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）基因组学和特定的挑战主题03-CA-101癌症早期检测和治疗指纹。 项目总结/摘要 染色体结构畸变包括易位、倒位、插入和缺失。这种改变可以直接破坏正常基因的结构，形成两个基因之间的融合基因。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被发现。许多染色体结构异常在肿瘤的发生发展中起着重要作用，并作为遗传标记广泛应用于临床诊断、治疗和预后判断。 虽然已经取得了很大的进展，但我们仍然远离全面了解癌症基因组中的结构畸变谱。在许多癌症中，遗传结构变化尚未确定。这些未知的基因突变可能具有特定的结构特征或影响较小的基因座，这些基因座可能难以使用常规技术进行识别。另一方面，对于已经确定的遗传结构畸变，仍然难以区分不是癌症原因而是肿瘤发生过程中的随机突变的“乘客”突变和直接有助于肿瘤发生的“驱动”突变。 mRNA是在给定条件下细胞中活性基因的功能读数。不相关的mRNA之间的融合转录本的存在可以提供直接的证据，在基因组中的基因组结构畸变的存在，并为它的功能参与肿瘤发生，这是关键的区分“驱动”突变从“乘客”突变。最近发展的RNA-Seq方法为检测融合转录本提供了有力的工具。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畸变提供了丰富的资源。 在本研究中，我们计划对急性髓性白血病（AML）的融合转录本及其染色体结构畸变进行系统分析。虽然在AML中已经确定了一致的染色体结构变化，但一半的AML病例不包含那些已知的染色体结构畸变。这些AML病例的临床结果与已知易位的AML病例不同，表明正常核型的AML可能含有不同的遗传畸变。在这项提案中，我们计划使用RNA-Seq方法从50个AML样本中获得全面的转录组。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，以定位其在疾病基因组中的原始结构畸变。 该研究的潜在影响将是提供AML中融合和遗传畸变的综合图谱，以识别AML中涉及的新候选基因，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AML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中的融合转录物进行全面检测，旨在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志物。

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.