Comprehensive identification of fusion transcripts in leukemia

描述(由申请人提供)：本申请涉及广泛的挑战领域(08)基因组学，以及针对癌症早期发现和治疗的特定挑战主题03-CA-101指纹。 项目摘要/摘要 染色体结构异常包括易位、倒位、插入和缺失。这种变化可能会直接破坏正常基因的结构，并在两个基因之间形成融合基因。这种变化在白血病中得到了很好的证明，在实体瘤中也越来越多地表现出来。许多染色体结构异常已被证明在肿瘤发生中起重要作用，并作为遗传标记广泛应用于临床诊断、治疗和预后。 虽然已经取得了很大的进展，但我们距离全面了解癌症基因组中的结构畸变谱还很远。在许多癌症中，尚未发现基因结构变化。这些未知的基因突变可能具有特定的结构特征，或者影响较小的基因座，而这些基因座可能很难用传统技术识别。另一方面，对于已经识别的基因结构异常，仍然很难区分不是癌症原因的、但在肿瘤发生过程中随机发生的“乘客”突变，以及直接导致肿瘤发生的“驱动因素”突变。 信使核糖核酸是细胞内活性基因在一定条件下的功能读数。不相关的mRNA之间融合转录本的存在可能为基因组中存在基因组结构异常及其参与肿瘤发生的功能提供直接证据，这是区分驱动突变和乘客突变的关键。最近发展起来的RNA-Seq方法为检测融合转录本提供了一个强有力的工具。它只需要简单的样品制备，可以从下一代DNA测序仪中以低成本收集大量的短cDNA序列。大量的序列为全面鉴定融合转录本及其原始基因组异常提供了丰富的资源。 在这个方案中，我们计划对AML(急性髓系白血病)的融合转录本及其染色体结构异常进行系统分析，AML是一种主要的白血病类型。尽管在AML中发现了一致的染色体结构变化，但有一半的AML病例不包含那些已知的染色体结构异常。这些AML患者的临床结局与已知易位的患者不同，提示正常核型AML可能包含不同的遗传异常。在这个方案中，我们计划使用RNA-Seq方法从50个AML样本中获得一个全面的转录组。我们计划进行广泛的信息学分析，以确定融合转录本和其他变化，以便定位它们在疾病基因组中的原始结构异常。 这项研究的潜在影响将是提供急性髓细胞白血病融合和遗传异常的全面图谱，识别与急性髓细胞白血病有关的新的候选基因，为识别“驱动”突变提供新的候选基因，并为癌症亚型分类和更好地诊断、治疗和预后提供新的遗传标记。 公共卫生相关性：该提案计划对急性髓系白血病的融合转录本进行全面检测，目的是识别导致这种疾病的新基因，并为这种疾病的临床诊断、治疗和预后确定新的标记物。

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (08) Genomics, and Specific Challenge Topic 03-CA-101 Fingerprints for the Early Detection and Treatment of Cancer. Project Summary /Abstract Chromosomal structural aberration includes translocation, inversion, insertion, and deletion. Such changes could directly disrupt the structure of normal genes and form fusion genes between two genes. Such changes have been well demonstrated in leukemia and increasingly revealed in solid tumors as well. Many chromosomal structural aberrations have been demonstrated to play important roles in tumorogenesis, and used widely as genetic markers in clinical applications including diagnosis, treatment and prognosis. Although great progress has been made, we are still far away from comprehensive understanding of the spectrum of structural aberrations in a cancer genome. In many cancers, genetic structural changes have not been identified. Those unknown genetic mutations could have specific structural features or affect smaller loci that may be difficult to identify using the conventional techniques. On the other hand, for the genetic structural aberrations already identified, it is still difficult to distinguish between the "passenger" mutations that are not the causes of the cancer but random mutations following the process of tumorogenesis, and the "driver" mutations that directly contribute to tumorogenesis. mRNA is the functional readouts of the active genes in the cell under a given condition. The presence of fusion transcripts between unrelated mRNAs may provide direct evidence for the presence of the genomic structural aberration in the genome, and for its functional involvement in tumorogenosis, which is critical in distinguishing the "driver" mutation from the "passenger" mutation. The recently developed RNA-Seq method provides a powerful tool for detecting the fusion transcripts. It only needs simple sample preparation and can collect massive short cDNA sequences from the next-generation DNA sequencers at low cost. The large quantity of sequences provides rich resources for comprehensive identification of fusion transcripts and their original genomic aberrations. In this proposal, we plan to perform a systematic analysis for the fusion transcripts and their chromosomal structural aberrations in AML (acute myeloid leukemia), a major type of leukemia. Although consistent chromosomal structural changes have been identified in AML, half of AML cases do not contain those known chromosomal structural aberrations. The clinical outcomes of these AML cases differ from those with known translocations, suggesting that the normal karyotype AML may contain different genetic aberrations. In this proposal, we plan to use the RNA-Seq method to obtain a comprehensive transcriptome from 50 AML samples. We plan to perform extensive informatics analysis to identify the fusion transcripts and other changes in order to locating their original structural aberrations in the disease genome. The potential impact of the study will be to provide a comprehensive map of fusion and genetic aberrations in AML, to identify new candidate genes involved in AML, to provide new candidate genes for identifying the "driver" mutations, and to provide new genetic markers for cancer subtype classification and for better diagnosis, treatment and prognosis of AML PUBLIC HEALTH RELEVANCE: The proposal plans to perform a comprehensive detection of fusion transcripts in acute myeloid leukemia, with the aims to identify new genes contributing to this disease and to identify new markers for clinical diagnosis, treatment and prognosis of this disease.