Expression and differential expression analysis of breast cancer patient samples and normal samples

Expression and differential expression analysis of breast cancer patient samples and normal samples from breast reduction operations. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Breast tissue samples from breast reduction operations were provided from the Colosseum Clinic, Oslo in co-operation with Akershus University Hospital, Lørenskog and are referred to as normal tissue. Expression and differential expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850. We analyzed 5 to 6 arrays each for breast cancer patient samples and normal samples.

本数据集针对乳腺癌患者样本与乳房缩小手术获取的正常乳腺组织样本，开展表达与差异表达分析。1995年至1998年间，研究人员从多家医院纳入的奥斯陆微转移（MicMa）研究——奥斯陆队列I的920例早期乳腺癌患者中，获取了新鲜冷冻的肿瘤活检样本，相关研究细节参见Naume等发表于《Mol Oncol》2007年第1卷160-171页的《骨髓微转移的存在与乳腺癌分子亚型内不同复发风险相关》，以及Wiedswang等发表于《J Clin Oncol》2003年第21卷3469-3478页的《骨髓中孤立肿瘤细胞的检测是乳腺癌的独立预后因素》。乳房缩小手术获取的乳腺组织样本由奥斯陆Colosseum诊所与勒伦斯克的阿克什胡斯大学医院合作提供，作为本次研究的正常对照组织。本研究采用安捷伦（Agilent）定制微阵列（244K，nONCOchip）完成表达与差异表达分析。该定制芯片包含针对以下三类基因组区域的探针：(i) 全细胞周期进程中差异表达的区域；(ii) 响应抗增殖、促凋亡p53通路的区域；(iii) 响应抗凋亡、促增殖STAT-3通路的区域，该探针设计基于TAS技术，相关细节参见Kampa等发表于《Genome Research》2004年第14卷331-342页的《对人类21号和22号染色体转录组的深度分析中发现的新型RNA》。此外，这款安捷伦（Agilent）定制微阵列（244K）还覆盖了经RNAz（相关研究参见Washietl等发表于《Proc Natl Acad Sci USA》2005年第102卷2454-2459页的《非编码RNA的快速可靠预测》）或Evofold（相关研究参见Pedersen等发表于《PLoS Comput Biol》2006年第2卷e33的《人类基因组中保守RNA二级结构的鉴定与分类》）预测的含有保守二级结构的基因组区域探针，同时包含公共数据库中的已知非编码RNA探针以及安捷伦mRNA探针集014850。本研究分别为乳腺癌患者样本与正常样本各制备了5至6张阵列芯片。