Featured Publications
The Human Pangenome Project: a global resource to map genomic diversity
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison N, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D. The Human Pangenome Project: a global resource to map genomic diversity. Nature 2022, 604: 437-446. PMID: 35444317, PMCID: PMC9402379, DOI: 10.1038/s41586-022-04601-8.Peer-Reviewed Original ResearchConceptsHuman reference genomeReference genomeGenomic diversityGenomic variationHuman genomic variationGlobal genomic diversitySingle nucleotide variantsGene-disease associationsDiploid genomeGenetic resourcesGenomeGenomic researchFuture biomedical researchHigh-quality referenceStructural variantsHuman geneticsRoutine assemblyCommon variantsFunctional elementsPolymorphic regionDiversityBiomedical researchVariantsMajor updateGeneticsMapping 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 effectsGeneticsCharacterizing 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
2024
Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies
Shyr D, Dey R, Li X, Zhou H, Boerwinkle E, Buyske S, Daly M, Gibbs R, Hall I, Matise T, Reeves C, Stitziel N, Zody M, Neale B, Lin X. Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies. American Journal Of Human Genetics 2024, 111: 2129-2138. PMID: 39270648, PMCID: PMC11480788, DOI: 10.1016/j.ajhg.2024.08.018.Peer-Reviewed Original ResearchHardy-Weinberg equilibriumWhole-genome sequencing studiesWhole-genome sequencingHomogeneous ancestryWGS studiesDownstream analysisAssociation analysisPresence of population structureAncestry groupsGenetic ancestry groupsPopulation structureSequencing studiesSelf-reported raceGenetic researchQuality variantsAncestrySubsets of samplesProgram centersVariantsIncreasing diversityHeterogeneous sampleAncestralAssociationGeneticsSequence
2017
The impact of rare variation on gene expression across tissues
Aguet F, Ardlie K, Cummings B, Gelfand E, Getz G, Hadley K, Handsaker R, Huang K, Kashin S, Karczewski K, Lek M, Li X, MacArthur D, Nedzel J, Nguyen D, Noble M, Segrè A, Trowbridge C, Tukiainen T, Abell N, Balliu B, Barshir R, Basha O, Battle A, Bogu G, Brown A, Brown C, Castel S, Chen L, Chiang C, Conrad D, Cox N, Damani F, Davis J, Delaneau O, Dermitzakis E, Engelhardt B, Eskin E, Ferreira P, Frésard L, Gamazon E, Garrido-Martín D, Gewirtz A, Gliner G, Gloudemans M, Guigo R, Hall I, Han B, He Y, Hormozdiari F, Howald C, Kyung Im H, Jo B, Yong Kang E, Kim Y, Kim-Hellmuth S, Lappalainen T, Li G, Li X, Liu B, Mangul S, McCarthy M, McDowell I, Mohammadi P, Monlong J, Montgomery S, Muñoz-Aguirre M, Ndungu A, Nicolae D, Nobel A, Oliva M, Ongen H, Palowitch J, Panousis N, Papasaikas P, Park Y, Parsana P, Payne A, Peterson C, Quan J, Reverter F, Sabatti C, Saha A, Sammeth M, Scott A, Shabalin A, Sodaei R, Stephens M, Stranger B, Strober B, Sul J, Tsang E, Urbut S, van de Bunt M, Wang G, Wen X, Wright F, Xi H, Yeger-Lotem E, Zappala Z, Zaugg J, Zhou Y, Akey J, Bates D, Chan J, Chen L, Claussnitzer M, Demanelis K, Diegel M, Doherty J, Feinberg A, Fernando M, Halow J, Hansen K, Haugen E, Hickey P, Hou L, Jasmine F, Jian R, Jiang L, Johnson A, Kaul R, Kellis M, Kibriya M, Lee K, Billy Li J, Li Q, Li X, Lin J, Lin S, Linder S, Linke C, Liu Y, Maurano M, Molinie B, Montgomery S, Nelson J, Neri F, Oliva M, Park Y, Pierce B, Rinaldi N, Rizzardi L, Sandstrom R, Skol A, Smith K, Snyder M, Stamatoyannopoulos J, Stranger B, Tang H, Tsang E, Wang L, Wang M, Van Wittenberghe N, Wu F, Zhang R, Nierras C, Branton P, Carithers L, Guan P, Moore H, Rao A, Vaught J, Gould S, Lockart N, Martin C, Struewing J, Volpi S, Addington A, Koester S, Little A, Brigham L, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber W, Lonsdale J, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas J, Walters G, Washington M, Wheeler J, Bridge J, Foster B, Gillard B, Karasik E, Kumar R, Miklos M, Moser M, Jewell S, Montroy R, Rohrer D, Valley D, Davis D, Mash D, Undale A, Smith A, Tabor D, Roche N, McLean J, Vatanian N, Robinson K, Sobin L, Barcus M, Valentino K, Qi L, Hunter S, Hariharan P, Singh S, Um K, Matose T, Tomaszewski M, Barker L, Mosavel M, Siminoff L, Traino H, Flicek P, Juettemann T, Ruffier M, Sheppard D, Taylor K, Trevanion S, Zerbino D, Craft B, Goldman M, Haeussler M, Kent W, Lee C, Paten B, Rosenbloom K, Vivian J, Zhu J. The impact of rare variation on gene expression across tissues. Nature 2017, 550: 239-243. PMID: 29022581, PMCID: PMC5877409, DOI: 10.1038/nature24267.Peer-Reviewed Original Research