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. 2018 Jan 4;46(D1):D1144-D1149.
doi: 10.1093/nar/gkx1018.

TumorFusions: an integrative resource for cancer-associated transcript fusions

Xin Hu  1   2 , Qianghu Wang  1   3 , Ming Tang  1 , Floris Barthel  4 , Samirkumar Amin  4 , Kosuke Yoshihara  5 , Frederick M Lang  1 , Emmanuel Martinez-Ledesma  6 , Soo Hyun Lee  1 , Siyuan Zheng  1   6 , Roel G W Verhaak  4
Affiliations

TumorFusions: an integrative resource for cancer-associated transcript fusions

Xin Hu et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1.
Figure 1.
The diagram of TumorFusions portal and its main features. The portal can be separated into three components, and the major features of each component are highlighted in rectangle. ‘Tissue’ in INPUT represents a TCGA cancer type.
Figure 2.
Figure 2.
Frequency of recurrent fusions across 33 cancer types. Y-axis represents percentage of cohort wherein the fusion is found. Only recurrent fusions are shown in the figure. The top frequent fusion in each cancer type is labeled and space permitting known cancer fusions are additionally shown.
Figure 3.
Figure 3.
Top frequent partner genes in recurrent fusion transcripts across 33 cancer types. Y-axis represents frequency of partner genes in the pan-cancer cohort.
See this image and copyright information in PMC

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