SpeedSeq: ultra-fast personal genome analysis and interpretation
Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nature Methods 2015, 12: 966-968. PMID: 26258291, PMCID: PMC4589466, DOI: 10.1038/nmeth.3505.Peer-Reviewed Original ResearchLUMPY: a probabilistic framework for structural variant discovery
Layer RM, Chiang C, Quinlan AR, Hall IM. LUMPY: a probabilistic framework for structural variant discovery. Genome Biology 2014, 15: r84. PMID: 24970577, PMCID: PMC4197822, DOI: 10.1186/gb-2014-15-6-r84.Peer-Reviewed Original ResearchBreakpoint 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 frequenciesCharacterizing complex structural variation in germline and somatic genomes
Quinlan AR, Hall IM. Characterizing complex structural variation in germline and somatic genomes. Trends In Genetics 2011, 28: 43-53. PMID: 22094265, PMCID: PMC3249479, DOI: 10.1016/j.tig.2011.10.002.Peer-Reviewed Original ResearchConceptsComplex structural variationsStructural variationsNext-generation DNA sequencingHallmarks of cancerSomatic genomeGenetic diversityMultiple chromosomesSingle locusDistinct lociRecombination eventsComplex variantsSingle mutationMapping experimentsDNA sequencingComplicated rearrangementsMammalsCurrent knowledgeMapping studiesLociSubtle alterationsVariantsGenomeSurprising numberChromosomesGermline