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 ResearchMeSH KeywordsChromosome MappingChromosomes, HumanDiploidyGenetic VariationGenome, HumanGenomicsHaplotypesHigh-Throughput Nucleotide SequencingHumansReference StandardsSequence Analysis, DNAConceptsDiploid 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 genomesHigh-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
Byrska-Bishop M, Evani U, Zhao X, Basile A, Abel H, Regier A, Corvelo A, Clarke W, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E, Consortium H, Eichler E, Korbel J, Lee C, Marschall T, Devine S, Harvey W, Zhou W, Mills R, Rausch T, Kumar S, Alkan C, Hormozdiari F, Chong Z, Chen Y, Yang X, Lin J, Gerstein M, Kai Y, Zhu Q, Yilmaz F, Xiao C, Flicek P, Germer S, Brand H, Hall I, Talkowski M, Narzisi G, Zody M. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell 2022, 185: 3426-3440.e19. PMID: 36055201, PMCID: PMC9439720, DOI: 10.1016/j.cell.2022.08.004.Peer-Reviewed Original ResearchFemaleGenome, HumanHigh-Throughput Nucleotide SequencingHumansINDEL MutationMalePolymorphism, Single NucleotideWhole Genome Sequencing
2020
Mapping 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 effectsGenetics
2019
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 variantsGenetics
2015
SpeedSeq: ultra-fast personal genome analysis and interpretation
Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nature Methods 2015, 12: 966-968. PMID: 26258291, PMCID: PMC4589466, DOI: 10.1038/nmeth.3505.Peer-Reviewed Original ResearchGenetic VariationGenome, HumanHigh-Throughput Nucleotide SequencingHumansMolecular Sequence AnnotationNeoplasmsPolymorphism, Single NucleotidePrecision MedicineSoftwareWorkflow