The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Genome Res. 2010 Apr;20(4):413-27. doi: 10.1101/gr.103697.109. Epub 2010 Feb 23.
Global studies of transcript structure and abundance in cancer cells enable the systematic discovery of aberrations that contribute to carcinogenesis, including gene fusions, alternative splice isoforms, and somatic mutations. We developed a systematic approach to characterize the spectrum of cancer-associated mRNA alterations through integration of transcriptomic and structural genomic data, and we applied this approach to generate new insights into melanoma biology. Using paired-end massively parallel sequencing of cDNA (RNA-seq) together with analyses of high-resolution chromosomal copy number data, we identified 11 novel melanoma gene fusions produced by underlying genomic rearrangements, as well as 12 novel readthrough transcripts. We mapped these chimeric transcripts to base-pair resolution and traced them to their genomic origins using matched chromosomal copy number information. We also used these data to discover and validate base-pair mutations that accumulated in these melanomas, revealing a surprisingly high rate of somatic mutation and lending support to the notion that point mutations constitute the major driver of melanoma progression. Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types.
对癌细胞中转录结构和丰度的全球研究使系统发现导致癌变的异常成为可能，包括基因融合、选择性剪接异构体和体细胞突变。我们开发了一种系统方法，通过整合转录组学和结构基因组学数据来描述癌症相关 mRNA 改变的范围，并将其应用于生成黑色素瘤生物学的新见解。使用 cDNA 的配对末端大规模平行测序（RNA-seq）以及高分辨率染色体拷贝数数据的分析，我们鉴定了 11 种由潜在基因组重排产生的新型黑色素瘤基因融合，以及 12 种新型通读转录本。我们将这些嵌合转录本映射到碱基分辨率，并使用匹配的染色体拷贝数信息追踪它们到其基因组起源。我们还使用这些数据发现并验证了在这些黑色素瘤中积累的碱基对突变，揭示了非常高的体细胞突变率，并支持点突变构成黑色素瘤进展的主要驱动因素的观点。总的来说，这些结果可能为黑色素瘤的靶点发现指明新的途径，同时也为许多肿瘤类型的大规模转录组研究提供模板。
