳酸化（Kla）可能是乳腺癌的一个新型治疗靶点

Abstract Background One of the most striking features of the childhood malignancy neuroblastoma (NB) is its clinical heterogeneity. Although there is a great need for better clinical and biological markers to distinguish between tumours with different severity and to improve treatment, no clear-cut prognostic factors have been found. Also, no major NB tumour suppressor genes have been identified. Methods In this study we performed expression analysis by quantitative real-time PCR (QPCR) on primary NB tumours divided into two groups, of favourable and unfavourable outcome respectively. Candidate genes were selected on basis of lower expression in unfavourable tumour types compared to favourables in our microarray expression analysis. Selected genes were studied in two steps: (1) using TaqMan Low Density Arrays (TLDA) targeting 89 genes on a set of 12 NB tumour samples, and (2) 12 genes were selected from the TLDA analysis for verification using individual TaqMan assays in a new set of 13 NB tumour samples. Results By TLDA analysis, 81 out of 87 genes were found to be significantly differentially expressed between groups, of which 14 have previously been reported as having an altered gene expression in NB. In the second verification round, seven out of 12 transcripts showed significantly lower expression in unfavourable NB tumours, ATBF1 , CACNA2D3 , CNTNAP2 , FUSIP1 , GNB1 , SLC35E2 , and TFAP2B . The gene that showed the highest fold change in the TLDA analysis, POU4F2 , was investigated for epigenetic changes (CpG methylation) and mutations in order to explore the cause of the differential expression. Moreover, the fragile site gene CNTNAP2 that showed the largest fold change in verification group 2 was investigated for structural aberrations by copy number analysis. However, the analyses of POU4F2 and CNTNAP2 showed no genetic alterations that could explain a lower expression in unfavourable NB tumours. Conclusion Through two steps of verification, seven transcripts were found to significantly discriminate between favourable and unfavourable NB tumours. Four of the transcripts, CACNA2D3 , GNB1 , SLC35E2 , and TFAP2B , have been observed in previous microarray studies, and are in this study independently verified. Our results suggest these transcripts to be markers of malignancy, which could have a potential usefulness in the clinic.

Kaisa Thorell

Annika Bergman

Helena Carén

Staffan Nilsson

Per Kogner

Tommy Martinsson

Frida Abel

Verification of genes differentially expressed in neuroblastoma tumours: a study of potential tumour suppressor genes

神经母细胞瘤肿瘤中差异表达基因的验证：一项潜在肿瘤抑制基因的研究

Abstract Background Parkinson’s disease (PD) is a progressive neurodegenerative disease with increasing prevalence. Effective diagnostic markers and therapeutic methods are still lacking. Exploring key molecular markers and mechanisms for PD can help with early diagnosis and treatment improvement. Methods Three datasets GSE174052, GSE77668, and GSE168496 were obtained from the GEO database to search differentially expressed circRNA (DECs), miRNAs (DEMis), and mRNAs (DEMs). GO and KEGG enrichment analyses, and protein–protein interaction (PPI) network construction were implemented to explore possible actions of DEMs. Hub genes were selected to establish circRNA-related competing endogenous RNA (ceRNA) networks. Results There were 1005 downregulated DECs, 21 upregulated and 21 downregulated DEMis, and 266 upregulated and 234 downregulated DEMs identified. The DEMs were significantly enriched in various PD-associated functions and pathways such as extracellular matrix organization, dopamine synthesis, PI3K-Akt, and calcium signaling pathways. Twenty-one hub genes were screened out, and a PD-related ceRNA regulatory network was constructed containing 31 circRNAs, one miRNA (miR-371a-3p), and one hub gene ( KCNJ6 ). Conclusion We identified PD-related molecular markers and ceRNA regulatory networks, providing new directions for PD diagnosis and treatment.

Zhenchao Huang

En’peng Song

Zhijie Chen

Peng Yu

Weiwen Chen

Huiqin Lin

Integrated bioinformatics analysis for exploring potential biomarkers related to Parkinson’s disease progression

综合生物信息学分析探索与帕金森病进展相关的潜在生物标志物

Pure partial trisomy 16q12.1q22.1 is a rare chromosome copy number variant (CNV). The primary clinical phenotypes associated with this syndrome include abnormal facial morphology, global developmental delay (GDD), short stature, and reported predisposing factors for atypical behavior, autism, the development of learning disabilities, and neuropsychiatric disorders. The dosage-sensitive genes associated with partial trisomy are not disclosed preventing to establish a genotype-phenotype correlation. We report a case of a Chinese patient diagnosed with GDD and an abnormal facial shape, who was found to have partial trisomy 16 through karyotyping and high-throughput sequencing analysis. Karyotype and CNV tracing analyses were also conducted on the biological parents of the patient to assess for any chromosomal structural abnormalities. Additionally, we included 29 patients with pure partial trisomy 16q, reported in the DECIPHER database and the literature. We and performed a genotype-phenotype correlation analysis. The proband, a 2-year-old female, was found to have a de novo 21.96 Mb duplication located between 16q12.1q22.1, with no other deletions observed on other chromosomes, indicating a pure partial trisomy of 16q. Through genotype and phenotype analysis of 29 individuals, we found that patients with the duplicated region located at the distal region of 16q may exhibit more severe symptoms than those with duplication at the proximal region; however, no relationship was identified between phenotype and the size of the duplicated segment. We report, for the first time, a patient with partial trisomy 16q validated by multiple genetic tests, including CNV-seq, whole exome sequencing (WES), and karyotyping. It is speculated that partial trisomy of 16q may be associated with continuous gene duplication. However, functional studies are necessary to identify the causative gene or critical region linked to duplication syndrome of chromosome 16q.

Dan Tang

Ai Chen

Jing Xu

Yu Huang

Jun Fan

Jin Wang

Hui Zhu

Guanghuan Pi

Li Yang

Fu Xiong

Zemin Luo

Gen Li

Lan Zeng

Shuyao Zhu

Genetic analysis of partial duplication of the long arm of chromosome 16

16号染色体长臂部分重复的遗传分析

Our previous study demonstrated that temperature-related microwave ablation (MWA) can safely modulate growth plates of piglets' vertebrae. Therefore, this study is designed to investigate the effects of different temperatures on chondrocyte viability and the underlying molecular mechanisms in vitro.

Wei Zhao

Yingsong Wang

Jingming Xie

Jin Zhou

Zhi Zhao

Tao Li

Zhiyue Shi

Jie Xiao

Effects of different temperatures on chondrocyte growth: a transcriptomic analysis

不同温度对软骨细胞生长的影响：转录组学分析

Hypertension (HTN) is a medical condition characterized by persistent systolic and diastolic blood pressures of ≥ 140 mmHg and ≥ 90 mmHg, respectively. With more than 1200 million adult patients aged 30-79 years worldwide according to the latest WHO data, HTN is a major health risk factor; more importantly, 46% of patients are unaware of this condition. Essential hypertension (EH), also known as primary hypertension, is the predominant subtype and has a complex etiology that involves both genetic and non-genetic factors. Majority of living organisms are influenced by the light and dark cycle of a day and respond to these changes through an intricate clock referred to as the "biological clock" or "circadian rhythm". The connection between circadian rhythm and blood pressure is well established, with many studies supporting the role of circadian rhythm gene mutation(s)/polymorphism(s) in EH. To date, no such data are available from any Indian population.

Shreya Sopori

Kavinay Kavinay

Sonali Bhan

Shreya Saxena

Medha Medha

Rakesh Kumar

Arti Dhar

Audesh Bhat

CLOCK gene 3’UTR and exon 9 polymorphisms show a strong association with essential hypertension in a North Indian population

CLOCK基因3'UTR和外显子9多态性与北印度人群原发性高血压密切相关

Prelingual hearing impairment (HI) is genetically highly heterogenous. Early diagnosis and intervention are essential for psychosocial development. In this study we investigated a consanguineous family from Pakistan with autosomal recessive (AR) non-syndromic sensorineural HI (NSHI). A DNA sample from an HI member of a consanguineous Pakistani family segregating ARNSHL underwent exome sequencing. Using Sanger sequencing select variants were validated and tested for segregation using DNA samples from additional family members. We further investigated RNA expression data for the candidate gene in mouse and human inner ear and human inner ear organoids using data obtained from the gene Expression Analysis Resource. We identified thrombospondin 1 (THBS1) as a new NSHI gene. A homozygous frameshift variant [c.1470del: p.(Ile491Serfs*45)] was observed in the three hearing-impaired and in the heterozygous state in three unaffected family members. Unlike for most ARNSHI, hearing-impaired individuals had audiograms with a sloping pattern, showing more pronounced HI in the mid and high frequencies (ranging from moderate to profound) compared to the low frequencies. RNA expression data indicates THBS1 is expressed during human inner ear development. Additionally, THBS1 is expressed in the cochlear epithelium and supporting cells of the mouse inner ear during embryonic and postnatal stages. Previously, THBS1 was demonstrated to affect hearing in knockout mice by influencing the formation and function of afferent synapses in the inner ear. Our findings highlight THBS1 as a potential novel candidate gene for human HI characterized by a sloping high-frequency audio profile. This discovery enhances our understanding of the genetic etiology of HI and will aid in advancing molecular diagnosis.

Thashi Bharadwaj

Anushree Acharya

Fati Ullah Khan

Saadullah Khan

Irfan Ullah

Isabelle Schrauwen

Wasim Ahmad

Suzanne M. Leal

THBS1 is a new autosomal recessive non-syndromic hearing impairment gene

THBS1是一种新的常染色体隐性非综合征性听力障碍基因

The role of the vitamin D receptor single nucleotide polymorphism FOKI (VDR-FOKI) (rs2228570) in genetic susceptibility to type 2 diabetic kidney disease (T2DKD) remains uncertain. This study investigated the relationship between VDR-FOKI and T2DKD within the Chinese Plateau Han population and analyzed the underlying mechanisms.

Yaping Zhao

Zehui Liu

Shiyu Feng

Rong yang

Zhenqin Ran

Rong Zhu

Lijuan Ma

Zizhou Wang

Lixin Chen

Rui Han

The association between vitamin D receptor gene polymorphism FokI and type 2 diabetic kidney disease and its molecular mechanism: a case control study

维生素D受体基因FokI多态性与2型糖尿病肾病的关联及其分子机制：一项病例对照研究

Abbreviation	BMC Med Genomics
Journal Impact	1.94
Quartiles(Global)	GENETICS & HEREDITY(Q3)

ISSN	1755-8794
h-index	94

Publication Information	Publisher: BioMed Central Ltd，Publishing cycle: Irregular，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 2009，Proportion of original research papers: 96.32%，Self Citation Rate:4.80%， Gold OA Rate: 100.00%
Average review cycle	网友分享经验：平均3.5月
Average recruitment ratio	网友分享经验：约50%

BMC Medical Genomics

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