Data from: Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression

The identification of gene fusions promises to play an important role in personalized cancer treatment decisions. Many rare gene fusion events have been identified in fresh frozen solid tumors from common cancers employing next-generation sequencing technology. However the ability to detect transcripts from gene fusions in RNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissues, which exist in very large sample repositories for which disease outcome is known, is still limited due to the low complexity of FFPE libraries and the lack of appropriate bioinformatics methods. We sought to develop a bioinformatics method, named gFuse, to detect fusion transcripts in FFPE tumor tissues. An integrated, cohort based strategy has been used in gFuse to examine single-end 50 base pair (bp) reads generated from FFPE RNA-Sequencing (RNA-Seq) datasets employing two breast cancer cohorts of 136 and 76 patients. In total, 118 fusion events were detected transcriptome-wide at base-pair resolution across the 212 samples. We selected 77 candidate fusions based on their biological relevance to cancer and supported 61% of these using TaqMan assays. Direct sequencing of 19 of the fusion sequences identified by TaqMan confirmed them. Three unique fused gene pairs were recurrent across the 212 patients with 6, 3, 2 individuals harboring these fusions respectively. We show here that a high frequency of fusion transcripts detected at the whole transcriptome level correlates with poor outcome (P<0.0005) in human breast cancer patients. This study demonstrates the ability to detect fusion transcripts as biomarkers from archival FFPE tissues, and the potential prognostic value of the fusion transcripts detected.基因融合的鉴定有望在癌症个性化治疗决策中发挥关键作用。借助下一代测序（next-generation sequencing）技术，研究人员已在常见癌症的新鲜冷冻实体瘤中发现了多种罕见基因融合事件。然而，福尔马林固定石蜡包埋（formalin-fixed paraffin-embedded, FFPE）肿瘤组织所提取的RNA，其制备的文库复杂度较低，且缺乏合适的生物信息学方法，导致对这类组织中基因融合转录本的检测能力仍十分有限——而这类组织拥有大量已知疾病转归的样本库。本研究旨在开发一款名为gFuse的生物信息学方法，用于检测FFPE肿瘤组织中的融合转录本。gFuse采用基于队列的整合分析策略，针对两个分别包含136名和76名乳腺癌患者的队列所产生的FFPE RNA测序（RNA-Sequencing, RNA-Seq）数据集生成的单端50碱基对（base pair, bp）读段进行分析。在全部212份样本中，我们以碱基分辨率在全转录组范围内共检测到118个融合事件。我们基于与癌症的生物学相关性筛选出77个候选融合基因，其中61%经TaqMan实验（TaqMan assays）验证。对19个经TaqMan鉴定出的融合序列进行直接测序，证实了这些融合的存在。在212名患者中，共有3组独特的融合基因对呈复现性，分别有6、3、2名患者携带这些融合。本研究表明，在人类乳腺癌患者中，全转录组水平检测到的融合转录本高频率与不良预后显著相关（P<0.0005）。本研究证实了从存档FFPE组织中检测作为生物标志物的融合转录本的可行性，以及所检测到的融合转录本的潜在预后价值。