Journal article
Processed pseudogenes acquired somatically during cancer development
SL Cooke, A Shlien, J Marshall, CP Pipinikas, I Martincorena, JMC Tubio, Y Li, A Menzies, L Mudie, M Ramakrishna, L Yates, H Davies, N Bolli, GR Bignell, PS Tarpey, S Behjati, S Nik-Zainal, E Papaemmanuil, VH Teixeira, K Raine Show all
Nature Communications | Published : 2014
DOI: 10.1038/ncomms4644
Abstract
Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5a €2 truncation (74%) and polyA tails (88%). Transcriptional consequenc..
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Awarded by Kay Kendall Leukaemia Fund
Funding Acknowledgements
This work was supported by the Health Innovation Challenge Fund, the Wellcome Trust (grant reference 077012/Z/05/Z), and the Kay Kendall Leukaemia Fund. P. J. C. and S. M. J. are personally funded through Wellcome Trust Senior Clinical Research Fellowships. A. S. is funded by the H. L. Holmes Award from the National Research Council Canada and an EMBO fellowship. UAM is personally supported by a Cancer Research UK Clinician Scientist Fellowship. NB was supported by a starter grant from the Academy of Medical Sciences and from Lady Tata Memorial Trust. The breast cancer sequencing was supported by the BASIS project. The BASIS project is a European research project funded by the European Community's Seventh Framework Programme (FP7/2010-2014) under the grant agreement number 242006. This research was supported in part by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences. We also acknowledge support for the sample banking and processing from UCL/UCLH NIHR Biomedical Centre, the Skeletal Cancer Action Trust (SCAT), especially Miss Dina Halai, and the Rosetrees Trust.