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
为了解新疆喀什地区鸽A群轮状病毒(group A rotavirus,RVA)的流行情况和遗传进化特征,使用实时荧光RT-PCR方法,对2024年从新疆喀什地区9个鸽场采集的165份鸽拭子样品进行RVA核酸检测,选取8份代表性阳性样品,针对RVA的2个中和基因VP7和VP...为了解新疆喀什地区鸽A群轮状病毒(group A rotavirus,RVA)的流行情况和遗传进化特征,使用实时荧光RT-PCR方法,对2024年从新疆喀什地区9个鸽场采集的165份鸽拭子样品进行RVA核酸检测,选取8份代表性阳性样品,针对RVA的2个中和基因VP7和VP4进行RT-PCR扩增及序列测定,并进行核苷酸同源性和遗传进化分析。结果显示:在165份鸽拭子样品中共检测出16份RVA阳性样品,个体阳性率为9.70%(16/165),阳性样品分布在8个鸽场;对代表性阳性样品进行VP7和VP4基因遗传进化分析发现,8份样品均属于G18P[17]基因型,其中VP7核苷酸同源性为85.2%~99.9%,与18株参考毒株的同源性为58.3%~98.7%,VP4核苷酸同源性为89.5%~99.7%,与18株参考毒株的同源性为52.8%~95.8%。阳性代表样品XJ-92、XJ-63、XJ-110、XJ-01均与美国鸽源毒株WVL21015-FL具有较高的亲缘性,推测可能来自同一次暴发或同一来源;XJ-71与其他阳性代表样品的亲缘性较远,同源性为89.5%~91.4%,与澳大利亚毒株VIC亲缘性最近,同源性为88.6%。结果表明:新疆喀什地区鸽群RVA感染严重,污染面较广,G18P[17]为优势流行基因型;新疆鸽群中流行的RVA属于同一进化分支或来自同一传染源,其在传播过程中可能发生了基因突变或基因组重配。建议持续强化RVA监测,加强养鸽场饲养管理,加快鸽RVA疫苗研发进程,以控制鸽RVA的流行与传播。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
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.
文摘为了解新疆喀什地区鸽A群轮状病毒(group A rotavirus,RVA)的流行情况和遗传进化特征,使用实时荧光RT-PCR方法,对2024年从新疆喀什地区9个鸽场采集的165份鸽拭子样品进行RVA核酸检测,选取8份代表性阳性样品,针对RVA的2个中和基因VP7和VP4进行RT-PCR扩增及序列测定,并进行核苷酸同源性和遗传进化分析。结果显示:在165份鸽拭子样品中共检测出16份RVA阳性样品,个体阳性率为9.70%(16/165),阳性样品分布在8个鸽场;对代表性阳性样品进行VP7和VP4基因遗传进化分析发现,8份样品均属于G18P[17]基因型,其中VP7核苷酸同源性为85.2%~99.9%,与18株参考毒株的同源性为58.3%~98.7%,VP4核苷酸同源性为89.5%~99.7%,与18株参考毒株的同源性为52.8%~95.8%。阳性代表样品XJ-92、XJ-63、XJ-110、XJ-01均与美国鸽源毒株WVL21015-FL具有较高的亲缘性,推测可能来自同一次暴发或同一来源;XJ-71与其他阳性代表样品的亲缘性较远,同源性为89.5%~91.4%,与澳大利亚毒株VIC亲缘性最近,同源性为88.6%。结果表明:新疆喀什地区鸽群RVA感染严重,污染面较广,G18P[17]为优势流行基因型;新疆鸽群中流行的RVA属于同一进化分支或来自同一传染源,其在传播过程中可能发生了基因突变或基因组重配。建议持续强化RVA监测,加强养鸽场饲养管理,加快鸽RVA疫苗研发进程,以控制鸽RVA的流行与传播。
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.
