Journal article
Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
J Schröder, A Hsu, SE Boyle, G Macintyre, M Cmero, RW Tothill, RW Johnstone, M Shackleton, AT Papenfuss
Bioinformatics | Published : 2014
Abstract
Motivation: Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital in cancer genomics. Available algorithms use one or more sources of evidence, such as read depth, paired-end reads or split reads to predict structural variants. However, the problem remains challenging due to the significant computational burden and high false-positive or false-negative rates.Results: In this article, we present Socrates (SOft Clip re-alignment To idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours that uses only split-read data. Socrates has single-nucleotide resolution, identifies micro-hom..
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Awarded by Victorian Cancer Agency
Funding Acknowledgements
This work was supported by a National Health and Medical Research Council (NHMRC) Project Grant (637357), Victorian State Government Operational Infrastructure Support, Australian Government NHMRC IRIISS, the Melbourne Melanoma Project, the Victorian Cancer Biobank and the Victorian Cancer Agency. S.B.was supported by a Cancer Council of Victoria scholarship. G.M.and M.C.were supported by NICTA. NICTA is funded by the Australian Government as represented by the Department of Broadband, Communications and the Digital Economy and the Australian Research Council through the ICT Centre of Excellence program. R.W.J.was supported by an NHMRC Principal Research Fellowship, as well as The Cancer Council Victoria, The Leukaemia Foundation of Australia and the Victorian Cancer Agency. M.S.was supported by fellowships from Pfizer Australia and VESKI. A.T.P.was supported by an NHMRC Career Development Fellowship (1003856) and The Lorenzo and Pamela Galli Melanoma Research Fellowship.