苏格拉底：通过重新比对软剪切读段来鉴定肿瘤基因组中的基因组重排。
Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.
作者信息
Schröder Jan, Hsu Arthur, Boyle Samantha E, Macintyre Geoff, Cmero Marek, Tothill Richard W, Johnstone Ricky W, Shackleton Mark, Papenfuss Anthony T
机构信息
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Department of Medical Biology, University of Melbourne, Victoria 3010, Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Department of Pathology, The University of Melbourne, Victoria 3010, NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, Department of Computing and Information Systems, University of Melbourne, Victoria 3010, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Department of Medical Biology, University of Melbourne, Victoria 3010, Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Department of Pathology, The University of Melbourne, Victoria 3010, NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, Department of Computing and Information Systems, University of Melbourne, Victoria 3010, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia.
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Department of Medical Biology, University of Melbourne, Victoria 3010, Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Department of Pathology, The University of Melbourne, Victoria 3010, NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, Department of Computing and Information Systems, University of Melbourne, Victoria 3010, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia.
出版信息
Bioinformatics. 2014 Apr 15;30(8):1064-1072. doi: 10.1093/bioinformatics/btt767. Epub 2014 Jan 2.
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-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. We demonstrate using simulated and real data that Socrates performs well compared with a number of existing structural variant detection tools.
AVAILABILITY AND IMPLEMENTATION
Socrates is released as open source and available from http://bioinf.wehi.edu.au/socrates CONTACT: papenfuss@wehi.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
动机
利用下一代测序检测肿瘤体细胞基因组重排的方法在癌症基因组学中至关重要。现有的算法使用一种或多种证据来源，如读深度、双端读段或分裂读段来预测结构变异。然而，由于巨大的计算负担以及高假阳性或假阴性率，该问题仍然具有挑战性。
结果
在本文中，我们提出了Socrates（用于识别结构变异的软剪切重比对），这是一种仅使用分裂读段数据来检测肿瘤基因组重排的高效且有效的方法。Socrates具有单核苷酸分辨率，可识别断点处的微同源性和非模板化序列，具有高灵敏度和高特异性，并利用并行性高效利用资源。我们使用模拟数据和真实数据证明，与许多现有的结构变异检测工具相比，Socrates表现良好。
可用性与实现
Socrates作为开源软件发布，可从http://bioinf.wehi.edu.au/socrates获取。联系方式：papenfuss@wehi.edu.au。补充信息：补充数据可在《生物信息学》在线获取。
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