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GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number

View ORCID ProfileDaniel L. Cameron, Jonathan Baber, Charles Shale, View ORCID ProfileAnthony T. Papenfuss, Jose Espejo Valle-Inclan, Nicolle Besselink, View ORCID ProfileEdwin Cuppen, View ORCID ProfilePeter Priestley
doi: https://doi.org/10.1101/781013
Daniel L. Cameron
1Hartwig Medical Foundation Australia, Sydney, Australia
5Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
6Department of Medical Biology, University of Melbourne, Australia
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Jonathan Baber
1Hartwig Medical Foundation Australia, Sydney, Australia
2Hartwig Medical Foundation, Science Park 408, Amsterdam, The Netherlands
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Charles Shale
1Hartwig Medical Foundation Australia, Sydney, Australia
2Hartwig Medical Foundation, Science Park 408, Amsterdam, The Netherlands
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Anthony T. Papenfuss
5Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
6Department of Medical Biology, University of Melbourne, Australia
7Peter MacCallum Cancer Centre, Melbourne, Australia
8Sir Peter MacCallum Department of Oncology, University of Melbourne, Australia
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Jose Espejo Valle-Inclan
4Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
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Nicolle Besselink
3Center for Personalized Cancer Treatment, The Netherlands
4Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
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Edwin Cuppen
2Hartwig Medical Foundation, Science Park 408, Amsterdam, The Netherlands
3Center for Personalized Cancer Treatment, The Netherlands
4Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
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Peter Priestley
1Hartwig Medical Foundation Australia, Sydney, Australia
2Hartwig Medical Foundation, Science Park 408, Amsterdam, The Netherlands
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  • ORCID record for Peter Priestley
  • For correspondence: p.priestley@hartwigmedicalfoundation.nl
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Abstract

We have developed a novel, integrated and comprehensive purity, ploidy, structural variant and copy number somatic analysis toolkit for whole genome sequencing data of paired tumor/normal samples. We show that the combination of using GRIDSS for somatic structural variant calling and PURPLE for somatic copy number alteration calling allows highly sensitive, precise and consistent copy number and structural variant determination, as well as providing novel insights for short structural variants and regions of complex local topology. LINX, an interpretation tool, leverages the integrated structural variant and copy number calling to cluster individual structural variants into higher order events and chains them together to predict local derivative chromosome structure. LINX classifies and extensively annotates genomic rearrangements including simple and reciprocal breaks, LINE, viral and pseudogene insertions, and complex events such as chromothripsis. LINX also comprehensively calls genic fusions including chained fusions. Finally, our toolkit provides novel visualisation methods providing insight into complex genomic rearrangements.

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Posted September 25, 2019.
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GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number
Daniel L. Cameron, Jonathan Baber, Charles Shale, Anthony T. Papenfuss, Jose Espejo Valle-Inclan, Nicolle Besselink, Edwin Cuppen, Peter Priestley
bioRxiv 781013; doi: https://doi.org/10.1101/781013
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GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number
Daniel L. Cameron, Jonathan Baber, Charles Shale, Anthony T. Papenfuss, Jose Espejo Valle-Inclan, Nicolle Besselink, Edwin Cuppen, Peter Priestley
bioRxiv 781013; doi: https://doi.org/10.1101/781013

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