Objective:To screen the blood group system genes of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems of Li ethnic group in Hainan Province and provide laboratory data for the rare blood group database in this ar...Objective:To screen the blood group system genes of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems of Li ethnic group in Hainan Province and provide laboratory data for the rare blood group database in this area.Methods:The alleles of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems of 300 voluntary participants of Li ethnic group in Hainan were detected by sequence-specific primer polymerase chain reaction,and the polymorphism was analyzed.Results:The allele frequencies of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems of Li ethnic groups in Hainan Province are 0.9583 for Fy^(a),0.0417 for Fy^(b),0.8350 for Au^(a),0.1650 for Au^(b),0.4500 for Jk^(a),0.5500 for Jk^(b),0.0667 for Di^(a),0.9333 for Di^(b),0.1017 for Doa and 0.8983 for Dob,respectively.The antigen incompatibility rates of Fy^(a)/Fy^(b),Au^(a)/Au^(b),Jk^(a)/Jk^(b),Di^(a)/Di^(b),Doa/Dob of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems were 7.67%,23.76%,37.25%,11.67%and 16.60%,respectively.Conclusion:The gene frequencies of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems of Li ethnic group in Hainan Province are polymorphic,and the antigen incompatibility rates of alleles are higher,which is quite different from that of other nationalities in China and with unique ethnic distribution characteristics.It is of great significance to establish the rare blood group database in this region.展开更多
<strong>Background:</strong><span style="font-family:""> This study is aimed towards an exploration of mutant genes in primary liver cancer (PLC) patients by using bioinformatics and d...<strong>Background:</strong><span style="font-family:""> This study is aimed towards an exploration of mutant genes in primary liver cancer (PLC) patients by using bioinformatics and data mining techniques. <b>Methods: </b>Peripheral blood or paraffin-embedded tissues from 8 patients with PLC were analyzed using a 551 cancer-related gene panel on an Illumina NextSeq500 Sequencer (Illumina). Meanwhile, the data of 396 PLC cases were downloaded from The Cancer Genome Atlas (TCGA) database. The common mutated genes were obtained after integrating the mutation information of the above two cohorts, followed by functional enrichment and protein-protein interaction (PPI) analyses. Three well-known databases, including Vogelstein’s list, the Network of Cancer Gene (NCG), and the Catalog of Somatic Mutations in Cancer (COSMIC) database were used to screen driver genes. Furthermore, the Chi-square and logistic analysis were performed to analyze the correlation between the driver genes and clinicopathological characteristics, and Kaplan</span><span style="font-family:"">-</span><span style="font-family:"">Meier (KM) method and multivariate Cox analysis were conducted to evaluate the overall survival outcome. <b>Results:</b> In total, 84 mutation genes were obtained after 8 PLC patients undergoing gene mutation detection with next-generation sequencing (NGS). The top 100 most mutate gene data from PLC patients in TCGA database were downloaded. After integrating the above two cohorts, 17 common mutated genes were identified. Next, 11 driver genes were screened out by analyzing the intersection of the 17 mutation genes and the genes in the three well-known databases. Among them, RB1, TP53, and KRAS gene mutations were connected with clinicopathological characteristics, while all the 11 gene mutations had no relationship with overall survival. <b>Conclusion:</b> This study investigated the mutant genes with significant clinical implications in PLC patients, which may improve the knowledge of gene mutations in PLC molecular pathogenesis.</span>展开更多
AIM To investigate the driver gene mutations associatedwith colorectal cancer (CRC) in the Taiwan Residentspopulation.METHODS: In this study, 103 patients with CRCwere evaluated. The samples consisted of 66 menand ...AIM To investigate the driver gene mutations associatedwith colorectal cancer (CRC) in the Taiwan Residentspopulation.METHODS: In this study, 103 patients with CRCwere evaluated. The samples consisted of 66 menand 37 women with a median age of 59 years and anage range of 26-86 years. We used high-resolutionmelting analysis (HRM) and direct DNA sequencing tocharacterize the mutations in 13 driver genes of CRCrelatedpathways. The HRM assays were conductedusing the LightCycler? 480 Instrument provided with the software LightCycler 480 Gene Scanning SoftwareVersion 1.5. We also compared the clinicopathologicaldata of CRC patients with the driver gene mutationstatus.RESULTS: Of the 103 patients evaluated, 73.79%had mutations in one of the 13 driver genes. Wediscovered 18 novel mutations in APC , MLH1 , MSH2 ,PMS2 , SMAD4 and TP53 that have not been previouslyreported. Additionally, we found 16 de novo mutationsin APC , BMPR1A , MLH1 , MSH2 , MSH6 , MUTYH andPMS2 in cancerous tissues previously reported in thedbSNP database; however, these mutations couldnot be detected in peripheral blood cells. The APCmutation correlates with lymph node metastasis(34.69% vs 12.96%, P = 0.009) and cancer stage(34.78% vs 14.04%, P = 0.013). No association wasobserved between other driver gene mutations andclinicopathological features. Furthermore, having twoor more driver gene mutations correlates with thedegree of lymph node metastasis (42.86% vs 24.07%,P = 0.043).CONCLUSION: Our findings confirm the importanceof 13 CRC-related pathway driver genes in the developmentof CRC in Taiwan Residents patients.展开更多
The identification of tumor driver genes facilitates accurate cancer diagnosis and treatment,playing a key role in precision oncology,along with gene signaling,regulation,and their interaction with protein complexes.T...The identification of tumor driver genes facilitates accurate cancer diagnosis and treatment,playing a key role in precision oncology,along with gene signaling,regulation,and their interaction with protein complexes.To tackle the challenge of distinguishing driver genes from a large number of genomic data,we construct a feature extraction framework for discovering pan-cancer driver genes based on multi-omics data(mutations,gene expression,copy number variants,and DNA methylation)combined with protein–protein interaction(PPI)networks.Using a network propagation algorithm,we mine functional information among nodes in the PPI network,focusing on genes with weak node information to represent specific cancer information.From these functional features,we extract distribution features of pan-cancer data,pan-cancer TOPSIS features of functional features using the ideal solution method,and SetExpan features of pan-cancer data from the gene functional features,a method to rank pan-cancer data based on the average inverse rank.These features represent the common message of pan-cancer.Finally,we use the lightGBM classification algorithm for gene prediction.Experimental results show that our method outperforms existing methods in terms of the area under the check precision-recall curve(AUPRC)and demonstrates better performance across different PPI networks.This indicates our framework’s effectiveness in predicting potential cancer genes,offering valuable insights for the diagnosis and treatment of tumors.展开更多
Rare earth elements(REE)are applied as micro-fertilizer in large scale in China and there is growing concern about the environmental effects of REE accumulation in soils. Accumulation of REE was simulated in lab by ad...Rare earth elements(REE)are applied as micro-fertilizer in large scale in China and there is growing concern about the environmental effects of REE accumulation in soils. Accumulation of REE was simulated in lab by adding REE to three soils and the survival of Pseudomonas fluorescence X16 strain marked with luxAB gene in soils was detected. Curvilinear regression method was applied to analyze the survival pattern. The stimulation values, EC_(50) and NOEC values for X16 strain were calculated to compare the toxic intensity of REE in different soils. The stimulation(peak)values in red soil, yellow fluovo-aquic soil and yellow cinnamon soil, are 11.55~18.08,(0~2.13), 2.37~4.62 mg·kg^(-1) , respectively. EC_(50) values are 13.47~39.12, 6.59~56.18, 372~1034 (mg·kg^(-1)), respectively.NOEC values are 5.62 ~21.41, 0.00~4.53, 133.3~327.1 mg·kg^(-1), respectively. Tangents values of regression equation of the survival of X16 strain in red soil are the maximum ones indicating that REE accumulation in red soil has stronger inhibitory effects than in other two soils. The soil order, reflecting toxic intensity of REE is as follows: red soil>yellow fluovic-aquic soil>yellow cinnamon soil.展开更多
Identification of cancer driver genes plays an important role in precision oncology research,which is helpful to understand cancer initiation and progression.However,most existing computational methods mainly used the...Identification of cancer driver genes plays an important role in precision oncology research,which is helpful to understand cancer initiation and progression.However,most existing computational methods mainly used the protein–protein interaction(PPI)networks,or treated the directed gene regulatory networks(GRNs)as the undirected gene–gene association networks to identify the cancer driver genes,which will lose the unique structure regulatory information in the directed GRNs,and then affect the outcome of the cancer driver gene identification.Here,based on the multi-omics pan-cancer data(i.e.,gene expression,mutation,copy number variation,and DNA methylation),we propose a novel method(called DGMP)to identify cancer driver genes by jointing directed graph convolutional network(DGCN)and multilayer perceptron(MLP).DGMP learns the multi-omics features of genes as well as the topological structure features in GRN with the DGCN model and uses MLP to weigh more on gene features for mitigating the bias toward the graph topological features in the DGCN learning process.The results on three GRNs show that DGMP outperforms other existing state-of-the-art methods.The ablation experimental results on the Dawn Net network indicate that introducing MLP into DGCN can offset the performance degradation of DGCN,and jointing MLP and DGCN can effectively improve the performance of identifying cancer driver genes.DGMP can identify not only the highly mutated cancer driver genes but also the driver genes harboring other kinds of alterations(e.g.,differential expression and aberrant DNA methylation)or genes involved in GRNs with other cancer genes.The source code of DGMP can be freely downloaded from https://github.com/NWPU-903PR/DGMP.展开更多
Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells.A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among availab...Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells.A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic mutations.To address this issue,we present the first webbased application,consensus cancer driver gene caller(C^3),to identify the consensus driver genes using six different complementary strategies,i.e.,frequency-based,machine learning-based,functional bias-based,clustering-based,statistics model-based,and network-based strategies.This application allows users to specify customized operations when calling driver genes,and provides solid statistical evaluations and interpretable visualizations on the integration results.C^3 is implemented in Python and is freely available for public use at http://drivergene.rwebox.com/c3.展开更多
The effects of Ce (Ⅳ) on callus growth, anthocyanin content, and expression of anthocyanin biosynthetic genes in callus suspension cultures of Solanum tuberosum cv. Chieftain were studied by the measurement of fres...The effects of Ce (Ⅳ) on callus growth, anthocyanin content, and expression of anthocyanin biosynthetic genes in callus suspension cultures of Solanum tuberosum cv. Chieftain were studied by the measurement of fresh weight, spectrophotometric assays, and semiquantitative RT-PCR. The results indicate that 0.1 mmol·L^- 1 Ce ( Ⅳ ) can promote callus growth, increase the accumulation of anthocyanins, and enhance the expression of five anthocyanin biosynthetic genes ( CHS, F3H, F3'5'H, DFR, and 3 GT) most efficiently. At high concentrations of 1 mmol·L^- 1, Ce (Ⅳ) partially inhibits callus growth and at 2 mmol· L^-1 eventually lends to cell death. The results show that Ce( Ⅳ ) can induce the expression of anthocyanin biosynthetic genes to produce and accumulate anthocyanins and increase the yield of anthocyanins.展开更多
The rats were fed with water dissolved Y^3+ at different levels (0, 53.4, 5340 mg·L^-1) for 7 months. The gene expression in brain tissue was detected with oligonucleotide microarray. The results show that, co...The rats were fed with water dissolved Y^3+ at different levels (0, 53.4, 5340 mg·L^-1) for 7 months. The gene expression in brain tissue was detected with oligonucleotide microarray. The results show that, compared to the control, 789 genes express differentially, 507 over-expressed genes and 282 under-expressed genes in the high-dose group (5340 mg· L^-1), of which, most were related to cell receptor, cell signal and transmission, and ionic passage. 44 genes were found to express differentially including 32 over-expressed genes and 12 under-expressed genes in the low-dose group (53. 40 mg· L^-1), of which, most were related to cell skeleton and movement, immunity, and DNA binding protein. These resuits suggest that Y^3. can change the expression of some genes, which may be responsible for the toxicity of rare earths on learning and memory.展开更多
基金Hainan Provincial Natural Science Foundation of China(No.820QN410)Hainan Province Clinical Medical Center(No.QWYH202175)。
文摘Objective:To screen the blood group system genes of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems of Li ethnic group in Hainan Province and provide laboratory data for the rare blood group database in this area.Methods:The alleles of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems of 300 voluntary participants of Li ethnic group in Hainan were detected by sequence-specific primer polymerase chain reaction,and the polymorphism was analyzed.Results:The allele frequencies of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems of Li ethnic groups in Hainan Province are 0.9583 for Fy^(a),0.0417 for Fy^(b),0.8350 for Au^(a),0.1650 for Au^(b),0.4500 for Jk^(a),0.5500 for Jk^(b),0.0667 for Di^(a),0.9333 for Di^(b),0.1017 for Doa and 0.8983 for Dob,respectively.The antigen incompatibility rates of Fy^(a)/Fy^(b),Au^(a)/Au^(b),Jk^(a)/Jk^(b),Di^(a)/Di^(b),Doa/Dob of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems were 7.67%,23.76%,37.25%,11.67%and 16.60%,respectively.Conclusion:The gene frequencies of Duffy,Lutheran,Kidd,Diego,Dombrock blood group systems of Li ethnic group in Hainan Province are polymorphic,and the antigen incompatibility rates of alleles are higher,which is quite different from that of other nationalities in China and with unique ethnic distribution characteristics.It is of great significance to establish the rare blood group database in this region.
文摘<strong>Background:</strong><span style="font-family:""> This study is aimed towards an exploration of mutant genes in primary liver cancer (PLC) patients by using bioinformatics and data mining techniques. <b>Methods: </b>Peripheral blood or paraffin-embedded tissues from 8 patients with PLC were analyzed using a 551 cancer-related gene panel on an Illumina NextSeq500 Sequencer (Illumina). Meanwhile, the data of 396 PLC cases were downloaded from The Cancer Genome Atlas (TCGA) database. The common mutated genes were obtained after integrating the mutation information of the above two cohorts, followed by functional enrichment and protein-protein interaction (PPI) analyses. Three well-known databases, including Vogelstein’s list, the Network of Cancer Gene (NCG), and the Catalog of Somatic Mutations in Cancer (COSMIC) database were used to screen driver genes. Furthermore, the Chi-square and logistic analysis were performed to analyze the correlation between the driver genes and clinicopathological characteristics, and Kaplan</span><span style="font-family:"">-</span><span style="font-family:"">Meier (KM) method and multivariate Cox analysis were conducted to evaluate the overall survival outcome. <b>Results:</b> In total, 84 mutation genes were obtained after 8 PLC patients undergoing gene mutation detection with next-generation sequencing (NGS). The top 100 most mutate gene data from PLC patients in TCGA database were downloaded. After integrating the above two cohorts, 17 common mutated genes were identified. Next, 11 driver genes were screened out by analyzing the intersection of the 17 mutation genes and the genes in the three well-known databases. Among them, RB1, TP53, and KRAS gene mutations were connected with clinicopathological characteristics, while all the 11 gene mutations had no relationship with overall survival. <b>Conclusion:</b> This study investigated the mutant genes with significant clinical implications in PLC patients, which may improve the knowledge of gene mutations in PLC molecular pathogenesis.</span>
基金research grant from the China Medical University Hospital,DMR-103-017
文摘AIM To investigate the driver gene mutations associatedwith colorectal cancer (CRC) in the Taiwan Residentspopulation.METHODS: In this study, 103 patients with CRCwere evaluated. The samples consisted of 66 menand 37 women with a median age of 59 years and anage range of 26-86 years. We used high-resolutionmelting analysis (HRM) and direct DNA sequencing tocharacterize the mutations in 13 driver genes of CRCrelatedpathways. The HRM assays were conductedusing the LightCycler? 480 Instrument provided with the software LightCycler 480 Gene Scanning SoftwareVersion 1.5. We also compared the clinicopathologicaldata of CRC patients with the driver gene mutationstatus.RESULTS: Of the 103 patients evaluated, 73.79%had mutations in one of the 13 driver genes. Wediscovered 18 novel mutations in APC , MLH1 , MSH2 ,PMS2 , SMAD4 and TP53 that have not been previouslyreported. Additionally, we found 16 de novo mutationsin APC , BMPR1A , MLH1 , MSH2 , MSH6 , MUTYH andPMS2 in cancerous tissues previously reported in thedbSNP database; however, these mutations couldnot be detected in peripheral blood cells. The APCmutation correlates with lymph node metastasis(34.69% vs 12.96%, P = 0.009) and cancer stage(34.78% vs 14.04%, P = 0.013). No association wasobserved between other driver gene mutations andclinicopathological features. Furthermore, having twoor more driver gene mutations correlates with thedegree of lymph node metastasis (42.86% vs 24.07%,P = 0.043).CONCLUSION: Our findings confirm the importanceof 13 CRC-related pathway driver genes in the developmentof CRC in Taiwan Residents patients.
基金National Natural Science Foundation of China,Grant/Award Numbers:61902215,61902216,61972226。
文摘The identification of tumor driver genes facilitates accurate cancer diagnosis and treatment,playing a key role in precision oncology,along with gene signaling,regulation,and their interaction with protein complexes.To tackle the challenge of distinguishing driver genes from a large number of genomic data,we construct a feature extraction framework for discovering pan-cancer driver genes based on multi-omics data(mutations,gene expression,copy number variants,and DNA methylation)combined with protein–protein interaction(PPI)networks.Using a network propagation algorithm,we mine functional information among nodes in the PPI network,focusing on genes with weak node information to represent specific cancer information.From these functional features,we extract distribution features of pan-cancer data,pan-cancer TOPSIS features of functional features using the ideal solution method,and SetExpan features of pan-cancer data from the gene functional features,a method to rank pan-cancer data based on the average inverse rank.These features represent the common message of pan-cancer.Finally,we use the lightGBM classification algorithm for gene prediction.Experimental results show that our method outperforms existing methods in terms of the area under the check precision-recall curve(AUPRC)and demonstrates better performance across different PPI networks.This indicates our framework’s effectiveness in predicting potential cancer genes,offering valuable insights for the diagnosis and treatment of tumors.
文摘Rare earth elements(REE)are applied as micro-fertilizer in large scale in China and there is growing concern about the environmental effects of REE accumulation in soils. Accumulation of REE was simulated in lab by adding REE to three soils and the survival of Pseudomonas fluorescence X16 strain marked with luxAB gene in soils was detected. Curvilinear regression method was applied to analyze the survival pattern. The stimulation values, EC_(50) and NOEC values for X16 strain were calculated to compare the toxic intensity of REE in different soils. The stimulation(peak)values in red soil, yellow fluovo-aquic soil and yellow cinnamon soil, are 11.55~18.08,(0~2.13), 2.37~4.62 mg·kg^(-1) , respectively. EC_(50) values are 13.47~39.12, 6.59~56.18, 372~1034 (mg·kg^(-1)), respectively.NOEC values are 5.62 ~21.41, 0.00~4.53, 133.3~327.1 mg·kg^(-1), respectively. Tangents values of regression equation of the survival of X16 strain in red soil are the maximum ones indicating that REE accumulation in red soil has stronger inhibitory effects than in other two soils. The soil order, reflecting toxic intensity of REE is as follows: red soil>yellow fluovic-aquic soil>yellow cinnamon soil.
基金supported in part by the National Natural Science Foundation of China(Grant Nos.62173271 and 61873202 to SWZ)。
文摘Identification of cancer driver genes plays an important role in precision oncology research,which is helpful to understand cancer initiation and progression.However,most existing computational methods mainly used the protein–protein interaction(PPI)networks,or treated the directed gene regulatory networks(GRNs)as the undirected gene–gene association networks to identify the cancer driver genes,which will lose the unique structure regulatory information in the directed GRNs,and then affect the outcome of the cancer driver gene identification.Here,based on the multi-omics pan-cancer data(i.e.,gene expression,mutation,copy number variation,and DNA methylation),we propose a novel method(called DGMP)to identify cancer driver genes by jointing directed graph convolutional network(DGCN)and multilayer perceptron(MLP).DGMP learns the multi-omics features of genes as well as the topological structure features in GRN with the DGCN model and uses MLP to weigh more on gene features for mitigating the bias toward the graph topological features in the DGCN learning process.The results on three GRNs show that DGMP outperforms other existing state-of-the-art methods.The ablation experimental results on the Dawn Net network indicate that introducing MLP into DGCN can offset the performance degradation of DGCN,and jointing MLP and DGCN can effectively improve the performance of identifying cancer driver genes.DGMP can identify not only the highly mutated cancer driver genes but also the driver genes harboring other kinds of alterations(e.g.,differential expression and aberrant DNA methylation)or genes involved in GRNs with other cancer genes.The source code of DGMP can be freely downloaded from https://github.com/NWPU-903PR/DGMP.
基金supported by the National Major Research and Innovation Program of China(Grant Nos.2017YFC0908500and 2016YFC1303205)National Natural Science Foundation of China(Grant No.61572361)+2 种基金Shanghai Rising-Star Program(Grant No.16QA1403900)Shanghai Natural Science Foundation Program(Grant No.17ZR1449400)Fundamental Research Funds for the Central Universities(Grant No.1501219106),China
文摘Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells.A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic mutations.To address this issue,we present the first webbased application,consensus cancer driver gene caller(C^3),to identify the consensus driver genes using six different complementary strategies,i.e.,frequency-based,machine learning-based,functional bias-based,clustering-based,statistics model-based,and network-based strategies.This application allows users to specify customized operations when calling driver genes,and provides solid statistical evaluations and interpretable visualizations on the integration results.C^3 is implemented in Python and is freely available for public use at http://drivergene.rwebox.com/c3.
基金Project Supported bythe International Cooperation Research of Jiangsu Province (BZ2003041)
文摘The effects of Ce (Ⅳ) on callus growth, anthocyanin content, and expression of anthocyanin biosynthetic genes in callus suspension cultures of Solanum tuberosum cv. Chieftain were studied by the measurement of fresh weight, spectrophotometric assays, and semiquantitative RT-PCR. The results indicate that 0.1 mmol·L^- 1 Ce ( Ⅳ ) can promote callus growth, increase the accumulation of anthocyanins, and enhance the expression of five anthocyanin biosynthetic genes ( CHS, F3H, F3'5'H, DFR, and 3 GT) most efficiently. At high concentrations of 1 mmol·L^- 1, Ce (Ⅳ) partially inhibits callus growth and at 2 mmol· L^-1 eventually lends to cell death. The results show that Ce( Ⅳ ) can induce the expression of anthocyanin biosynthetic genes to produce and accumulate anthocyanins and increase the yield of anthocyanins.
文摘The rats were fed with water dissolved Y^3+ at different levels (0, 53.4, 5340 mg·L^-1) for 7 months. The gene expression in brain tissue was detected with oligonucleotide microarray. The results show that, compared to the control, 789 genes express differentially, 507 over-expressed genes and 282 under-expressed genes in the high-dose group (5340 mg· L^-1), of which, most were related to cell receptor, cell signal and transmission, and ionic passage. 44 genes were found to express differentially including 32 over-expressed genes and 12 under-expressed genes in the low-dose group (53. 40 mg· L^-1), of which, most were related to cell skeleton and movement, immunity, and DNA binding protein. These resuits suggest that Y^3. can change the expression of some genes, which may be responsible for the toxicity of rare earths on learning and memory.