文章：

全转录组霰弹枪测序方法在费城阳性急性淋巴细胞白血病研究中的应用

Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia

原文发布日期：2012-03-09

DOI: 10.1038/bcj.2012.6

类型: Original Article

开放获取: 是

英文摘要：

Although the pathogenesis of BCR–ABL1-positive acute lymphoblastic leukemia (ALL) is mainly related to the expression of the BCR–ABL1 fusion transcript, additional cooperating genetic lesions are supposed to be involved in its development and progression. Therefore, in an attempt to investigate the complex landscape of mutations, changes in expression profiles and alternative splicing (AS) events that can be observed in such disease, the leukemia transcriptome of a BCR–ABL1-positive ALL patient at diagnosis and at relapse was sequenced using a whole-transcriptome shotgun sequencing (RNA-Seq) approach. A total of 13.9 and 15.8 million sequence reads was generated from de novo and relapsed samples, respectively, and aligned to the human genome reference sequence. This led to the identification of five validated missense mutations in genes involved in metabolic processes (DPEP1, TMEM46), transport (MVP), cell cycle regulation (ABL1) and catalytic activity (CTSZ), two of which resulted in acquired relapse variants. In all, 6390 and 4671 putative AS events were also detected, as well as expression levels for 18 315 and 18 795 genes, 28% of which were differentially expressed in the two disease phases. These data demonstrate that RNA-Seq is a suitable approach for identifying a wide spectrum of genetic alterations potentially involved in ALL.

摘要翻译： 

尽管BCR–ABL1阳性急性淋巴细胞白血病（ALL）的发病机制主要与BCR–ABL1融合转录本的表达有关，但其发生和进展被认为还涉及其他协同遗传损伤。因此，为探究该疾病中可能存在的复杂突变景观、表达谱变化及可变剪接（AS）事件，研究人员采用全转录组鸟枪法测序（RNA-Seq）对一名BCR–ABL1阳性ALL患者初诊及复发期的白血病转录组进行了测序。初诊与复发样本分别产生1390万和1580万条序列读数，并与人基因组参考序列进行比对。通过分析鉴定出5个已验证的错义突变，涉及代谢过程（DPEP1、TMEM46）、运输（MVP）、细胞周期调控（ABL1）和催化活性（CTSZ）相关基因，其中两个突变表现为获得性复发变异。同时检测到6390个和4671个推定可变剪接事件，以及18315个和18795个基因的表达水平——其中28%的基因在两个疾病阶段存在差异表达。这些数据表明RNA-Seq是识别ALL潜在广泛遗传变异的有效方法。

原文链接：

Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia