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GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

Daniel L Cameron, Jan Schroeder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, View ORCID ProfileAlexander Dobrovic, View ORCID ProfileTerence P Speed, View ORCID ProfileAnthony T Papenfuss
doi: https://doi.org/10.1101/110387
Daniel L Cameron
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
2Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
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Jan Schroeder
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
2Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
3Department of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
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Jocelyn Sietsma Penington
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
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Hongdo Do
4Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, 3084, Australia
5Department of Pathology, University of Melbourne, Parkville, Victoria, 3010, Australia
6School of Cancer Medicine, La Trobe University, Bundoora, Victoria, 3084, Australia
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Ramyar Molania
4Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, 3084, Australia
7Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, 3084, Australia
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Alexander Dobrovic
4Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, 3084, Australia
5Department of Pathology, University of Melbourne, Parkville, Victoria, 3010, Australia
6School of Cancer Medicine, La Trobe University, Bundoora, Victoria, 3084, Australia
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  • ORCID record for Alexander Dobrovic
Terence P Speed
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
8Department of Mathematics and Statistics, University of Melbourne, VIC 3010, Australia
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Anthony T Papenfuss
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
2Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
8Department of Mathematics and Statistics, University of Melbourne, VIC 3010, Australia
9Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Melbourne, 3000, Australia
10Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, 3010, Australia
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  • ORCID record for Anthony T Papenfuss
  • For correspondence: papenfuss@wehi.edu.au
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ABSTRACT

The identification of genomic rearrangements, particularly in cancers, with high sensitivity and specificity using massively parallel sequencing remains a major challenge. Here, we describe the Genome Rearrangement IDentification Software Suite (GRIDSS), a high-speed structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph assembler. By combining assembly, split read and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line and patient tumour data, recently winning SV sub-challenge #5 of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods. GRIDSS identifies non-template sequence insertions, micro-homologies and large imperfect homologies, and supports multi-sample analysis. GRIDSS is freely available at https://github.com/PapenfussLab/gridss.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 21, 2017.
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GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
Daniel L Cameron, Jan Schroeder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence P Speed, Anthony T Papenfuss
bioRxiv 110387; doi: https://doi.org/10.1101/110387
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GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
Daniel L Cameron, Jan Schroeder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence P Speed, Anthony T Papenfuss
bioRxiv 110387; doi: https://doi.org/10.1101/110387

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