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Pan-cancer study of heterogeneous RNA aberrations

Item Type:Preprint
Title:Pan-cancer study of heterogeneous RNA aberrations
Creators Name:Fonseca, N.A. and Kahles, A. and Lehmann, K.V. and Calabrese, C. and Chateigner, A. and Davidson, N.R. and Demircioglu, D. and He, Y. and Lamaze, F.C. and Li, S. and Liu, D. and Liu, F. and Perry, M.D. and Su, H. and Xiang, L. and Zhang, J. and Amin, S.B. and Bailey, P. and Craft, B. and Frenkel-Morgenstern, M. and Goldman, M. and Greger, L. and Hoadley, K.A. and Hou, Y. and Khurana, E. and Korbel, J.O. and Li, C. and Li, X. and Li, X. and Liu, X. and Lu, Y. and Marin, M.G. and Meyerson, M. and Nandi, T. and Nielsen, M.M. and Ojesina, A.I. and Ouellette, B.F.F. and Pan-Hammarstroem, Q. and Pedamallu, C.S. and Pedersen, J.S. and Shiraishi, Y. and Siebert, R. and Soulette, C.M. and Stark, S.G. and Tan, P. and Teh, B.T. and Valencia, A. and Wang, J. and Xing, R. and Xiong, H. and Yakneen, S. and Ye, C. and Yung, C. and Zhang, F. and Zhang, X. and Zheng, L. and Zhu, J. and Zhu, S. and Awadalla, P. and Creighton, C.J. and Goeke, J. and Schwarz, R.F. and Stegle, O. and Wu, K. and Yang, H. and Zhang, Z. and Brazma, A. and Raetsch, G. and Brooks, A.N.
Abstract:Pan-cancer studies have transformed our understanding of recurrent somatic mutations that contribute to cancer pathogenesis; however, there has yet to be a full investigation of the multiple mechanisms in which genes can be somatically altered, particularly at the transcriptome level. We present the most comprehensive catalogue of cancer-associated gene alterations through extensive characterization of tumor transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project with matched whole-genome sequence data. We processed the RNA-seq data with a unified analysis pipeline that included both sequence alignment and extensive quality control. Subsequently, we identified gene alterations through gene expression, alternative splicing, alternative transcription starts, allele-specific expression, RNA-edited sites, and gene fusions, and by comparing with RNA-Seq from a panel of normal tissue samples from the Genotype-Tissue Expression (GTEx) project. Our data represent an extensive pan-cancer catalog of RNA-level aberrations for each gene and will be the basis for further analyses within PCAWG. NOTE TO READERS: This is a draft of a marker paper from the PCAWG Transcriptome Working Group and is intended to describe technical aspects of RNA-Seq analysis associated with the PCAWG project. The full marker paper is currently in preparation.
Publisher:Cold Spring Harbor Laboratory Press
Article Number:183889
Date:3 September 2017
Official Publication:https://doi.org/10.1101/183889

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