Mapping and characterization of structural variation in 17,795 human genomes
Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S, Matise T, Muzny D, Zody M, Lander E, Dutcher S, Stitziel N, Hall I. Mapping and characterization of structural variation in 17,795 human genomes. Nature 2020, 583: 83-89. PMID: 32460305, PMCID: PMC7547914, DOI: 10.1038/s41586-020-2371-0.Peer-Reviewed Original ResearchConceptsStructural variantsWhole-genome sequencingHuman genomeUltra-rare structural variantsRare structural variantsSuch structural variantsSingle nucleotide variantsNoncoding elementsDosage sensitivityGenomeHuman geneticsSmall insertionsComplex rearrangementsDeletion variantsSmall variantsStructural variationsGenesSequencingAllelesForm of variationVariantsElement classesSite frequency dataDeleterious effectsGeneticsBreakpoint 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 frequenciesGenome Sequencing of Mouse Induced Pluripotent Stem Cells Reveals Retroelement Stability and Infrequent DNA Rearrangement during Reprogramming
Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM. Genome Sequencing of Mouse Induced Pluripotent Stem Cells Reveals Retroelement Stability and Infrequent DNA Rearrangement during Reprogramming. Cell Stem Cell 2011, 9: 366-373. PMID: 21982236, PMCID: PMC3975295, DOI: 10.1016/j.stem.2011.07.018.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell LineageCellular ReprogrammingChimeraDNA Copy Number VariationsFalse Negative ReactionsGene RearrangementGene SilencingGenomeGenomic InstabilityHumansInduced Pluripotent Stem CellsMiceMolecular Sequence DataMutagenesis, InsertionalOrgan SpecificityRetroelementsSequence Analysis, DNAConceptsPluripotent stem cellsClasses of SVsPaired-end DNA sequencingStem cellsGenomic structural variationMouse Induced Pluripotent Stem CellsStructural variationsDNA copy number variationsEmbryonic stem cellsMost iPSC linesMouse iPSC linesIPSC linesInduced pluripotent stem cellsCopy number variationsGenome stabilityGene-disrupting mutationsRecent microarray studiesDNA rearrangementsGenome sequencingSpontaneous mutationsMicroarray studiesDeleterious genetic mutationsNumber variationsDNA sequencingComplex rearrangements