Please use this identifier to cite or link to this item: https://ahro.austin.org.au/austinjspui/handle/1/18219
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dc.contributor.authorCameron, Daniel L-
dc.contributor.authorSchröder, Jan-
dc.contributor.authorPenington, Jocelyn Sietsma-
dc.contributor.authorDo, Hongdo-
dc.contributor.authorMolania, Ramyar-
dc.contributor.authorDobrovic, Alexander-
dc.contributor.authorSpeed, Terence P-
dc.contributor.authorPapenfuss, Anthony T-
dc.date2017-11-02-
dc.date.accessioned2018-08-24T06:49:09Z-
dc.date.available2018-08-24T06:49:09Z-
dc.date.issued2017-12-
dc.identifier.citationGenome research 2017; 27(12): 2050-2060-
dc.identifier.urihttps://ahro.austin.org.au/austinjspui/handle/1/18219-
dc.description.abstractThe identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based 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 tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods while matching or exceeding their sensitivity. GRIDSS identifies nontemplate sequence insertions, microhomologies, and large imperfect homologies, estimates a quality score for each breakpoint, stratifies calls into high or low confidence, and supports multisample analysis.-
dc.language.isoeng-
dc.titleGRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.-
dc.typeJournal Article-
dc.identifier.journaltitleGenome research-
dc.identifier.affiliationBioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia-
dc.identifier.affiliationDepartment of Medical Biology, University of Melbourne, Parkville, Victoria, Australia-
dc.identifier.affiliationDepartment of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia-
dc.identifier.affiliationTranslational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia-
dc.identifier.affiliationDepartment of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia -
dc.identifier.affiliationDepartment of Pathology, University of Melbourne, Parkville, Victoria, 3010, Australia-
dc.identifier.affiliationSchool of Cancer Medicine, La Trobe University, Bundoora, Victoria, 3084, Australia-
dc.identifier.affiliationDepartment of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia-
dc.identifier.affiliationPeter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Melbourne, Australia-
dc.identifier.affiliationSir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia-
dc.identifier.doi10.1101/gr.222109.117-
dc.identifier.orcid0000-0002-0951-7116-
dc.identifier.orcid0000-0001-5270-0605-
dc.identifier.orcid0000-0003-1561-0074-
dc.identifier.orcid0000-0003-3414-112X-
dc.identifier.orcid0000-0002-5403-7998-
dc.identifier.orcid0000-0002-1102-8506-
dc.identifier.pubmedid29097403-
dc.type.austinEvaluation Studies-
dc.type.austinJournal Article-
dc.type.austinResearch Support, Non-U.S. Gov't-
local.name.researcherDobrovic, Alexander
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.cerifentitytypePublications-
item.fulltextNo Fulltext-
item.grantfulltextnone-
item.languageiso639-1en-
item.openairetypeJournal Article-
crisitem.author.deptOlivia Newton-John Cancer Research Institute-
crisitem.author.deptSurgery (University of Melbourne)-
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