2021
Comprehensive identification of somatic nucleotide variants in human brain tissue
Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino F, Moran J, Urban A, Kidd J, Mills R, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biology 2021, 22: 92. PMID: 33781308, PMCID: PMC8006362, DOI: 10.1186/s13059-021-02285-3.Peer-Reviewed Original ResearchConceptsSomatic SNVsSomatic single nucleotide variantsWhole-genome sequencing dataSequencing dataBulk DNA samplesCell lineage treesSomatic mosaicismSingle nucleotide variantsLineage treesSomatic nucleotide variantsCellular processesDNA replicationHuman genomeSomatic tissuesDNA repairNucleotide variantsComprehensive identificationDNA samplesMosaic variantsNon-cancerous tissuesDNASingle individualMultiple replicatesHuman brain tissueVariantsLandmarks of human embryonic development inscribed in somatic mutations
Bizzotto S, Dou Y, Ganz J, Doan R, Kwon M, Bohrson C, Kim S, Bae T, Abyzov A, Network† N, Park P, Walsh C. Landmarks of human embryonic development inscribed in somatic mutations. Science 2021, 371: 1249-1253. PMID: 33737485, PMCID: PMC8170505, DOI: 10.1126/science.abe1544.Peer-Reviewed Original ResearchConceptsSomatic single nucleotide variantsHuman embryonic developmentEmbryonic developmentEarly embryonic cell divisionsTransposase-accessible chromatin sequencingSingle cellsSingle-nucleus assayHigh-depth whole-genome sequencingSingle-nucleus RNA sequencingEmbryonic cell divisionCell lineage informationDistinct germ layersOnset of gastrulationSingle nucleotide variantsOrganismal developmentWhole-genome sequencingExtraembryonic tissuesCell divisionRNA sequencingProgenitor poolLineage informationGerm layersEarly progenitorsMultiple tissuesSequencing
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
Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors
Mitra A, Mukherjee U, Harding T, Jang J, Stessman H, Li Y, Abyzov A, Jen J, Kumar S, Rajkumar V, Van Ness B. Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors. Leukemia 2015, 30: 1094-1102. PMID: 26710886, DOI: 10.1038/leu.2015.361.Peer-Reviewed Original ResearchConceptsSingle cellsIndividual cellsSignificant genetic diversitySingle-cell analysisGene expression profile signaturesSingle-cell levelGenetic diversityTranscriptome analysisDrug responseCellular responsesDrug sensitivityBulk populationInhibitor sensitivitySubclonal architectureProfiling studiesPCR analysisPrediction programsCell linesMyeloma cell linesTumor progressionCellsIntratumor heterogeneityProfile signaturesProteasome inhibitor sensitivitySubclonal levelUnderstanding genome structural variations
Abyzov A, Li S, Gerstein MB. Understanding genome structural variations. Oncotarget 2015, 7: 7370-7371. PMID: 26657727, PMCID: PMC4884923, DOI: 10.18632/oncotarget.6485.Peer-Reviewed Original ResearchAn 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 variationsMetaSV: an accurate and integrative structural-variant caller for next generation sequencing
Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinformatics 2015, 31: 2741-2744. PMID: 25861968, PMCID: PMC4528635, DOI: 10.1093/bioinformatics/btv204.Peer-Reviewed Original ResearchMeSH KeywordsGenetic VariationHigh-Throughput Nucleotide SequencingMutagenesis, InsertionalSequence DeletionSoftwareConceptsCoverage information
2014
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications
Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics 2014, 31: 1469-1471. PMID: 25524895, PMCID: PMC4410653, DOI: 10.1093/bioinformatics/btu828.Peer-Reviewed Original ResearchMeSH KeywordsComputer SimulationGenetic VariationGenomicsHigh-Throughput Nucleotide SequencingHumansMutationNeoplasmsSequence AlignmentSoftwareConceptsMap data structureCompute frameworkGraphical reportsData structureParallel computationValidation frameworkRead alignmentSupplementary dataValidation toolReal dataHigh-fidelity simulationHigh-throughput genome sequencingDetailed statisticsFrameworkValidation resultsPythonInformationJavaSimulatorSupplementary informationComputationBioinformaticsRealistic modelCodeImplementation
2013
Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Consortium 1, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics. Science 2013, 342: 1235587. PMID: 24092746, PMCID: PMC3947637, DOI: 10.1126/science.1235587.Peer-Reviewed Original Research
2008
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. MSB: A mean-shift-based approach for the analysis of structural variation in the genome. Genome Research 2008, 19: 106-117. PMID: 19037015, PMCID: PMC2612956, DOI: 10.1101/gr.080069.108.Peer-Reviewed Original ResearchConceptsProbability density functionNumber of segmentsGood parameter initializationLikelihood functionArray CGH experimentsKernel-based approachUnderlying distributionModel parametersParameter initializationParticular assumptionsNonparametric methodsExpectation maximizationComputational methodsConvergenceGlobal criterionLocal gradients