Featured Publications
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Ganel L, Chen L, Christ R, Vangipurapu J, Young E, Das I, Kanchi K, Larson D, Regier A, Abel H, Kang CJ, Scott A, Havulinna A, Chiang CWK, Service S, Freimer N, Palotie A, Ripatti S, Kuusisto J, Boehnke M, Laakso M, Locke A, Stitziel NO, Hall IM. Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences. Human Genomics 2021, 15: 34. PMID: 34099068, PMCID: PMC8185936, DOI: 10.1186/s40246-021-00335-2.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedApoptosis Regulatory ProteinsCell LineageDNA Copy Number VariationsDNA, MitochondrialExome SequencingFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyGenome, MitochondrialGTP-Binding ProteinsHumansMaleMembrane ProteinsMendelian Randomization AnalysisMiddle AgedPhenotypePolymorphism, Single NucleotideProto-Oncogene Proteins c-mybSequence Analysis, DNAConceptsCell type compositionGenome copy numberBlood-derived DNAMitochondrial genome copy numberCombination of genomesCopy numberBulk DNA sequencingDNA sequencingPolygenic risk scoresNumber of mitochondriaExome sequencing dataRelated traitsSequencing dataMetabolic traitsTraitsCommon variantsLociRare variantsSequencingDNAFinnish individualsMendelian randomization frameworkUK BiobankMetS traitsGenome
2023
Gaps and complex structurally variant loci in phased genome assemblies
Porubsky D, Vollger M, Harvey W, Rozanski A, Ebert P, Hickey G, Hasenfeld P, Sanders A, Stober C, Consortium H, Korbel J, Paten B, Marschall T, Eichler E, Abel H, Antonacci-Fulton L, Asri M, Baid G, Baker C, Belyaeva A, Billis K, Bourque G, Buonaiuto S, Carroll A, Chaisson M, Chang P, Chang X, Cheng H, Chu J, Cody S, Colonna V, Cook D, Cook-Deegan R, Cornejo O, Diekhans M, Doerr D, Ebert P, Ebler J, Eichler E, Eizenga J, Fairley S, Fedrigo O, Felsenfeld A, Feng X, Fischer C, Flicek P, Formenti G, Frankish A, Fulton R, Gao Y, Garg S, Garrison E, Garrison N, Giron C, Green R, Groza C, Guarracino A, Haggerty L, Hall I, Harvey W, Haukness M, Haussler D, Heumos S, Hickey G, Hoekzema K, Hourlier T, Howe K, Jain M, Jarvis E, Ji H, Kenny E, Koenig B, Kolesnikov A, Korbel J, Kordosky J, Koren S, Lee H, Lewis A, Li H, Liao W, Lu S, Lu T, Lucas J, Magalhães H, Marco-Sola S, Marijon P, Markello C, Marschall T, Martin F, McCartney A, McDaniel J, Miga K, Mitchell M, Monlong J, Mountcastle J, Munson K, Mwaniki M, Nattestad M, Novak A, Nurk S, Olsen H, Olson N, Paten B, Pesout T, Phillippy A, Popejoy A, Porubsky D, Prins P, Puiu D, Rautiainen M, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Sibbesen J, Sirén J, Smith M, Sofia H, Tayoun A, Thibaud-Nissen F, Tomlinson C, Tricomi F, Villani F, Vollger M, Wagner J, Walenz B, Wang T, Wood J, Zimin A, Zook J. Gaps and complex structurally variant loci in phased genome assemblies. Genome Research 2023, 33: 496-510. PMID: 37164484, PMCID: PMC10234299, DOI: 10.1101/gr.277334.122.Peer-Reviewed Original ResearchConceptsProtein-coding genesGenome assemblyMbp of DNALinked-read dataLarge segmental duplicationsStrand-seqDiversity panelInversion polymorphismHaploid genomeSegmental duplicationsEuchromatic DNAMore haplotypesIdentical repeatsHaploid assembliesVariant lociDNAHaplotypesGenesFrequent expansionAssembly gapsImportant targetAssemblyHuman speciesHuman samplesMBP