Featured Publications
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen J, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2020, 578: 102-111. PMID: 32025015, PMCID: PMC7054214, DOI: 10.1038/s41586-020-1965-x.Peer-Reviewed Original ResearchConceptsInternational Cancer Genome ConsortiumStructural variantsPoint mutationsDriver discoveryProtein-coding genesNon-coding genesNon-coding regionsPan-cancer analysisDriver point mutationsSomatic driversCancer Genome AtlasRegulatory sequencesCancer genomesUntranslated regionGenome ConsortiumFocal deletionsGenesGenome AtlasGenomeNovel candidatesMutationsRecurrent breakpointsRegion of TP53DiscoveryVariantsSystematic analysis of telomere length and somatic alterations in 31 cancer types
Barthel F, Wei W, Tang M, Martinez-Ledesma E, Hu X, Amin S, Akdemir K, Seth S, Song X, Wang Q, Lichtenberg T, Hu J, Zhang J, Zheng S, Verhaak R. Systematic analysis of telomere length and somatic alterations in 31 cancer types. Nature Genetics 2017, 49: 349-357. PMID: 28135248, PMCID: PMC5571729, DOI: 10.1038/ng.3781.Peer-Reviewed Original ResearchThe Cancer Genome Atlas Pan-Cancer analysis project
Chang K, Creighton C, Davis C, Donehower L, Drummond J, Wheeler D, Ally A, Balasundaram M, Birol I, Butterfield Y, Chu A, Chuah E, Chun H, Dhalla N, Guin R, Hirst M, Hirst C, Holt R, Jones S, Lee D, Li H, Marra M, Mayo M, Moore R, Mungall A, Robertson A, Schein J, Sipahimalani P, Tam A, Thiessen N, Varhol R, Beroukhim R, Bhatt A, Brooks A, Cherniack A, Freeman S, Gabriel S, Helman E, Jung J, Meyerson M, Ojesina A, Pedamallu C, Saksena G, Schumacher S, Tabak B, Zack T, Lander E, Bristow C, Hadjipanayis A, Haseley P, Kucherlapati R, Lee S, Lee E, Luquette L, Mahadeshwar H, Pantazi A, Parfenov M, Park P, Protopopov A, Ren X, Santoso N, Seidman J, Seth S, Song X, Tang J, Xi R, Xu A, Yang L, Zeng D, Auman J, Balu S, Buda E, Fan C, Hoadley K, Jones C, Meng S, Mieczkowski P, Parker J, Perou C, Roach J, Shi Y, Silva G, Tan D, Veluvolu U, Waring S, Wilkerson M, Wu J, Zhao W, Bodenheimer T, Hayes D, Hoyle A, Jeffreys S, Mose L, Simons J, Soloway M, Baylin S, Berman B, Bootwalla M, Danilova L, Herman J, Hinoue T, Laird P, Rhie S, Shen H, Triche T, Weisenberger D, Carter S, Cibulskis K, Chin L, Zhang J, Getz G, Sougnez C, Wang M, Saksena G, Carter S, Cibulskis K, Chin L, Zhang J, Getz G, Dinh H, Doddapaneni H, Gibbs R, Gunaratne P, Han Y, Kalra D, Kovar C, Lewis L, Morgan M, Morton D, Muzny D, Reid J, Xi L, Cho J, DiCara D, Frazer S, Gehlenborg N, Heiman D, Kim J, Lawrence M, Lin P, Liu Y, Noble M, Stojanov P, Voet D, Zhang H, Zou L, Stewart C, Bernard B, Bressler R, Eakin A, Iype L, Knijnenburg T, Kramer R, Kreisberg R, Leinonen K, Lin J, Liu Y, Miller M, Reynolds S, Rovira H, Shmulevich I, Thorsson V, Yang D, Zhang W, Amin S, Wu C, Wu C, Akbani R, Aldape K, Baggerly K, Broom B, Casasent T, Cleland J, Creighton C, Dodda D, Edgerton M, Han L, Herbrich S, Ju Z, Kim H, Lerner S, Li J, Liang H, Liu W, Lorenzi P, Lu Y, Melott J, Mills G, Nguyen L, Su X, Verhaak R, Wang W, Weinstein J, Wong A, Yang Y, Yao J, Yao R, Yoshihara K, Yuan Y, Yung A, Zhang N, Zheng S, Ryan M, Kane D, Aksoy B, Ciriello G, Dresdner G, Gao J, Gross B, Jacobsen A, Kahles A, Ladanyi M, Lee W, Lehmann K, Miller M, Ramirez R, Rätsch G, Reva B, Sander C, Schultz N, Senbabaoglu Y, Shen R, Sinha R, Sumer S, Sun Y, Taylor B, Weinhold N, Fei S, Spellman P, Benz C, Carlin D, Cline M, Craft B, Ellrott K, Goldman M, Haussler D, Ma S, Ng S, Paull E, Radenbaugh A, Salama S, Sokolov A, Stuart J, Swatloski T, Uzunangelov V, Waltman P, Yau C, Zhu J, Hamilton S, Getz G, Sougnez C, Abbott S, Abbott R, Dees N, Delehaunty K, Ding L, Dooling D, Eldred J, Fronick C, Fulton R, Fulton L, Kalicki-Veizer J, Kanchi K, Kandoth C, Koboldt D, Larson D, Ley T, Lin L, Lu C, Magrini V, Mardis E, McLellan M, McMichael J, Miller C, O'Laughlin M, Pohl C, Schmidt H, Smith S, Walker J, Wallis J, Wendl M, Wilson R, Wylie T, Zhang Q, Burton R, Jensen M, Kahn A, Pihl T, Pot D, Wan Y, Levine D, Black A, Bowen J, Frick J, Gastier-Foster J, Harper H, Helsel C, Leraas K, Lichtenberg T, McAllister C, Ramirez N, Sharpe S, Wise L, Zmuda E, Chanock S, Davidsen T, Demchok J, Eley G, Felau I, Ozenberger B, Sheth M, Sofia H, Staudt L, Tarnuzzer R, Wang Z, Yang L, Zhang J, Omberg L, Margolin A, Raphael B, Vandin F, Wu H, Leiserson M, Benz S, Vaske C, Noushmehr H, Knijnenburg T, Wolf D, Veer L, Collisson E, Anastassiou D, Yang T, Lopez-Bigas N, Gonzalez-Perez A, Tamborero D, Xia Z, Li W, Cho D, Przytycka T, Hamilton M, McGuire S, Nelander S, Johansson P, Jörnsten R, Kling T, Sanchez J. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics 2013, 45: 1113-1120. PMID: 24071849, PMCID: PMC3919969, DOI: 10.1038/ng.2764.Peer-Reviewed Original Research
2022
Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer
Yi E, Gujar A, Guthrie M, Kim H, Zhao D, Johnson K, Amin S, Costa M, Yu Q, Das S, Jillette N, Clow P, Cheng A, Verhaak R. Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer. Cancer Discovery 2022, 12: 468-483. PMID: 34819316, PMCID: PMC8831456, DOI: 10.1158/2159-8290.cd-21-1376.Peer-Reviewed Original ResearchConceptsExtrachromosomal DNA elementsDNA elementsUneven segregationRNA polymerase IILive-cell imagingPolymerase IIOffspring cellsGene transcriptionCell line modelsEcDNAsRandom segregationGenetic materialLiving cellsCopy numberLive cellsIndividual cellsTumor evolutionMitosisInheritance patternBreakpoint sequencesIssue featureTranscriptionFluorescent markersPatient tissuesCells
2021
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer
Kocakavuk E, Anderson K, Varn F, Johnson K, Amin S, Sulman E, Lolkema M, Barthel F, Verhaak R. Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer. Nature Genetics 2021, 53: 1088-1096. PMID: 34045764, PMCID: PMC8483261, DOI: 10.1038/s41588-021-00874-3.Peer-Reviewed Original ResearchConceptsWorse clinical outcomesNon-irradiated tumorsClinical outcomesRecurrent cancerPatient survivalPoor outcomeMetastatic tumorsRecurrent gliomaRadiation therapyRadiation-induced DNA damageDNA damageGlioma Longitudinal Analysis ConsortiumMutational signature analysisCancer treatmentDeletion burdenRadiotherapyMedical FoundationAPOBEC mutagenesisSignificant increaseTumorsCancerDNA damage repairDeletion signatureMutational spectrumSmall deletions
2020
Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure
Akdemir K, Le V, Kim J, Killcoyne S, King D, Lin Y, Tian Y, Inoue A, Amin S, Robinson F, Nimmakayalu M, Herrera R, Lynn E, Chan K, Seth S, Klimczak L, Gerstung M, Gordenin D, O’Brien J, Li L, Deribe Y, Verhaak R, Campbell P, Fitzgerald R, Morrison A, Dixon J, Andrew Futreal P. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. Nature Genetics 2020, 52: 1178-1188. PMID: 33020667, PMCID: PMC8350746, DOI: 10.1038/s41588-020-0708-0.Peer-Reviewed Original ResearchConceptsCancer genomesMutational processesGenome organizationThree-dimensional genome organizationThree-dimensional chromatin structureSomatic mutationsSpatial genome organizationMutation rate variationDifferent human cancer typesDifferent mutational processesWhole-genome datasetsActive mutational processesSpecific mutational processesChromatin structureHuman cancer typesMutation distributionInactive domainsDevelopment of cancerDriver genesGenomeMutational loadActive domainHuman cancersMutationsNovel therapeutic strategiesExtrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers
Kim H, Nguyen N, Turner K, Wu S, Gujar A, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin S, Yi E, Menghi F, Schulte J, Henssen A, Chang H, Beck C, Mischel P, Bafna V, Verhaak R. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nature Genetics 2020, 52: 891-897. PMID: 32807987, PMCID: PMC7484012, DOI: 10.1038/s41588-020-0678-2.Peer-Reviewed Original ResearchConceptsOncogene amplificationPoor outcomeCancer typesEcDNA amplificationShorter survivalCancer patientsMost cancer typesExtrachromosomal DNA amplificationsClinical impactMultiple cancersPatientsNormal tissuesCancerTranscript fusionsEnhanced chromatin accessibilityIntratumoral genetic heterogeneityOncogene transcriptionChromosomal amplificationOutcomesGenetic heterogeneityHigh levelsDNA amplificationTissue typesBlood
2017
TumorFusions: an integrative resource for cancer-associated transcript fusions
Hu X, Wang Q, Tang M, Barthel F, Amin S, Yoshihara K, Lang F, Martinez-Ledesma E, Lee S, Zheng S, Verhaak R. TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Research 2017, 46: gkx1018-. PMID: 29099951, PMCID: PMC5753333, DOI: 10.1093/nar/gkx1018.Peer-Reviewed Original ResearchConceptsTranscript fusionsGene fusionsWhole-genome sequencing dataSomatic DNA rearrangementsTranscript-level expressionGenome sequencing dataGene annotationCopy number levelsCancer samplesCancer Genome AtlasDNA rearrangementsUniform pipelineFunctional fusionSequencing dataIntegrative resourceLevel expressionPartner genesGenome AtlasChromosomal alterationsMutational patternsCancer typesFusion transcriptsNon-neoplastic samplesMolecular aberrationsNumber levels
2012
Integrative analysis of gene and miRNA expression profiles with transcription factor–miRNA feed-forward loops identifies regulators in human cancers
Yan Z, Shah P, Amin S, Samur M, Huang N, Wang X, Misra V, Ji H, Gabuzda D, Li C. Integrative analysis of gene and miRNA expression profiles with transcription factor–miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Research 2012, 40: e135-e135. PMID: 22645320, PMCID: PMC3458521, DOI: 10.1093/nar/gks395.Peer-Reviewed Original ResearchConceptsFeed-forward loopTranscription factorsMiRNA expression profilesExpression profilesNovel feed-forward loopCancer-related transcription factorsExpression dataTF target genesMiRNA-mRNA interactionsCommon target genesMiR-15/miRMiRNA expression dataMiRNA partnersTranscriptome changesTarget genesDifferential genesIntegrative analysisMultiple cancer typesGenesMiRNA expressionHuman cancersLiterature validationBiological conditionsMiRNAsRegulator