High Definition Clonal Analyses of Archival Pancreatic Adenocarcinoma Samples

存档胰腺腺癌样本的高清克隆分析

• 批准号: 7778986
• 负责人: Michael T Barrett
• 金额: $ 25.73万
• 依托单位: TRANSLATIONAL GENOMICS RESEARCH INST
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-03-01 至 2013-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7778986
• 关键词: Adenocarcinoma Cell; Admixture; Aneuploid Cells; Aneuploidy; Biocompatible Materials; Biological Assay; Biopsy; Cell Fraction; Cell Line; Cells; Clinical; Clonal Evolution; Complex; Cytokeratin; DNA; Data; Detection; Development; Diagnostic; Diploid Cells; Diploidy; Flow Cytometry; Formalin; Freezing; Genome; Genomic Instability; Genomics; Growth; Heterogeneity; Human; Human Characteristics; Individual; Intervention; Lead; Lesion; Malignant Neoplasms; Malignant neoplasm of pancreas; Maps; Masks; Measures; Methods; Molecular; Neoplasms; Normal Cell; Oligonucleotides; Organ; Outcome; Pancreas; Pancreatic Adenocarcinoma; Pancreatic carcinoma; Paraffin Embedding; Pathway interactions; Patients; Pattern; Ploidies; Population; Preparation; Process; Protocols documentation; Resistance; Resolution; Resources; Sampling; Site; Solid; Sorting - Cell Movement; Specimen; System; Technology; Therapeutic; Tissues; Tumor Tissue; Validation; Work; anticancer research; aurora-A kinase; base; cancer genome; cancer therapy; follow-up; hypoxia inducible factor 1; improved; in vivo; interest; neoplastic; neoplastic cell; new therapeutic target; next generation; novel; research study; tumor; Adenocarcinoma Cell; Admixture; Aneuploid Cells; Aneuploidy; Biocompatible Materials; Biological Assay; Biopsy; Cell Fraction; Cell Line; Cells; Clinical; Clonal Evolution; Complex; Cytokeratin; DNA; Data; Detection; Development; Diagnostic; Diploid Cells; Diploidy; Flow Cytometry; Formalin; Freezing; Genome; Genomic Instability; Genomics; Growth; Heterogeneity; Human; Human Characteristics; Individual; Intervention; Lead; Lesion; Malignant Neoplasms; Malignant neoplasm of pancreas; Maps; Masks; Measures; Methods; Molecular; Neoplasms; Normal Cell; Oligonucleotides; Organ; Outcome; Pancreas; Pancreatic Adenocarcinoma; Pancreatic carcinoma; Paraffin Embedding; Pathway interactions; Patients; Pattern; Ploidies; Population; Preparation; Process; Protocols documentation; Resistance; Resolution; Resources; Sampling; Site; Solid; Sorting - Cell Movement; Specimen; System; Technology; Therapeutic; Tissues; Tumor Tissue; Validation; Work; anticancer research; aurora-A kinase; base; cancer genome; cancer therapy; follow-up; hypoxia inducible factor 1; improved; in vivo; interest; neoplastic; neoplastic cell; new therapeutic target; next generation; novel; research study; tumor

DESCRIPTION (provided by applicant): Genomic instability appears to cooperate with Darwinian selection to promote cancer formation through a process in which genomic aberrations occur at accelerated rates, and those alterations that provide a selective growth advantage lead to clonal evolution and expansion. Consequently the patterns of genomic aberrations in cancers can vary extensively, even in tumors arising in the same organ site. A fundamental hypothesis of current cancer genome efforts is that tumor cells become differentially resistant or sensitive to available clinical interventions according to selected aberrations present in each sample and the pathways that they target. Thus the identification of selected aberrations in patient samples will help develop novel therapeutic targets that can be advanced for improved more personalized approach to the treatment of cancer. Recent advances in genomic technologies provide highly detailed analyses of samples of interest. For example oligonucleotide CGH arrays can distinguish single copy changes across an entire genome at intragenic mapping resolution with probe error rates of <5%. A challenge in studying complex tissues is the presence of admixtures of cells and the polyclonal nature of human neoplasias. Furthermore, in addition to masking critical genomic aberrations, the presence of clonal mixtures of neoplastic cell populations in biopsies makes it prohibitively difficult to discern which genomic aberrations occur concurrently and to comprehensively define the genomic contexts of patient samples. Formalin fixed paraffin embedded (FFPE) tissues are a vast resource of clinically annotated samples with patient follow-up data including diagnostic and therapeutic outcomes. As such, these samples represent highly desirable and informative materials for the application of high definition genomics that could improve patient management and provide the molecular basis for the selection of personalized therapeutics. However a major limitation to the use of these samples for high resolution genomic analyses to date is the highly variable quality of the DNA extracted from samples of interest. Flow cytometry has been used to identify and isolate neoplastic clones from primary biopsies in a variety of tissues using objective quantifiable markers. Once identified individual populations can be flow purified to greater than 95% purity for subsequent molecular analyses. We have recently developed methods that adapt single parameter flow cytometry of fresh frozen samples to high definition clonal aCGH analyses of pancreatic cancer. The overall objective of this application is to extend these methods by developing and validating multiparameter flow cytometry assays that are compatible with high definition array CGH analyses and next generation sequencing of clinical samples. These will include diploid and aneuploid cell populations from formulin fixed paraffin embedded (FFPE) samples of pancreatic adenocarcinomas.

描述（由申请人提供）：基因组不稳定性似乎与达尔文主义的选择合作，通过以加速速率发生基因组畸变的过程来促进癌症形成，以及那些提供选择性增长优势的变化导致克隆进化和扩张。因此，即使在同一器官部位出现的肿瘤中，癌症中基因组畸变的模式也会有所不同。当前癌症基因组努力的基本假设是，根据每个样品中存在的某些畸变及其靶向途径，肿瘤细胞对可用的临床干预具有差异性或敏感。因此，鉴定患者样品中选定的畸变将有助于开发新型的治疗靶标，这些靶标可以改善癌症治疗的更多个性化方法。基因组技术的最新进展提供了对感兴趣样本的高度详细分析。例如，寡核苷酸CGH阵列可以以探测错误率<5％的概率分辨率区分整个基因组的单拷贝变化。研究复杂组织的一个挑战是细胞的混合物和人类肿瘤的多克隆性质。此外，除了掩盖了临界基因组畸变外，活检中肿瘤细胞种群的克隆混合物的存在使得非常难以识别哪些基因组畸变同时发生并全面定义患者样品的基因组环境。福尔马林固定的石蜡嵌入（FFPE）组织是临床注释样品的广泛资源，并具有患者的随访数据，包括诊断和治疗结果。因此，这些样品代表了高清晰基因组学的应用高度可取且信息丰富的材料，这些基因组学可以改善患者的管理并为选择个性化治疗剂的选择提供分子基础。但是，迄今为止，将这些样品用于高分辨率基因组分析的主要局限性是从感兴趣的样品中提取的DNA的高度可变质量。流式细胞仪已用于使用客观可量化标记来识别和分离各种组织中的肿瘤克隆。一旦确定的单个种群可以被纯化至大于95％的纯度，以进行随后的分子分析。我们最近开发了将新鲜冷冻样品的单个参数流式细胞仪调整为胰腺癌的克隆ACGH分析的方法。该应用的总体目的是通过开发和验证与高清阵列CGH分析和临床样本的下一代测序兼容的多参数流式细胞仪测定法来扩展这些方法。这些将包括胰岛固定石蜡（FFPE）胰腺腺癌样品的二倍体和非整倍型细胞群。