Specimen Acquistition and Expression Profiling

髓系白血病患者临床标本的受控采集和处理， 骨髓增生异常综合征仍然是一个关键的活动，为准确，有效，全面 获取本计划项目所需的基因组数据。同样，一个质量控制和 标准化的肿瘤基因表达、基因拷贝数和对应于这些的基因分型数据 标本将继续有助于阐明AMI的基因组基础。程序改进和 在受管制的实验室环境中操作微阵列分析平台将进一步准备这一点。 该技术用于白血病患者的分子临床试验。因此，这 核心有两个具体目标： 具体目标1：我们将收集、储存和处理所有患者的组织标本， 在该机构看到的AML和MDS诊断。我们将包括来自骨骼的恶性细胞群 骨髓抽吸物和外周血以及皮肤穿刺活检和口腔灌洗标本 代表非恶性细胞群。将采集血清和血浆用于将来的蛋白质组学研究。 生物标记物研究。将在每例患者的整个病程中采集标本（初始 表现、缓解、复发），并且在适当情况下，将 被收回。将样本处理为细胞RNA、基因组DNA、全基因组扩增DNA， 和蛋白质提取物。细胞群也将被可行地冷冻以备将来使用。 异种移植研究。特别注意标本采集（例如，快速处理白血病细胞， 保存转录本概况）和质量控制。 具体目标二：利用Affychip平台，我们将产生全基因组 本研究期间收集的所有AML标本的表达、拷贝数和等位基因丢失数据， 根据国家认可的实验室准则。亲和素全基因组（U133Plus2）和外显子特异性 表达阵列将用于生成定量和定性转录谱， 全基因组基因分型（500K和1M SNP）阵列将用于同时产生生殖系 来自肿瘤和非恶性肿瘤的基因型数据、体细胞拷贝数变化数据和等位基因丢失（洛）数据 样本对。重点将放在开发快速周转的新方法上。

The controlled collection and processing of clinical specimens from patients with myeloid leukemia and myelodysplastic syndrome continues to be a critical activity for the accurate, efficient, and comprehensive acquisition of genomic data required for this program project. Similarly, a repository of quality controlled and standardized tumor gene expression, gene copy number, and genotyping data corresponding to these specimens will continue to aid in elucidating the genomic basis of AMI. Procedural enhancements and operation of microarray analytical platforms in a regulated laboratory environment will further prepare this technology for use in the context of molecular-based clinical trials for leukemia patients. Accordingly, this Core has two Specific Aims: Specific Aim 1: We will collect, store, and process tissue specimens from all patients with a diagnosis of AML and MDS seen at this institution. We will include malignant cell populations from bone marrow aspirates and peripheral blood as well as skin punch biopsy and buccal lavage specimens representing non-malignant cell populations. Serum and plasma will be collected for future proteomic biomarker studies. Specimens will be collected throughout each patient's disease course (initial presentation, remission, relapse) and where appropriate, archival specimens from previous malignancies will be retrieved. Specimens will be processed to cellular RNA, genomic DMA, whole genome amplified DNA, and protein extracts as required for each study. Cellular populations will also be viably frozen for future xenograft studies. Particular attention to specimen procurement (e.g. rapid processing of leukemia cells to preserve transcript profiles) and quality control will be practiced. Specific Aim 2: Using the Affymetrix GeneChip¿ platform, we will generate whole genome expression, copy number, and allelic loss data from all AML specimens collected during this study, under nationally accredited laboratory guidelines. Affymetrix whole genome (U133Plus2) and exonspecific expression arrays will be used to generate quantitative and qualitative transcriptional profiles while whole genome genotyping (500K and 1M SNP) arrays will be used to simultaneously generate germline genotype data, somatic copy number change data, and allelic loss (LOH) data from tumor and non-malignant sample pairs. Emphasis will be place on developing new methods for rapid turnaround.