Identification and analysis of tissue-specific (TS) genes and their regulatory activities play an important role in understanding the mechanisms of the organism, disease diagnosis and drug design. Although so far we a...Identification and analysis of tissue-specific (TS) genes and their regulatory activities play an important role in understanding the mechanisms of the organism, disease diagnosis and drug design. Although so far we are not clear about the mechanisms totally, the sequence features of TS genes are becoming an important clue. In this paper we used an integrated pipeline to discover sequences motifs for the promoter regions of TS genes. To test the significances of those motifs in a specific tissue, we used hypotheses test approaches including Bayesian hypothesis, Binomial distribution and traditional z-test. We finally got 2784, 1204 and 703 motifs respectively out of 3244 motifs obtained in discovery phase using above three tests from 3954 TS genes across 83 human tissues. 52.7% of those motifs can be found in public databases available.展开更多
The traditional method for creating a gene score to predict a given outcome is to use the most statistically significant single nucleotide polymorphisms (SNPs) from all SNPs which were tested. There are several disadv...The traditional method for creating a gene score to predict a given outcome is to use the most statistically significant single nucleotide polymorphisms (SNPs) from all SNPs which were tested. There are several disadvantages of this approach such as excluding SNPs that do not have strong single effects when tested on their own but do have strong joint effects when tested together with other SNPs. The interpretation of results from the traditional gene score may lack biological insight since the functional unit of interest is often the gene, not the single SNP. In this paper we present a new gene scoring method, which overcomes these problems as it generates a gene score for each gene, and the total gene score for all the genes available. First, we calculate a gene score for each gene and second, we test the association between this gene score and the outcome of interest (i.e. trait). Only the gene scores which are significantly associated with the outcome after multiple testing correction for the number of gene tests (not SNPs) are considered in the total gene score calculation. This method controls false positive results caused by multiple tests within genes and between genes separately, and has the advantage of identifying multi-locus genetic effects, compared with the Bonferroni correction, false discovery rate (FDR), and permutation tests for all SNPs. Another main feature of this method is that we select the SNPs, which have different effects within a gene by using adjustment in multiple regressions and then combine the information from the selected SNPs within a gene to create a gene score. A simulation study has been conducted to evaluate finite sample performance of the proposed method.展开更多
Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena i PLEX chemistry and matrix-assisted laser desorption ioniza...Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena i PLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on Mass ARRAY mass spectrometry platform.Methods: We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a Lung Carta^(TM) kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencing EGFR and KRAS genes in 100 lung cancer cases.Results: The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with Lung Carta^(TM) kit. However, an FGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively.Conclusions: The proposed Mass ARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues.展开更多
Over the last twenty years,with the development of gene-driven therapies,numerous new drugs have entered clinical use.Very few of these new drugs are suitable for a large number of patients,and all require molecular g...Over the last twenty years,with the development of gene-driven therapies,numerous new drugs have entered clinical use.Very few of these new drugs are suitable for a large number of patients,and all require molecular genetic testing.In lung cancer,gene-targeted therapy has evolved rapidly and has placed demands on the development of diagnostics and tissue sample preparation and logistics.Rapid diagnosis and prevalence assessment are necessary to determine the prognosis of a lung cancer patient based on the latest research findings.Therefore,the molecular-genetic diagnostic pathway must also be accelerated and matured to do the necessary analyses on small samples.Because lung cancer rebiopsy can be difficult,liquid biopsy techniques should be developed to cover more of the treatable mutations.There are obstacles related to tissue sampling,new genomic techniques and access to gene-driven cancer drugs,including their affordability.With this review and case study,we go into the obstacles faced by our clinic and discuss how to tackle these obstacles in lung cancer.We use lung cancer as an example due to its complexity,though these same obstacles are found in different cancers on a minor scale.展开更多
This experiment was conducted to clarify species and drug resistance of pathogen from the diseased Procambarus clarkia. Pathogenic bacteria from hepatopancreas of the diseased P. clarkia were examined using convention...This experiment was conducted to clarify species and drug resistance of pathogen from the diseased Procambarus clarkia. Pathogenic bacteria from hepatopancreas of the diseased P. clarkia were examined using conventional methods,and then were isolated. The further tests and analysis of the isolated strain were developed,including the regression experiment to P. clarkia,the morphology,physiological and biochemical characteristics,sequence analysis of their 16 S rRNA and gyr B genes,and the susceptibility test to antibiotics. Large colonies with similar morphology and color were obtained. Strain X120523 was identified as Citrobacter freundii,proved to have strong pathogenicity,and was susceptible to quinolones and aminoglycosides.展开更多
Transmission disequilibrium test (TDT) is a popular family based genetic association method. Under multiplicative assumption, a conditional logistic regression for matched pair, affected offspring with allele transmit...Transmission disequilibrium test (TDT) is a popular family based genetic association method. Under multiplicative assumption, a conditional logistic regression for matched pair, affected offspring with allele transmitted from parents and pseudo-offspring (control) with allele non-transmitted from parents, was built to detect the <span style="font-family:Verdana;">main </span><span style="font-family:Verdana;">effects of genes and gene-covariate interaction</span><span style="font-family:Verdana;">s</span><span style="font-family:;" "=""><span style="font-family:Verdana;">. When there exist genotype uncertainties, expectation-maximization (EM) algorithm was adopted to estimate the coefficients. The transmission model was applied to detect the association between M235T polymorphism in AGT gene and essential hypertension (ESH). Most of parents are not available in the 126 families from HongKong Chinese population. The results </span><span style="font-family:Verdana;">showed M235T is associat</span></span><span style="font-family:Verdana;">ed</span><span style="font-family:Verdana;"> with hypertension and there is interaction between M235T and the case’s sex. The allele T is higher risk for male than female</span><span style="font-family:Verdana;">.</span>展开更多
目的:分析江苏省汉族人群亲子鉴定中39个短串联重复序列(short tandem repeat,STR)基因座的突变特征。方法:选取2019年1月—2024年12月南京医科大学第一附属医院司法鉴定所受理的6812例亲子鉴定案例,采用GoldenEye^(TM) DNA身份鉴定系...目的:分析江苏省汉族人群亲子鉴定中39个短串联重复序列(short tandem repeat,STR)基因座的突变特征。方法:选取2019年1月—2024年12月南京医科大学第一附属医院司法鉴定所受理的6812例亲子鉴定案例,采用GoldenEye^(TM) DNA身份鉴定系统检测39个STR基因座的突变情况,对突变率、突变来源和步数进行统计分析。结果:在6812例认定亲子关系的案例中,三联体1680例,二联体5132例。共发现214例突变案例,总突变率2.52%。其中,D12S391基因座突变率最高,达0.3297%(28/8492),其次为Penta E、FGA、D21S11、D18S51、D3S1358基因座,突变率均在0.20%以上。突变来源分析中,父源突变189例,母源突变20例,不明原因突变5例,父源突变显著高于母源(P<0.001)。203例(94.86%)突变为一步突变,二步突变9例,FGA和D21S11基因座三步突变各1例。结论:亲子鉴定中39个STR基因座总突变率较高,达2.52%,具有性别和地区差异,在亲子鉴定实践中需加以重视,该结果为江苏地区汉族人群STR基因座突变情况提供数据支撑,有助于提升复杂亲缘关系鉴定的准确性。展开更多
Soybean (Glycine max L.) plays an essential role in human nutrition as a protein source, and in plant nutrition as a N source. The rate of N fixation varies depending on the cultivars and compatibility between the ino...Soybean (Glycine max L.) plays an essential role in human nutrition as a protein source, and in plant nutrition as a N source. The rate of N fixation varies depending on the cultivars and compatibility between the inoculated Rhizobium strain and the host cultivar. Characterizing the nodulation regulatory (Rj) genes is necessary to determine the compatibility of cultivars and Rhizobium strains. Rj genes were previously identified based on inoculation tests and PCR analyses. The six cultivars Yezin-3, Yezin-7, Yezin-11, Shan Seine (Local), Madaya (Local), and Hinthada (Local) were identified as harboring the Rj4 gene. Two cultivars, Yezin-6 and Yezin-8, were classified as non-Rj-gene harboring. Two other cultivars, Yezin-9 and Yezin-10, were identified as Rj3- and Rj2Rj3-gene harboring, respectively. Ours is the first report on Rj3- and Rj2Rj3-gene harboring cultivars in Myanmar. We evaluated Myanmar soybean cultivars for symbiotic effectiveness, relying on the standard strain Bradyrhizobium japonicum USDA110. In our first experiment, the soybean cultivar Yezin-11 (Rj4) showed the highest N fixing potential. Based on their potential for fixing N and nodulation, the top six soybean cultivars were Yezin-11 (Rj4), Yezin-9 (Rj3), Yezin-6 (non-Rj), Yezin-8 (non-Rj), Yezin-3 (Rj4) and Yezin-10 (Rj2Rj3). These cultivars were selected for a second experiment, which revealed that the N fixation, nodulation, and plant growth of Yezin-11 (Rj4) *Corresponding author. A. Z. Htwe et al. 2800 were superior to the other cultivars. We conclude that Yezin-11 (Rj4) is the most efficient cultivar for nodulation and N fixation when inoculated with B. japonicum USDA110.展开更多
文摘Identification and analysis of tissue-specific (TS) genes and their regulatory activities play an important role in understanding the mechanisms of the organism, disease diagnosis and drug design. Although so far we are not clear about the mechanisms totally, the sequence features of TS genes are becoming an important clue. In this paper we used an integrated pipeline to discover sequences motifs for the promoter regions of TS genes. To test the significances of those motifs in a specific tissue, we used hypotheses test approaches including Bayesian hypothesis, Binomial distribution and traditional z-test. We finally got 2784, 1204 and 703 motifs respectively out of 3244 motifs obtained in discovery phase using above three tests from 3954 TS genes across 83 human tissues. 52.7% of those motifs can be found in public databases available.
文摘The traditional method for creating a gene score to predict a given outcome is to use the most statistically significant single nucleotide polymorphisms (SNPs) from all SNPs which were tested. There are several disadvantages of this approach such as excluding SNPs that do not have strong single effects when tested on their own but do have strong joint effects when tested together with other SNPs. The interpretation of results from the traditional gene score may lack biological insight since the functional unit of interest is often the gene, not the single SNP. In this paper we present a new gene scoring method, which overcomes these problems as it generates a gene score for each gene, and the total gene score for all the genes available. First, we calculate a gene score for each gene and second, we test the association between this gene score and the outcome of interest (i.e. trait). Only the gene scores which are significantly associated with the outcome after multiple testing correction for the number of gene tests (not SNPs) are considered in the total gene score calculation. This method controls false positive results caused by multiple tests within genes and between genes separately, and has the advantage of identifying multi-locus genetic effects, compared with the Bonferroni correction, false discovery rate (FDR), and permutation tests for all SNPs. Another main feature of this method is that we select the SNPs, which have different effects within a gene by using adjustment in multiple regressions and then combine the information from the selected SNPs within a gene to create a gene score. A simulation study has been conducted to evaluate finite sample performance of the proposed method.
基金supported by the Special Fund for Research in the Public Interest from the National Health and Family Planning Commission of PRC (Grant No. 201402031)the Key Lab System Project of the Guangdong Science and Technology Department (Grant No. 2012A061400006)the Special Fund for Research in the Public Interest and Capacity Building from the Guangdong Science and Technology Department (Grant No. 2014A020212225)
文摘Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena i PLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on Mass ARRAY mass spectrometry platform.Methods: We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a Lung Carta^(TM) kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencing EGFR and KRAS genes in 100 lung cancer cases.Results: The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with Lung Carta^(TM) kit. However, an FGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively.Conclusions: The proposed Mass ARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues.
文摘Over the last twenty years,with the development of gene-driven therapies,numerous new drugs have entered clinical use.Very few of these new drugs are suitable for a large number of patients,and all require molecular genetic testing.In lung cancer,gene-targeted therapy has evolved rapidly and has placed demands on the development of diagnostics and tissue sample preparation and logistics.Rapid diagnosis and prevalence assessment are necessary to determine the prognosis of a lung cancer patient based on the latest research findings.Therefore,the molecular-genetic diagnostic pathway must also be accelerated and matured to do the necessary analyses on small samples.Because lung cancer rebiopsy can be difficult,liquid biopsy techniques should be developed to cover more of the treatable mutations.There are obstacles related to tissue sampling,new genomic techniques and access to gene-driven cancer drugs,including their affordability.With this review and case study,we go into the obstacles faced by our clinic and discuss how to tackle these obstacles in lung cancer.We use lung cancer as an example due to its complexity,though these same obstacles are found in different cancers on a minor scale.
基金Supported by the Science and Technology Innovative Research Team of Anhui Academy of Agricultural Sciences(14C0504)the Youth Innovation Foundation of President of Anhui Academy of Agricultural Sciences(14B0529)Anhui Aquaculture Industry Technology System for Shrimp and Crab
文摘This experiment was conducted to clarify species and drug resistance of pathogen from the diseased Procambarus clarkia. Pathogenic bacteria from hepatopancreas of the diseased P. clarkia were examined using conventional methods,and then were isolated. The further tests and analysis of the isolated strain were developed,including the regression experiment to P. clarkia,the morphology,physiological and biochemical characteristics,sequence analysis of their 16 S rRNA and gyr B genes,and the susceptibility test to antibiotics. Large colonies with similar morphology and color were obtained. Strain X120523 was identified as Citrobacter freundii,proved to have strong pathogenicity,and was susceptible to quinolones and aminoglycosides.
文摘Transmission disequilibrium test (TDT) is a popular family based genetic association method. Under multiplicative assumption, a conditional logistic regression for matched pair, affected offspring with allele transmitted from parents and pseudo-offspring (control) with allele non-transmitted from parents, was built to detect the <span style="font-family:Verdana;">main </span><span style="font-family:Verdana;">effects of genes and gene-covariate interaction</span><span style="font-family:Verdana;">s</span><span style="font-family:;" "=""><span style="font-family:Verdana;">. When there exist genotype uncertainties, expectation-maximization (EM) algorithm was adopted to estimate the coefficients. The transmission model was applied to detect the association between M235T polymorphism in AGT gene and essential hypertension (ESH). Most of parents are not available in the 126 families from HongKong Chinese population. The results </span><span style="font-family:Verdana;">showed M235T is associat</span></span><span style="font-family:Verdana;">ed</span><span style="font-family:Verdana;"> with hypertension and there is interaction between M235T and the case’s sex. The allele T is higher risk for male than female</span><span style="font-family:Verdana;">.</span>
文摘目的:分析江苏省汉族人群亲子鉴定中39个短串联重复序列(short tandem repeat,STR)基因座的突变特征。方法:选取2019年1月—2024年12月南京医科大学第一附属医院司法鉴定所受理的6812例亲子鉴定案例,采用GoldenEye^(TM) DNA身份鉴定系统检测39个STR基因座的突变情况,对突变率、突变来源和步数进行统计分析。结果:在6812例认定亲子关系的案例中,三联体1680例,二联体5132例。共发现214例突变案例,总突变率2.52%。其中,D12S391基因座突变率最高,达0.3297%(28/8492),其次为Penta E、FGA、D21S11、D18S51、D3S1358基因座,突变率均在0.20%以上。突变来源分析中,父源突变189例,母源突变20例,不明原因突变5例,父源突变显著高于母源(P<0.001)。203例(94.86%)突变为一步突变,二步突变9例,FGA和D21S11基因座三步突变各1例。结论:亲子鉴定中39个STR基因座总突变率较高,达2.52%,具有性别和地区差异,在亲子鉴定实践中需加以重视,该结果为江苏地区汉族人群STR基因座突变情况提供数据支撑,有助于提升复杂亲缘关系鉴定的准确性。
文摘Soybean (Glycine max L.) plays an essential role in human nutrition as a protein source, and in plant nutrition as a N source. The rate of N fixation varies depending on the cultivars and compatibility between the inoculated Rhizobium strain and the host cultivar. Characterizing the nodulation regulatory (Rj) genes is necessary to determine the compatibility of cultivars and Rhizobium strains. Rj genes were previously identified based on inoculation tests and PCR analyses. The six cultivars Yezin-3, Yezin-7, Yezin-11, Shan Seine (Local), Madaya (Local), and Hinthada (Local) were identified as harboring the Rj4 gene. Two cultivars, Yezin-6 and Yezin-8, were classified as non-Rj-gene harboring. Two other cultivars, Yezin-9 and Yezin-10, were identified as Rj3- and Rj2Rj3-gene harboring, respectively. Ours is the first report on Rj3- and Rj2Rj3-gene harboring cultivars in Myanmar. We evaluated Myanmar soybean cultivars for symbiotic effectiveness, relying on the standard strain Bradyrhizobium japonicum USDA110. In our first experiment, the soybean cultivar Yezin-11 (Rj4) showed the highest N fixing potential. Based on their potential for fixing N and nodulation, the top six soybean cultivars were Yezin-11 (Rj4), Yezin-9 (Rj3), Yezin-6 (non-Rj), Yezin-8 (non-Rj), Yezin-3 (Rj4) and Yezin-10 (Rj2Rj3). These cultivars were selected for a second experiment, which revealed that the N fixation, nodulation, and plant growth of Yezin-11 (Rj4) *Corresponding author. A. Z. Htwe et al. 2800 were superior to the other cultivars. We conclude that Yezin-11 (Rj4) is the most efficient cultivar for nodulation and N fixation when inoculated with B. japonicum USDA110.
