Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Program in Bioinformatics and Biostatistics, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
Nucleic Acids Res. 2018 Jan 4;46(D1):D1144-D1149. doi: 10.1093/nar/gkx1018.
Gene fusion represents a class of molecular aberrations in cancer and has been exploited for therapeutic purposes. In this paper we describe TumorFusions, a data portal that catalogues 20 731 gene fusions detected in 9966 well characterized cancer samples and 648 normal specimens from The Cancer Genome Atlas (TCGA). The portal spans 33 cancer types in TCGA. Fusion transcripts were identified via a uniform pipeline, including filtering against a list of 3838 transcript fusions detected in a panel of 648 non-neoplastic samples. Fusions were mapped to somatic DNA rearrangements identified using whole genome sequencing data from 561 cancer samples as a means of validation. We observed that 65% of transcript fusions were associated with a chromosomal alteration, which is annotated in the portal. Other features of the portal include links to SNP array-based copy number levels and mutational patterns, exon and transcript level expressions of the partner genes, and a network-based centrality score for prioritizing functional fusions. Our portal aims to be a broadly applicable and user friendly resource for cancer gene annotation and is publicly available at http://www.tumorfusions.org.
基因融合代表了一类癌症中的分子异常，并被用于治疗目的。在本文中，我们描述了 TumorFusions，这是一个数据门户，它对来自癌症基因组图谱（TCGA）的 9966 个特征明确的癌症样本和 648 个正常样本中检测到的 20731 个基因融合进行了编目。该门户涵盖了 TCGA 中的 33 种癌症类型。融合转录本是通过一个统一的管道识别出来的，包括过滤掉在 648 个非肿瘤样本的面板中检测到的 3838 个转录融合列表。融合被映射到体细胞 DNA 重排，这些重排是使用来自 561 个癌症样本的全基因组测序数据确定的，作为验证方法。我们观察到，65%的转录融合与染色体改变有关，该门户对其进行了注释。该门户的其他功能包括与 SNP 芯片拷贝数水平和突变模式、伙伴基因的外显子和转录本水平表达的链接，以及基于网络的中心性评分，用于优先考虑功能融合。我们的门户旨在成为一个广泛适用且用户友好的癌症基因注释资源，并在 http://www.tumorfusions.org 上公开提供。
