目的利用再测序芯片对北京市首例人禽流感病例进行病原筛查和验证。方法采集病例咽拭子和气管抽吸物标本,利用real-ti me RT-PCR进行禽流感病毒H5N1亚型核酸检测;应用病原体再测序芯片对其进行复核,并对其它呼吸道病原体和流感病毒其它...目的利用再测序芯片对北京市首例人禽流感病例进行病原筛查和验证。方法采集病例咽拭子和气管抽吸物标本,利用real-ti me RT-PCR进行禽流感病毒H5N1亚型核酸检测;应用病原体再测序芯片对其进行复核,并对其它呼吸道病原体和流感病毒其它亚型进行筛查。结果气管抽吸物标本经real-ti me RT-PCR检测为禽流感病毒H5N1核酸阳性;再测序芯片检测的结果是获得了H5N1的非结构蛋白基因(NS)特异序列,通过与GenBank进行序列比对,确定为禽流感病毒H5N1核酸,并排除了30种流感病毒亚型和其它33种呼吸道病原体的感染。结论病原体再测序芯片具有高灵敏性和特异性,在北京市首例人禽流感病例的病原学筛查和验证中发挥了重要作用。展开更多
Objective: Genetic as well as hormonal factors are known to influence the development and clinical course of endometriosis. We aimed to investigate the association among 10 single nucleotide polymorphisms (SNPs) invol...Objective: Genetic as well as hormonal factors are known to influence the development and clinical course of endometriosis. We aimed to investigate the association among 10 single nucleotide polymorphisms (SNPs) involved in the estrogen metabolism and endometriosis and to develop a multiple genetic model. METHODS: In a case-control study, we investigated the genotype frequencies of 10 estrogen metabolizing SNPs in 32 patients with endometriosis and 790 healthy controls using sequencing-on-chip-technology with solid-phase polymerase chain reaction on oligonucleotide microarrays: catechol-O-methy-ltransferase, Val158Met G->A, 17-β-hydroxysteroid dehydrogenase type 1 (HSD17), vIV A->C, cytochrome P450 (CYP), 17 A2 allele T->C, CYP1A1 Mspl RFLP T->C, CYP1A1 Ile462ValA->G, CYP19 Arg264-Cys C->T, CYP19 C1558T C->T, CYP 1B1 Leu432Val, CYP1B1 Asn453Ser, and estrogen receptor alpha. IVS1-401>C. Associations and 2-way interaction models between SNPs were calculated by stepwise logistic regression models. RESULTS: In a univariate model, HSD17 vIV A->C was associated with a significantly increased risk of endometriosis (P = .004; odds ratio 3.9, 95%confidence interval 1.6-9.8). When all 2-way interactions of investigated SNPs were ascertained, no significant interactions among SNPs were observed. In a multivariate model, HSD17 vIV A->C was also significantly associated with endometriosis (P = .002). CONCLUSION: We present data on multiple SNPs in patients with endometriosis indicating an association between HSD17 gene variation and the disease. Although not able to demonstrate interaction models of SNPs, we provide evidence of HSD17 vIV A->C as a low penetrance genetic marker of endometriosis.展开更多
[目的]本试验旨在利用基因芯片测序技术分析宿主miRNA在调控流感病毒感染小鼠肺组织过程中的作用。[方法]应用低致病性H_7N_9亚型A/Anhui/1/2013流感病毒及PBS感染BALB/c小鼠,感染后3 d取小鼠肺组织分别利用转录组测序技术和miRNA芯片...[目的]本试验旨在利用基因芯片测序技术分析宿主miRNA在调控流感病毒感染小鼠肺组织过程中的作用。[方法]应用低致病性H_7N_9亚型A/Anhui/1/2013流感病毒及PBS感染BALB/c小鼠,感染后3 d取小鼠肺组织分别利用转录组测序技术和miRNA芯片测序技术筛选差异表达mRNA和miRNA,并利用RT-qPCR验证差异miRNA。之后分别采用Targetscan、PITA及microRNAorg软件预测靶基因并结合转录组mRNA信息筛选候选miRNA的假定靶基因,最后利用Gene Ontology(GO)和Kyoto Encyclopedia of Gene and Genomes(KEGG)分析差异miRNA的生物学功能及其可能调控的信号通路。[结果]与PBS组相比,低致病性H_7N_9病毒感染组共筛选到265个差异表达miRNA,其中143个miRNA显著上调,122个miRNA显著下调。差异表达miRNA经RT-qPCR验证,10条候选miRNA的RT-qPCR结果与芯片结果有非常好的一致性。进一步KEGG分析表明,这些差异表达miRNA主要富集在Rap1、PI3K-Akt、Hippo、MAPK、Wnt、黏着斑、自噬等免疫相关信号通路中。结合差异mRNA信息进行miRNA-mRNA调控网络分析,显示主要有15条差异表达miRNA和31个差异靶基因富集到这些信号通路中。[结论]成功筛选到了低致病性H_7N_9感染小鼠肺组织后引起的差异表达miRNA,且RT-qPCR证明其与基因芯片测序结果表达趋势具有很好的一致性,为深入研究宿主miRNA在调控低致病性H_7N_9流感病毒与宿主相互作用的分子机制奠定了基础。展开更多
Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer (GA) platform.The protocol involves two-stage library construction.The specifi...Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer (GA) platform.The protocol involves two-stage library construction.The specificity of exome enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target region at an average sequencing depth of 33-fold.Comparison of our results with whole genome shot-gun resequencing results showed that the exome SNP calls gave only 0.97% false positive and 6.27% false negative variants.Our protocol is also well suited for use with whole genome amplified DNA.The results presented here indicate that there is a promising future for large-scale population genomics and medical studies using a whole exome sequencing approach.展开更多
文摘目的利用再测序芯片对北京市首例人禽流感病例进行病原筛查和验证。方法采集病例咽拭子和气管抽吸物标本,利用real-ti me RT-PCR进行禽流感病毒H5N1亚型核酸检测;应用病原体再测序芯片对其进行复核,并对其它呼吸道病原体和流感病毒其它亚型进行筛查。结果气管抽吸物标本经real-ti me RT-PCR检测为禽流感病毒H5N1核酸阳性;再测序芯片检测的结果是获得了H5N1的非结构蛋白基因(NS)特异序列,通过与GenBank进行序列比对,确定为禽流感病毒H5N1核酸,并排除了30种流感病毒亚型和其它33种呼吸道病原体的感染。结论病原体再测序芯片具有高灵敏性和特异性,在北京市首例人禽流感病例的病原学筛查和验证中发挥了重要作用。
文摘目的研究单核苷酸多态性(Single Nucleotide Polymorphism,SNP)微阵列和新一代基因捕获测序技术的联合应用对智力障碍或精神发育迟缓儿童的诊断价值。方法通过资料分析法选取2018年9月至2020年3月在南京医科大学附属儿童医院康复门诊接受治疗的智力障碍或精神发育迟缓儿童19名,年龄在6个月至14岁,男童11人和女童8人。分别采用发育诊断量表和韦氏儿童智力量表中国修订本(WISC-RC)对其进行智力评定,发育商低于49分或智商低于51分者纳入本次研究,进行全基因组拷贝数变异(Copy Number Variation,CNV)及致病基因变异分析,对检测的CNV采用定量PCR法进行先证者及父母验证,对明确或疑似致病性基因变异采用双脱氧法测序进行验证和家庭基因谱核查。结果研究表明19名入选者中有16名患儿的SNP微阵列分析结果为阴性,其中6例确认患有单一遗传疾病、7例阴性、3例存在可疑的基因病变(表现在11q24.1q25、21q22.2q22.3、12q22.1q23区域,其是诱发智力障碍和精神发育迟缓的主要病因)。结论SNP微阵列和新一代基因捕获测序技术的联合应用可显著提高不明原因的智力障碍或精神发育迟缓儿童的分子遗传病因诊断概率,通过寻根朔源方式也可为后续诊治方向提供可靠依据,具有重要的临床意义。
文摘Objective: Genetic as well as hormonal factors are known to influence the development and clinical course of endometriosis. We aimed to investigate the association among 10 single nucleotide polymorphisms (SNPs) involved in the estrogen metabolism and endometriosis and to develop a multiple genetic model. METHODS: In a case-control study, we investigated the genotype frequencies of 10 estrogen metabolizing SNPs in 32 patients with endometriosis and 790 healthy controls using sequencing-on-chip-technology with solid-phase polymerase chain reaction on oligonucleotide microarrays: catechol-O-methy-ltransferase, Val158Met G->A, 17-β-hydroxysteroid dehydrogenase type 1 (HSD17), vIV A->C, cytochrome P450 (CYP), 17 A2 allele T->C, CYP1A1 Mspl RFLP T->C, CYP1A1 Ile462ValA->G, CYP19 Arg264-Cys C->T, CYP19 C1558T C->T, CYP 1B1 Leu432Val, CYP1B1 Asn453Ser, and estrogen receptor alpha. IVS1-401>C. Associations and 2-way interaction models between SNPs were calculated by stepwise logistic regression models. RESULTS: In a univariate model, HSD17 vIV A->C was associated with a significantly increased risk of endometriosis (P = .004; odds ratio 3.9, 95%confidence interval 1.6-9.8). When all 2-way interactions of investigated SNPs were ascertained, no significant interactions among SNPs were observed. In a multivariate model, HSD17 vIV A->C was also significantly associated with endometriosis (P = .002). CONCLUSION: We present data on multiple SNPs in patients with endometriosis indicating an association between HSD17 gene variation and the disease. Although not able to demonstrate interaction models of SNPs, we provide evidence of HSD17 vIV A->C as a low penetrance genetic marker of endometriosis.
文摘[目的]本试验旨在利用基因芯片测序技术分析宿主miRNA在调控流感病毒感染小鼠肺组织过程中的作用。[方法]应用低致病性H_7N_9亚型A/Anhui/1/2013流感病毒及PBS感染BALB/c小鼠,感染后3 d取小鼠肺组织分别利用转录组测序技术和miRNA芯片测序技术筛选差异表达mRNA和miRNA,并利用RT-qPCR验证差异miRNA。之后分别采用Targetscan、PITA及microRNAorg软件预测靶基因并结合转录组mRNA信息筛选候选miRNA的假定靶基因,最后利用Gene Ontology(GO)和Kyoto Encyclopedia of Gene and Genomes(KEGG)分析差异miRNA的生物学功能及其可能调控的信号通路。[结果]与PBS组相比,低致病性H_7N_9病毒感染组共筛选到265个差异表达miRNA,其中143个miRNA显著上调,122个miRNA显著下调。差异表达miRNA经RT-qPCR验证,10条候选miRNA的RT-qPCR结果与芯片结果有非常好的一致性。进一步KEGG分析表明,这些差异表达miRNA主要富集在Rap1、PI3K-Akt、Hippo、MAPK、Wnt、黏着斑、自噬等免疫相关信号通路中。结合差异mRNA信息进行miRNA-mRNA调控网络分析,显示主要有15条差异表达miRNA和31个差异靶基因富集到这些信号通路中。[结论]成功筛选到了低致病性H_7N_9感染小鼠肺组织后引起的差异表达miRNA,且RT-qPCR证明其与基因芯片测序结果表达趋势具有很好的一致性,为深入研究宿主miRNA在调控低致病性H_7N_9流感病毒与宿主相互作用的分子机制奠定了基础。
基金supported by the Chinese Academy of Sciences (Grant Nos.GJHZ0701-6 and KSCX-YWN-023)the National Natural Science Foundation of China (Grant Nos.30725008,90403130,90608010,30221004,90612019 and 30392130)the National Basic Research Program of China (Grant Nos.2007CB815701,2007CB815703 and 2007CB815705)
文摘Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer (GA) platform.The protocol involves two-stage library construction.The specificity of exome enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target region at an average sequencing depth of 33-fold.Comparison of our results with whole genome shot-gun resequencing results showed that the exome SNP calls gave only 0.97% false positive and 6.27% false negative variants.Our protocol is also well suited for use with whole genome amplified DNA.The results presented here indicate that there is a promising future for large-scale population genomics and medical studies using a whole exome sequencing approach.
