Association of structural variation with cardiometabolic traits in Finns
Chen L, Abel HJ, Das I, Larson DE, Ganel L, Kanchi KL, Regier AA, Young EP, Kang CJ, Scott AJ, Chiang C, Wang X, Lu S, Christ R, Service SK, Chiang CWK, Havulinna AS, Kuusisto J, Boehnke M, Laakso M, Palotie A, Ripatti S, Freimer NB, Locke AE, Stitziel NO, Hall IM. Association of structural variation with cardiometabolic traits in Finns. American Journal Of Human Genetics 2021, 108: 583-596. PMID: 33798444, PMCID: PMC8059371, DOI: 10.1016/j.ajhg.2021.03.008.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCardiovascular DiseasesCholesterolDNA Copy Number VariationsFemaleFinlandGenome, HumanGenomic Structural VariationGenotypeHigh-Throughput Nucleotide SequencingHumansMaleMitochondrial ProteinsPromoter Regions, GeneticPyruvate Dehydrogenase (Lipoamide)-PhosphatasePyruvic AcidSerum Albumin, HumanConceptsSingle nucleotide variantsCopy number variantsQuantitative traitsGenome-wide significant associationStructural variationsTrait mapping studiesDeep whole-genome sequencing dataGenome structural variationsWhole-genome sequencing dataStrong phenotypic effectsComplex genomic regionsCardiometabolic traitsLow-frequency structural variationsEvolutionary timeGenomic regionsPhenotypic effectsSequencing dataNucleotide variantsGenotype dataGene deletionNumber variantsTraitsGenetic associationCandidate associationsExome sequencingMapping 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 effectsGeneticsSVScore: an impact prediction tool for structural variation
Ganel L, Abel HJ, , Hall IM. SVScore: an impact prediction tool for structural variation. Bioinformatics 2017, 33: 1083-1085. PMID: 28031184, PMCID: PMC5408916, DOI: 10.1093/bioinformatics/btw789.Peer-Reviewed Original ResearchCharacterizing 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 numberChromosomesGermlineGenome 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