• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>BMC Medical Genomics >Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL ? platform
【24h】

Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL ? platform

机译：使用DASL®上的癌症特异性基因组和全基因组基因组对福尔马林固定石蜡包埋的原发性乳腺肿瘤进行表达谱分析平台

获取原文
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Background The c D NA-mediated A nnealing, extension, S election and L igation (DASL) assay has become a suitable gene expression profiling system for degraded RNA from paraffin-embedded tissue. We examined assay characteristics and the performance of the DASL 502-gene Cancer Panelv1 (1.5K) and 24,526-gene panel (24K) platforms at differentiating nine human epidermal growth factor receptor 2- positive (HER2+) and 11 HER2-negative (HER2-) paraffin-embedded breast tumors. Methods Bland-Altman plots and Spearman correlations evaluated intra/inter-panel agreement of normalized expression values. Unequal-variance t -statistics tested for differences in expression levels between HER2 + and HER2 - tumors. Regulatory network analysis was performed using Metacore (GeneGo Inc., St. Joseph, MI). Results Technical replicate correlations ranged between 0.815-0.956 and 0.986-0.997 for the 1.5K and 24K panels, respectively. Inter-panel correlations of expression values for the common 498 genes across the two panels ranged between 0.485-0.573. Inter-panel correlations of expression values of 17 probes with base-pair sequence matches between the 1.5K and 24K panels ranged between 0.652-0.899. In both panels, erythroblastic leukemia viral oncogene homolog 2 ( ERBB2 ) was the most differentially expressed gene between the HER2 + and HER2 - tumors and seven additional genes had p-values |0.5| in expression between HER2 + and HER2 - tumors: topoisomerase II alpha ( TOP2A ), cyclin a2 ( CCNA2 ), v-fos fbj murine osteosarcoma viral oncogene homolog ( FOS ), wingless-type mmtv integration site family, member 5a ( WNT5A ), growth factor receptor-bound protein 7 ( GRB7 ), cell division cycle 2 ( CDC2 ), and baculoviral iap repeat-containing protein 5 ( BIRC5 ). The top 52 discriminating probes from the 24K panel are enriched with genes belonging to the regulatory networks centered around v-myc avian myelocytomatosis viral oncogene homolog ( MYC ), tumor protein p53 ( TP53 ), and estrogen receptor α ( ESR1 ). Network analysis with a two-step extension also showed that the eight discriminating genes common to the 1.5K and 24K panels are functionally linked together through MYC , TP53 , and ESR1 . Conclusions The relative RNA abundance obtained from two highly differing density gene panels are correlated with eight common genes differentiating HER2 + and HER2 - breast tumors. Network analyses demonstrated biological consistency between the 1.5K and 24K gene panels.
机译：背景技术c D NA介导的退火，延伸，S选择和连接（DASL）分析已成为从石蜡包埋的组织中降解的RNA的合适基因表达谱系统。我们检查了DASL 502基因癌症小组 v1 （1.5K）和24,526基因小组（24K）平台在区分9种人类表皮生长因子受体2阳性（HER2 +）时的测定特征和性能和11种HER2阴性（HER2-）石蜡包埋的乳腺肿瘤。方法使用Bland-Altman图和Spearman相关性评估标准化表达值的面板内/面板间一致性。测试了HER2 +和HER2-肿瘤之间表达水平差异的等方差t统计量。使用Metacore（GeneGo Inc.，St.Joseph，MI）进行监管网络分析。结果1.5K和24K面板的技术重复相关性分别在0.815-0.956和0.986-0.997之间。跨两个面板的常见498个基因的表达值在面板间的相关性介于0.485-0.573之间。 1.5K和24K面板之间碱基对序列匹配的17个探针的表达值与面板之间的相关性介于0.652-0.899之间。在两个组中，红细胞白血病病毒癌基因同源物2（ERBB2）是HER2 +和HER2-肿瘤之间表达最差的基因，另外七个基因的p值| 0.5 |。在HER2 +和HER2-肿瘤之间的表达中：拓扑异构酶IIα（TOP2A），细胞周期蛋白a2（CCNA2），v-fos fbj鼠骨肉瘤病毒癌基因同源物（FOS），无翼型mmtv整合位点家族，成员5a（WNT5A），生长因子受体结合蛋白7（GRB7），细胞分裂周期2（CDC2）和杆状病毒Iap重复蛋白5（BIRC5）。来自24K小组的前52个区分探针富含以v-myc禽骨髓细胞瘤病病毒癌基因同源物（MYC），肿瘤蛋白p53（TP53）和雌激素受体α（ESR1）为中心的调控网络基因。通过两步扩展的网络分析还显示，1.5K和24K面板共有的八个区分基因通过MYC，TP53和ESR1在功能上链接在一起。结论从两个高度不同的密度基因组获得的相对RNA丰度与区分HER2 +和HER2-乳腺肿瘤的八个常见基因相关。网络分析表明1.5K和24K基因组之间的生物学一致性。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号