2019
Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
Zhou B, Ho S, Greer S, Zhu X, Bell J, Arthur J, Spies N, Zhang X, Byeon S, Pattni R, Ben-Efraim N, Haney M, Haraksingh R, Song G, Ji H, Perrin D, Wong W, Abyzov A, Urban A. Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562. Genome Research 2019, 29: 472-484. PMID: 30737237, PMCID: PMC6396411, DOI: 10.1101/gr.234948.118.Peer-Reviewed Original ResearchConceptsWhole-genome analysisStructural variantsFunctional genomicsEpigenomic dataAllele-specific DNA methylationComprehensive whole-genome analysisWhole-genome bisulfite sequencing dataGenomic structural featuresCopy numberLinked-read sequencingAllele-specific expressionEntire chromosome armsBisulfite sequencing dataAllele-specific deletionsComplex structural variantsTumor suppressor geneEpigenomic characteristicsChromosome armsGenome sequenceChromosome segmentsDNA methylationRNA-seqGenome characteristicsRetrotransposon insertionGenomic variant information
2015
An integrated map of structural variation in 2,504 human genomes
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills R, Gerstein M, Bashir A, Stegle O, Devine S, Lee C, Eichler E, Korbel J. An integrated map of structural variation in 2,504 human genomes. Nature 2015, 526: 75-81. PMID: 26432246, PMCID: PMC4617611, DOI: 10.1038/nature15394.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceGenetic Predisposition to DiseaseGenetic VariationGenetics, MedicalGenetics, PopulationGenome-Wide Association StudyGenome, HumanGenomicsGenotypeHaplotypesHomozygoteHumansMolecular Sequence DataMutation RatePhysical Chromosome MappingPolymorphism, Single NucleotideQuantitative Trait LociSequence Analysis, DNASequence DeletionConceptsStructural variantsHuman genomeExpression quantitative trait lociGenome-wide association studiesIndividual mutational eventsQuantitative trait lociComplex structural variantsHomozygous gene knockoutsDNA sequencing dataLoci subjectTrait lociHuman genesGene knockoutIntegrated mapSequencing dataAssociation studiesMutational eventsHaplotype blocksVariant classesFunctional impactPopulation stratificationGenomeNumerous diseasesHuman populationStructural variations