Featured Publications
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 sequencingSVScore: 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 ResearchMeSH KeywordsGene FrequencyGenomic Structural VariationGenomicsHumansPolymorphism, Single NucleotideSequence DeletionSoftwareCharacterizing 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
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 ResearchMeSH KeywordsAnimalsDatabases, FactualGene DeletionGenetics, PopulationGenomic Structural VariationGenomicsHumansHydraSequence AlignmentSoftwareConceptsNumber 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 toolsDiscoverySAMBLASTER: fast duplicate marking and structural variant read extraction
Faust GG, Hall IM. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics 2014, 30: 2503-2505. PMID: 24812344, PMCID: PMC4147885, DOI: 10.1093/bioinformatics/btu314.Peer-Reviewed Original Research