Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform.
Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform.
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DOI：
10.1186/1755-8794-3-60
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发表时间：
2010-12-20
影响因子：
2.7
通讯作者：
Lingle WL
中科院分区：
文献类型：
--
作者：
Reinholz MM;Eckel-Passow JE;Anderson SK;Asmann YW;Zschunke MA;Oberg AL;McCullough AE;Dueck AC;Chen B;April CS;Wickham-Garcia E;Jenkins RB;Cunningham JM;Jen J;Perez EA;Fan JB;Lingle WL
基因表达谱分析已成为一种适合石蜡包埋组织中降解RNA的基因表达谱分析方法。我们检测了DASL 502基因的癌症面板1(1.5K)和24,526基因面板(24K)平台在区分9个人表皮生长因子受体2阳性(HER2+)和11个HER2阴性(HER2-)石蜡包埋乳腺肿瘤时的检测特征和性能。Bland-Altman图和Spearman相关性评估归一化表达值的小组内/小组间的一致性。非均方差t统计检验HER2+和HER2-肿瘤之间表达水平的差异。使用MetaCore(GeneGo Inc.，St.Joseph，MI)进行调控网络分析。1.5K和24K面板的技术重复相关系数分别在0.815-0.956和0.986-0.997之间。两组间共有的498个基因的表达值的组间相关性在0.485-0.573之间。17个探针的表达值与1.5K和24K面板之间的碱基对序列匹配的面板间相关性在0.652-0.899之间。在这两个研究小组中，红细胞白血病病毒癌基因同源2(ERBB2)是HER2+和HER2-肿瘤中表达差异最大的基因，另外7个基因有p值和log2倍变化。在HER2+和HER2-肿瘤之间的表达：拓扑异构酶IIα(TOP2A)、细胞周期蛋白A2(CcNA2)、v-fos fbj小鼠骨肉瘤病毒癌基因同源基因(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)和含杆状病毒IAP重复序列的蛋白5(BIRC5)。来自24K小组的前52个识别探针富含属于以v-myc禽骨髓细胞瘤病毒癌基因同源(Myc)、肿瘤蛋白p53(Tp53)和雌激素受体α(Esr1)为中心的调控网络的基因。两步延伸的网络分析还表明，1.5K和24K面板共有的8个区分基因通过MYC、TP53和ESR1在功能上连接在一起。从两个高度不同密度的基因板获得的相对RNA丰度与区分HER2+和HER2-乳腺肿瘤的八个常见基因相关。网络分析证明了1.5K和24K基因面板之间的生物学一致性。
The cDNA-mediated Annealing, extension, Selection and Ligation (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. 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). 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 < 0.05 and log2 -fold changes > |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. 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.
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影响因子：
3
作者：
Li Z;Su Z;Wen Z;Shi L;Chen T
通讯作者：
Chen T
影响因子：
11.2
作者：
Li, HR;Wang-Rodriguez, J;Fan, JB
通讯作者：
Fan, JB
影响因子：
5.8
作者：
Ballman, KV;Grill, DE;Therneau, TM
通讯作者：
Therneau, TM
影响因子：
4.4
作者：
Bibikova, Marina;Chudin, Eugene;Wang-Rodriguez, Jessica
通讯作者：
Wang-Rodriguez, Jessica
影响因子：
4.3
作者：
Huang, Erich S.;Black, Esther P.;Nevins, Joseph R.
通讯作者：
Nevins, Joseph R.