Featured Publications
Genomic Analysis in the Age of Human Genome Sequencing
Lappalainen T, Scott AJ, Brandt M, Hall IM. Genomic Analysis in the Age of Human Genome Sequencing. Cell 2019, 177: 70-84. PMID: 30901550, PMCID: PMC6532068, DOI: 10.1016/j.cell.2019.02.032.Peer-Reviewed Original ResearchMeSH KeywordsBiological Specimen BanksChromosome MappingGenetic Predisposition to DiseaseGenetic TestingGenetic VariationGenome, HumanGenome-Wide Association StudyGenomicsHigh-Throughput Nucleotide SequencingHuman Genome ProjectHumansPolymorphism, Single NucleotideSequence Analysis, DNAWhole Genome SequencingConceptsFunctional genomics approachAllele frequency spectrumHuman genome sequencingGene mapping studiesGenome sequencing technologiesRare human diseasesWhole-genome sequencingGenomic approachesGenetic variant discoveryGenome variationHuman genomeGenome analysisGenomic analysisSequencing technologiesGenome sequencingVariant discoveryHuman diseasesHuman geneticsGenomeFunctional interpretationMapping studiesFunctional effectsSequencingGermline variantsGeneticsThe impact of structural variation on human gene expression
Chiang C, Scott AJ, Davis JR, Tsang EK, Li X, Kim Y, Hadzic T, Damani FN, Ganel L, Montgomery S, Battle A, Conrad D, Hall I. The impact of structural variation on human gene expression. Nature Genetics 2017, 49: 692-699. PMID: 28369037, PMCID: PMC5406250, DOI: 10.1038/ng.3834.Peer-Reviewed Original ResearchRecurrent DNA copy number variation in the laboratory mouse
Egan CM, Sridhar S, Wigler M, Hall IM. Recurrent DNA copy number variation in the laboratory mouse. Nature Genetics 2007, 39: 1384-1389. PMID: 17965714, DOI: 10.1038/ng.2007.19.Peer-Reviewed Original ResearchConceptsCopy number variationsCopy numberNumber variationsGenome-wide analysisDNA copy number variationsRecent common ancestryGenerations of inbreedingRecurrent copy number variationsHigh-resolution microarraysCommon ancestryNatural variationGenetic differencesDifferent speciesDifferent lociGenerational timeLaboratory miceNonrandom processGenomeRecurrent mutationsLociAdditional strainsInbreedingLineagesGenesDiscrete segments
2022
Semi-automated assembly of high-quality diploid human reference genomes
Jarvis E, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger M, Porubsky D, Cheng H, Asri M, Logsdon G, Carnevali P, Chaisson M, Chin C, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton R, Fulton L, Garg S, Gerton J, Ghurye J, Granat A, Green R, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger E, Jain M, Kirsche M, Kolmogorov M, Korbel J, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell M, McDaniel J, Nie F, Olsen H, Olson N, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg S, Sanders A, Schatz M, Schmitt A, Schneider V, Selvaraj S, Shafin K, Shumate A, Stitziel N, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin A, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook J, Eichler E, Phillippy A, Paten B, Howe K, Miga K. Semi-automated assembly of high-quality diploid human reference genomes. Nature 2022, 611: 519-531. PMID: 36261518, PMCID: PMC9668749, DOI: 10.1038/s41586-022-05325-5.Peer-Reviewed Original ResearchConceptsDiploid genome assemblyGenome assemblyProtein-coding genesGlobal genetic variationCurrent human reference genomeDiploid human genomeHigh-quality assemblyAccurate long readsNon-synonymous amino acid changesHuman reference genomeAmino acid changesMost chromosomesReference assemblyReference genomeHuman genomeCentromeric regionsGenetic variationHigh diversityGenome sequencingLong readsSingle nucleotideGenomeAcid changesManual curationBiological genomes