2017
Landscape and variation of novel retroduplications in 26 human populations
Zhang Y, Li S, Abyzov A, Gerstein MB. Landscape and variation of novel retroduplications in 26 human populations. PLOS Computational Biology 2017, 13: e1005567. PMID: 28662076, PMCID: PMC5510864, DOI: 10.1371/journal.pcbi.1005567.Peer-Reviewed Original ResearchConceptsParent genesSequencing dataHigh-coverage exomesLow-coverage whole-genome sequencing dataHuman populationWhole-genome sequencing dataExon-exon junctionsGenomes Phase 3Young L1 elementsPaired-end readsPotential disease associationsRetrotranspositional activityGenomic elementsNucleosome positioningPhylogenetic treeRetroduplicationExome sequencing dataReference genomeGenomic featuresInsertion eventsL1 elementsComprehensive discoveryPopulation markersSNP callingFunctional regions
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, HumanGenome-Wide Association StudyGenomicsGenotypeHaplotypesHomozygoteHumansMolecular 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
2013
Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division
Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Consortium T, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Research 2013, 23: 2042-2052. PMID: 24026178, PMCID: PMC3847774, DOI: 10.1101/gr.154625.113.Peer-Reviewed Original ResearchConceptsCell divisionCorrect phylogenetic treeGenomes Project ConsortiumHuman populationTranscription of mRNARetroduplicationPhylogenetic treeParent genesGenomic integrationCell cycleG1 transitionMore copiesGenesRetrotranspositionHuman subpopulationsMultiple linesRetrogenesPseudogenesTranscriptionDivisionRNAVariantsProteinMRNACopies