Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads

Bioinformatics
Jan SchröderAnthony T Papenfuss

Abstract

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. 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. 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.

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Citations

Feb 3, 2016·Nature Communications·Chloé LescaleLudovic Deriano
Oct 9, 2015·Thrombosis and Haemostasis·Marisa L R CunhaSaskia Middeldorp
Apr 17, 2015·Briefings in Functional Genomics·Geòrgia EscaramísRaquel Rabionet
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Apr 18, 2019·Genome Research·Roven Rommel FuentesNickolai Alexandrov
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Aug 28, 2020·Frontiers in Genetics·Jinxin DongXiguo Yuan
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Jul 22, 2017·BMC Bioinformatics·Jan SchröderAnthony T Papenfuss
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Related Concepts

Malignant Neoplasms
Computer Programs and Programming
Sequence Determinations, DNA
Computational Molecular Biology
Genomics
High-Throughput Nucleotide Sequencing
Malignant Neoplasms
Gene Rearrangement
Genome
Neoplasms

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