Featured Publications
Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms
Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Research 2013, 23: 762-776. PMID: 23410887, PMCID: PMC3638133, DOI: 10.1101/gr.143677.112.Peer-Reviewed Original ResearchConceptsComplex genomic rearrangementsSingle mutational eventCancer genomesMutational eventsBreakpoint clusterDNA double-strand breaksHomology-independent mechanismsComplex rearrangementsDouble-strand breaksLarge-scale rearrangementsGenome architectureGenome rearrangementsNonhomologous repairGenomic rearrangementsChromothripsis eventsSelective advantageMore chromosomesTumor genomesGenomeGlioblastoma samplesTemplated insertionsState profilingPunctuated changeBreakpoint sequencesAllele frequencies
2014
Population-based structural variation discovery with Hydra-Multi
Lindberg MR, Hall IM, Quinlan AR. Population-based structural variation discovery with Hydra-Multi. Bioinformatics 2014, 31: 1286-1289. PMID: 25527832, PMCID: PMC4393510, DOI: 10.1093/bioinformatics/btu771.Peer-Reviewed Original ResearchConceptsNumber of genomesSV analysisStructural variation discoveryStructural variant detectionHuman genomeCancer Genome AtlasVariation discoveryGenomic rearrangementsGenome ProjectSequence alignmentSignal integrationIndel discoveryGenome AtlasGenomeMultiple individualsSupplementary dataSize variabilityVariant detectionCommodity hardwarePoor scalabilityAvailable datasetsAnalysis workflowScalabilityExtant toolsDiscovery