Featured Publications
Comparative Molecular Life History of Spontaneous Canine and Human Gliomas
Amin S, Anderson K, Boudreau C, Martinez-Ledesma E, Kocakavuk E, Johnson K, Barthel F, Varn F, Kassab C, Ling X, Kim H, Barter M, Lau C, Ngan C, Chapman M, Koehler J, Long J, Miller A, Miller C, Porter B, Rissi D, Mazcko C, LeBlanc A, Dickinson P, Packer R, Taylor A, Rossmeisl J, Woolard K, Heimberger A, Levine J, Verhaak R. Comparative Molecular Life History of Spontaneous Canine and Human Gliomas. Cancer Cell 2020, 37: 243-257.e7. PMID: 32049048, PMCID: PMC7132629, DOI: 10.1016/j.ccell.2020.01.004.Peer-Reviewed Original ResearchConceptsComparative genomic analysisDNA methylation patternsReceptor tyrosine kinasesCell cycle pathwayGenomic analysisMethylation sequencingLife historyMutational processesTyrosine kinaseHigh similarityHuman gliomasTumorigenic mechanismsHost environmentMutational rateSomatic alterationsSporadic gliomasIDH1 R132Canine gliomasMolecular profileGlioma etiologyHuman pediatricPediatric gliomasTranscriptomeKinaseUnique insightsAnalyses 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 TP53DiscoveryVariantsTruncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma
Lissanu Deribe Y, Shi Y, Rai K, Nezi L, Amin S, Wu C, Akdemir K, Mahdavi M, Peng Q, Chang Q, Hornigold K, Arold S, Welch H, Garraway L, Chin L. Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: e1296-e1305. PMID: 26884185, PMCID: PMC4780599, DOI: 10.1073/pnas.1513801113.Peer-Reviewed Original ResearchConceptsPREX2 mutationsCross-species gene expression analysisGuanine nucleotide exchange factor activityNucleotide exchange factor activityGene expression regulationPI3K/PTEN/Akt pathwayExchange factor activityMelanoma developmentPTEN/AKT pathwayCell cycle regulatorsGene expression analysisExpression regulationGEF activityCytoskeleton organizationCDKN1C geneRegulatory regionsExpression analysisGene expressionCycle regulatorsDNA hypomethylationCell cycleChromosome 11Tumor suppressorBiological pathwaysMechanistic basis
2022
Glioma progression is shaped by genetic evolution and microenvironment interactions
Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R, Consortium T, Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Alfaro K, Amin S, Ashley D, Bock C, Brodbelt A, Bulsara K, Castro A, Connelly J, Costello J, de Groot J, Finocchiaro G, French P, Golebiewska A, Hau A, Hong C, Horbinski C, Kannan K, Kouwenhoven M, Lasorella A, LaViolette P, Ligon K, Lowman A, Mehta S, Miletic H, Molinaro A, Ng H, Niclou S, Niers J, Phillips J, Rabadan R, Rao G, Reifenberger G, Sanai N, Short S, Smitt P, Sloan A, Smits M, Snyder J, Suzuki H, Tabatabai G, Tanner G, Tomaszewski W, Wells M, Westerman B, Wheeler H, Xie J, Yung W, Zadeh G, Zhao J, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell 2022, 185: 2184-2199.e16. PMID: 35649412, PMCID: PMC9189056, DOI: 10.1016/j.cell.2022.04.038.Peer-Reviewed Original ResearchConceptsSpecific ligand-receptor interactionsMicroenvironment interactionsDNA sequencing dataGlioma progressionLigand-receptor interactionsNeoplastic cellsSignaling programsCell statesSequencing dataGenetic evolutionGenetic changesIDH wild-type tumorsIsocitrate dehydrogenaseMesenchymal transitionSomatic alterationsDistinct mannerActive tumor growthIDH-mutant gliomasPotential targetTherapy resistanceAdult patientsDisease progressionPossible roleCellsTumor growth
2021
Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy
Terranova C, Tang M, Maitituoheti M, Raman A, Ghosh A, Schulz J, Amin S, Orouji E, Tomczak K, Sarkar S, Oba J, Creasy C, Wu C, Khan S, Lazcano R, Wani K, Singh A, Barrodia P, Zhao D, Chen K, Haydu L, Wang W, Lazar A, Woodman S, Bernatchez C, Rai K. Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. Cell Reports 2021, 36: 109410. PMID: 34289358, PMCID: PMC8369408, DOI: 10.1016/j.celrep.2021.109410.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell Line, TumorCell ProliferationChromatinEnhancer of Zeste Homolog 2 ProteinFemaleGTP PhosphohydrolasesHistonesHumansMelanocytesMelanomaMembrane ProteinsMesodermMice, NudeMitogen-Activated Protein Kinase KinasesMutationNeoplasm MetastasisPolycomb Repressive Complex 2Transcription, GeneticTumor BurdenConceptsHistone H3 lysine 27 trimethylationH3 lysine 27 trimethylationBivalent chromatin stateCell identity genesLysine 27 trimethylationKey epigenetic alterationsNRAS mutantsMaster transcription factorBivalent domainsChromatin statePRC2 inhibitionEpigenetic elementsTranscription factorsEpigenetic alterationsGenetic driversMesenchymal phenotypeNRAS-mutant melanomaState profilingTherapeutic vulnerabilitiesInvasive capacityPharmacological inhibitionMutantsTherapeutic strategiesMelanoma samplesMutant melanoma patients
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 strategiesKMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer
Alam H, Tang M, Maitituoheti M, Dhar S, Kumar M, Han C, Ambati C, Amin S, Gu B, Chen T, Lin Y, Chen J, Muller F, Putluri N, Flores E, DeMayo F, Baseler L, Rai K, Lee M. KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer. Cancer Cell 2020, 37: 599-617.e7. PMID: 32243837, PMCID: PMC7178078, DOI: 10.1016/j.ccell.2020.03.005.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinoma of LungAnimalsAntimetabolitesApoptosisBiomarkers, TumorCell ProliferationDeoxyglucoseDNA-Binding ProteinsEnhancer Elements, GeneticGene Expression Regulation, NeoplasticGlycolysisHistone-Lysine N-MethyltransferaseHistonesHumansLung NeoplasmsMiceMice, KnockoutMice, NudeMutationMyeloid-Lymphoid Leukemia ProteinNeoplasm ProteinsPeriod Circadian ProteinsPrognosisTumor Cells, CulturedXenograft Model Antitumor AssaysConceptsLung cancerLung-specific lossHuman lung cancer cellsExpression of Per2Lung cancer cellsHistone methyltransferase KMT2DLung tumor suppressorTumor suppressive roleMultiple glycolytic genesLung tumorigenesisEpigenetic modifiersPharmacological inhibitionTherapeutic vulnerabilitiesGlycolytic inhibitorCancerCancer cellsKMT2DFunction mutationsTumor suppressorPer2GlycolysisGlycolytic genesMutationsMiceMolecular and clonal evolution in recurrent metastatic gliosarcoma
Anderson K, Tan A, Parkinson J, Back M, Kastelan M, Newey A, Brewer J, Wheeler H, Hudson A, Amin S, Johnson K, Barthel F, Verhaak R, Khasraw M. Molecular and clonal evolution in recurrent metastatic gliosarcoma. Molecular Case Studies 2020, 6: a004671. PMID: 31896544, PMCID: PMC6996521, DOI: 10.1101/mcs.a004671.Peer-Reviewed Original ResearchConceptsFirst recurrenceExtracranial metastasesIntracranial tumorsFrontal lobeRight iliac boneLeft frontal lobeOrigin of metastasesFrontal recurrenceMetastatic gliosarcomaConcurrent radiotherapyFurther surgeryFurther recurrenceRecurrent tumorsMetastatic tumorsIliac boneMetastasisRecurrenceTumorsMesenchymal typeSurgeryClonal relationshipRadiotherapyGliosarcomaMolecular profilePelvic bones
2019
Longitudinal molecular trajectories of diffuse glioma in adults
Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW. Longitudinal molecular trajectories of diffuse glioma in adults. Nature 2019, 576: 112-120. PMID: 31748746, PMCID: PMC6897368, DOI: 10.1038/s41586-019-1775-1.Peer-Reviewed Original ResearchConceptsAdult patientsDiffuse gliomasRecurrent gliomaOverall survivalPoor outcomeCurrent therapiesChromosome arms 1p/19qAcquired alterationsMajor subtypesTherapeutic resistanceGliomasGlioma developmentGene alterationsIDH mutationsGlioma subtypesPatientsHypermutator phenotypeDriver genesSubtypesClinical annotationSurvivalSubclonal selectionCell cycleAlterationsLittle evidence
2017
Navigating the Cancer Transcriptome by Decoding Divergent Oncogenic States
Amin S, Verhaak R. Navigating the Cancer Transcriptome by Decoding Divergent Oncogenic States. Cell Systems 2017, 5: 90-92. PMID: 28837814, DOI: 10.1016/j.cels.2017.08.006.Peer-Reviewed Original ResearchConceptsAvailable therapeutic options
2015
The Molecular Taxonomy of Primary Prostate Cancer
Network T, Abeshouse A, Ahn J, Akbani R, Ally A, Amin S, Andry C, Annala M, Aprikian A, Armenia J, Arora A, Auman J, Balasundaram M, Balu S, Barbieri C, Bauer T, Benz C, Bergeron A, Beroukhim R, Berrios M, Bivol A, Bodenheimer T, Boice L, Bootwalla M, dos Reis R, Boutros P, Bowen J, Bowlby R, Boyd J, Bradley R, Breggia A, Brimo F, Bristow C, Brooks D, Broom B, Bryce A, Bubley G, Burks E, Butterfield Y, Button M, Canes D, Carlotti C, Carlsen R, Carmel M, Carroll P, Carter S, Cartun R, Carver B, Chan J, Chang M, Chen Y, Cherniack A, Chevalier S, Chin L, Cho J, Chu A, Chuah E, Chudamani S, Cibulskis K, Ciriello G, Clarke A, Cooperberg M, Corcoran N, Costello A, Cowan J, Crain D, Curley E, David K, Demchok J, Demichelis F, Dhalla N, Dhir R, Doueik A, Drake B, Dvinge H, Dyakova N, Felau I, Ferguson M, Frazer S, Freedland S, Fu Y, Gabriel S, Gao J, Gardner J, Gastier-Foster J, Gehlenborg N, Gerken M, Gerstein M, Getz G, Godwin A, Gopalan A, Graefen M, Graim K, Gribbin T, Guin R, Gupta M, Hadjipanayis A, Haider S, Hamel L, Hayes D, Heiman D, Hess J, Hoadley K, Holbrook A, Holt R, Holway A, Hovens C, Hoyle A, Huang M, Hutter C, Ittmann M, Iype L, Jefferys S, Jones C, Jones S, Juhl H, Kahles A, Kane C, Kasaian K, Kerger M, Khurana E, Kim J, Klein R, Kucherlapati R, Lacombe L, Ladanyi M, Lai P, Laird P, Lander E, Latour M, Lawrence M, Lau K, LeBien T, Lee D, Lee S, Lehmann K, Leraas K, Leshchiner I, Leung R, Libertino J, Lichtenberg T, Lin P, Linehan W, Ling S, Lippman S, Liu J, Liu W, Lochovsky L, Loda M, Logothetis C, Lolla L, Longacre T, Lu Y, Luo J, Ma Y, Mahadeshwar H, Mallery D, Mariamidze A, Marra M, Mayo M, McCall S, McKercher G, Meng S, Mes-Masson A, Merino M, Meyerson M, Mieczkowski P, Mills G, Shaw K, Minner S, Moinzadeh A, Moore R, Morris S, Morrison C, Mose L, Mungall A, Murray B, Myers J, Naresh R, Nelson J, Nelson M, Nelson P, Newton Y, Noble M, Noushmehr H, Nykter M, Pantazi A, Parfenov M, Park P, Parker J, Paulauskis J, Penny R, Perou C, Piché A, Pihl T, Pinto P, Prandi D, Protopopov A, Ramirez N, Rao A, Rathmell W, Rätsch G, Ren X, Reuter V, Reynolds S, Rhie S, Rieger-Christ K, Roach J, Robertson A, Robinson B, Rubin M, Saad F, Sadeghi S, Saksena G, Saller C, Salner A, Sanchez-Vega F, Sander C, Sandusky G, Sauter G, Sboner A, Scardino P, Scarlata E, Schein J, Schlomm T, Schmidt L, Schultz N, Schumacher S, Seidman J, Neder L, Seth S, Sharp A, Shelton C, Shelton T, Shen H, Shen R, Sherman M, Sheth M, Shi Y, Shih J, Shmulevich I, Simko J, Simon R, Simons J, Sipahimalani P, Skelly T, Sofia H, Soloway M, Song X, Sorcini A, Sougnez C, Stepa S, Stewart C, Stewart J, Stuart J, Sullivan T, Sun C, Sun H, Tam A, Tan D, Tang J, Tarnuzzer R, Tarvin K, Taylor B, Teebagy P, Tenggara I, Têtu B, Tewari A, Thiessen N, Thompson T, Thorne L, Tirapelli D, Tomlins S, Trevisan F, Troncoso P, True L, Tsourlakis M, Tyekucheva S, Van Allen E, Van Den Berg D, Veluvolu U, Verhaak R, Vocke C, Voet D, Wan Y, Wang Q, Wang W, Wang Z, Weinhold N, Weinstein J, Weisenberger D, Wilkerson M, Wise L, Witte J, Wu C, Wu J, Wu Y, Xu A, Yadav S, Yang L, Yang L, Yau C, Ye H, Yena P, Zeng T, Zenklusen J, Zhang H, Zhang J, Zhang J, Zhang W, Zhong Y, Zhu K, Zmuda E. The Molecular Taxonomy of Primary Prostate Cancer. Cell 2015, 163: 1011-1025. PMID: 26544944, PMCID: PMC4695400, DOI: 10.1016/j.cell.2015.10.025.Peer-Reviewed Original ResearchConceptsPrimary prostate cancerProstate cancerVariable clinical courseAndrogen receptor activityPrimary prostate carcinomasSubtype-specific mannerSubstantial heterogeneityMolecular taxonomyCancer Genome AtlasClinical courseSpecific gene fusionsProstate carcinomaMutant tumorsReceptor activityComprehensive molecular analysisMolecular abnormalitiesCancerDNA repair genesMethylator phenotypeActionable lesionsGenome AtlasPI3KRepair genesEpigenetic profilesTumorsGenomic Classification of Cutaneous Melanoma
Network T, Akbani R, Akdemir K, Aksoy B, Albert M, Ally A, Amin S, Arachchi H, Arora A, Auman J, Ayala B, Baboud J, Balasundaram M, Balu S, Barnabas N, Bartlett J, Bartlett P, Bastian B, Baylin S, Behera M, Belyaev D, Benz C, Bernard B, Beroukhim R, Bir N, Black A, Bodenheimer T, Boice L, Boland G, Bono R, Bootwalla M, Bosenberg M, Bowen J, Bowlby R, Bristow C, Brockway-Lunardi L, Brooks D, Brzezinski J, Bshara W, Buda E, Burns W, Butterfield Y, Button M, Calderone T, Cappellini G, Carter C, Carter S, Cherney L, Cherniack A, Chevalier A, Chin L, Cho J, Cho R, Choi Y, Chu A, Chudamani S, Cibulskis K, Ciriello G, Clarke A, Coons S, Cope L, Crain D, Curley E, Danilova L, D’Atri S, Davidsen T, Davies M, Delman K, Demchok J, Deng Q, Deribe Y, Dhalla N, Dhir R, DiCara D, Dinikin M, Dubina M, Ebrom J, Egea S, Eley G, Engel J, Eschbacher J, Fedosenko K, Felau I, Fennell T, Ferguson M, Fisher S, Flaherty K, Frazer S, Frick J, Fulidou V, Gabriel S, Gao J, Gardner J, Garraway L, Gastier-Foster J, Gaudioso C, Gehlenborg N, Genovese G, Gerken M, Gershenwald J, Getz G, Gomez-Fernandez C, Gribbin T, Grimsby J, Gross B, Guin R, Gutschner T, Hadjipanayis A, Halaban R, Hanf B, Haussler D, Haydu L, Hayes D, Hayward N, Heiman D, Herbert L, Herman J, Hersey P, Hoadley K, Hodis E, Holt R, Hoon D, Hoppough S, Hoyle A, Huang F, Huang M, Huang S, Hutter C, Ibbs M, Iype L, Jacobsen A, Jakrot V, Janning A, Jeck W, Jefferys S, Jensen M, Jones C, Jones S, Ju Z, Kakavand H, Kang H, Kefford R, Khuri F, Kim J, Kirkwood J, Klode J, Korkut A, Korski K, Krauthammer M, Kucherlapati R, Kwong L, Kycler W, Ladanyi M, Lai P, Laird P, Lander E, Lawrence M, Lazar A, Łaźniak R, Lee D, Lee J, Lee J, Lee K, Lee S, Lee W, Leporowska E, Leraas K, Li H, Lichtenberg T, Lichtenstein L, Lin P, Ling S, Liu J, Liu O, Liu W, Long G, Lu Y, Ma, Ma Y, Mackiewicz A, Mahadeshwar H, Malke J, Mallery D, Manikhas G, Mann G, Marra M, Matejka B, Mayo M, Mehrabi S, Meng S, Meyerson M, Mieczkowski P, Miller J, Miller M, Mills G, Moiseenko F, Moore R, Morris S, Morrison C, Morton D, Moschos S, Mose L, Muller F, Mungall A, Murawa D, Murawa P, Murray B, Nezi L, Ng S, Nicholson D, Noble M, Osunkoya A, Owonikoko T, Ozenberger B, Pagani E, Paklina O, Pantazi A, Parfenov M, Parfitt J, Park P, Park W, Parker J, Passarelli F, Penny R, Perou C, Pihl T, Potapova O, Prieto V, Protopopov A, Quinn M, Radenbaugh A, Rai K, Ramalingam S, Raman A, Ramirez N, Ramirez R, Rao U, Rathmell W, Ren X, Reynolds S, Roach J, Robertson A, Ross M, Roszik J, Russo G, Saksena G, Saller C, Samuels Y, Sander C, Sander C, Sandusky G, Santoso N, Saul M, Saw R, Schadendorf D, Schein J, Schultz N, Schumacher S, Schwallier C, Scolyer R, Seidman J, Sekhar P, Sekhon H, Senbabaoglu Y, Seth S, Shannon K, Sharpe S, Sharpless N, Shaw K, Shelton C, Shelton T, Shen R, Sheth M, Shi Y, Shiau C, Shmulevich I, Sica G, Simons J, Sinha R, Sipahimalani P, Sofia H, Soloway M, Song X, Sougnez C, Spillane A, Spychała A, Stretch J, Stuart J, Suchorska W, Sucker A, Sumer S, Sun Y, Synott M, Tabak B, Tabler T, Tam A, Tan D, Tang J, Tarnuzzer R, Tarvin K, Tatka H, Taylor B, Teresiak M, Thiessen N, Thompson J, Thorne L, Thorsson V, Trent J, Triche T, Tsai K, Tsou P, Van Den Berg D, Van Allen E, Veluvolu U, Verhaak R, Voet D, Voronina O, Walter V, Walton J, Wan Y, Wang Y, Wang Z, Waring S, Watson I, Weinhold N, Weinstein J, Weisenberger D, White P, Wilkerson M, Wilmott J, Wise L, Wiznerowicz M, Woodman S, Wu C, Wu C, Wu J, Wu Y, Xi R, Xu A, Yang D, Yang L, Yang L, Zack T, Zenklusen J, Zhang H, Zhang J, Zhang W, Zhao X, Zhu J, Zhu K, Zimmer L, Zmuda E, Zou L. Genomic Classification of Cutaneous Melanoma. Cell 2015, 161: 1681-1696. PMID: 26091043, PMCID: PMC4580370, DOI: 10.1016/j.cell.2015.05.044.Peer-Reviewed Original ResearchConceptsGenomic classificationProtein-based analysesComplex structural rearrangementsImmune gene expressionMutant RASGene expressionIntegrative analysisFocal amplificationGenomic alterationsStructural rearrangementsProtein expressionMutant BRAFCell markersExpressionGenesRNADNAMutationsCutaneous melanomaKIT mutationsNF1RASRearrangementEnrichmentLandscape