2020
Pan-cancer analysis of whole genomes
Aaltonen L, Abascal F, Abeshouse A, Aburatani H, Adams D, Agrawal N, Ahn K, Ahn S, Aikata H, Akbani R, Akdemir K, Al-Ahmadie H, Al-Sedairy T, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov L, Ally A, Alsop K, Alvarez E, Amary F, Amin S, Aminou B, Ammerpohl O, Anderson M, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum E, Arai Y, Aretz A, Arihiro K, Ariizumi S, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman J, Aure M, Awadalla P, Aymerich M, Bader G, Baez-Ortega A, Bailey M, Bailey P, Balasundaram M, Balu S, Bandopadhayay P, Banks R, Barbi S, Barbour A, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe O, Baumhoer D, Bavi P, Baylin S, Bazant W, Beardsmore D, Beck T, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann A, Bergstrom E, Berman B, Berney D, Bernhart S, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle S, Biankin A, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas N, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono J, Boot A, Bootwalla M, Borg A, Borkhardt A, Boroevich K, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros P, Bova G, Bowen D, Bowlby R, Bowtell D, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer D, Brinkman A, Bristow R, Broaddus R, Brock J, Brock M, Broeks A, Brooks A, Brooks D, Brors B, Brunak S, Bruxner T, Bruzos A, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns K, Busanovich J, Bustamante C, Butler A, Butte A, Byrne N, Børresen-Dale A, Caesar-Johnson S, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell P, Campo E, Cantù C, Cao S, Carey T, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick D, Chakravarty D, Chalmers D, Chan C, Chan K, Chan-Seng-Yue M, Chandan V, Chang D, Chanock S, Chantrill L, Chateigner A, Chatterjee N, Chayama K, Chen H, Chen J, Chen K, Chen Y, Chen Z, Cherniack A, Chien J, Chiew Y, Chin S, Cho J, Cho S, Choi J, Choi W, Chomienne C, Chong Z, Choo S, Chou A, Christ A, Christie E, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins C, Connor A, Cooke S, Cooper C, Cope L, Corbo V, Cordes M, Cordner S, Cortés-Ciriano I, Covington K, Cowin P, Craft B, Craft D, Creighton C, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg R, Danilova L, Davi M, Davidson N, Davies H, Davis I, Davis-Dusenbery B, Dawson K, De La Vega F, De Paoli-Iseppi R, Defreitas T, Dei Tos A, Delaneau O, Demchok J, Demeulemeester J, Demidov G, Demircioğlu D, Dennis N, Denroche R, Dentro S, Desai N, Deshpande V, Deshwar A, Desmedt C, Deu-Pons J, Dhalla N, Dhani N, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh H, Dirix L, Doddapaneni H, Donmez N, Dow M, Drapkin R, Drechsel O, Drews R, Serge S, Dudderidge T, Dueso-Barroso A, Dunford A, Dunn M, Dursi L, Duthie F, Dutton-Regester K, Eagles J, Easton D, Edmonds S, Edwards P, Edwards S, Eeles R, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu S, Estivill X, Etemadmoghadam D, Eyfjord J, Faltas B, Fan D, Fan Y, Faquin W, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson M, Ferretti V, Feuerbach L, Field M, Fink J, Finocchiaro G, Fisher C, Fittall M, Fitzgerald A, Fitzgerald R, Flanagan A, Fleshner N, Flicek P, Foekens J, Fong K, Fonseca N, Foster C, Fox N, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick C, Fujimoto A, Fujita M, Fukayama M, Fulton L, Fulton R, Furuta M, Futreal P, Füllgrabe A, Gabriel S, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed D, Gehlenborg N, Gelpi J, George J, Gerhard D, Gerhauser C, Gershenwald J, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama N, Gibbs R, Gibson B, Gill A, Gill P, Giri D, Glodzik D, Gnanapragasam V, Goebler M, Goldman M, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin D, Gossage J, Gotoh K, Govindan R, Grabau D, Graham J, Grant R, Green A, Green E, Greger L, Grehan N, Grimaldi S, Grimmond S, Grossman R, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut I, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber J, Habermann N, Hach F, Haider S, Hama N, Hamdy F, Hamilton A, Hamilton M, Han L, Hanna G, Hansmann M, Haradhvala N, Harismendy O, Harliwong I, Harmanci A, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes D, Hayes S, Hayward N, Hazell S, He Y, Heath A, Heath S, Hedley D, Hegde A, Heiman D, Heinold M, Heins Z, Heisler L, Hellstrom-Lindberg E, Helmy M, Heo S, Hepperla A, Heredia-Genestar J, Herrmann C, Hersey P, Hess J, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley K, Hobolth A, Hodzic E, Hoell J, Hoffmann S, Hofmann O, Holbrook A, Holik A, Hollingsworth M, Holmes O, Holt R, Hong C, Hong E, Hong J, Hooijer G, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle A, Hruban R, Hu J, Hu T, Hua X, Huang K, Huang M, Huang M, Huang V, Huang Y, Huber W, Hudson T, Hummel M, Hung J, Huntsman D, Hupp T, Huse J, Huska M, Hutter B, Hutter C, Hübschmann D, Iacobuzio-Donahue C, Imbusch C, Imielinski M, Imoto S, Isaacs W, Isaev K, Ishikawa S, Iskar M, Islam S, Ittmann M, Ivkovic S, Izarzugaza J, Jacquemier J, Jakrot V, Jamieson N, Jang G, Jang J, Jayaseelan J, Jayasinghe R, Jefferys S, Jegalian K, Jennings J, Jeon S, Jerman L, Ji Y, Jiao W, Johansson P, Johns A, Johns J, Johnson R, Johnson T, Jolly C, Joly Y, Jonasson J, Jones C, Jones D, Jones D, Jones N, Jones S, Jonkers J, Ju Y, Juhl H, Jung J, Juul M, Juul R, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser V, Kakavand H, Kalimuthu S, von Kalle C, Kang K, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn K, Katai H, Kato M, Katoh H, Kawakami Y, Kay J, Kazakoff S, Kazanov M, Keays M, Kebebew E, Kefford R, Kellis M, Kench J, Kennedy C, Kerssemakers J, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim H, Kim H, Kim H, Kim H, Kim J, Kim J, Kim J, Kim Y, King T, Klapper W, Kleinheinz K, Klimczak L, Knappskog S, Kneba M, Knoppers B, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel J, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai P, Laird P, Lakhani S, Lalansingh C, Lalonde E, Lamaze F, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau L, Lawerenz C, Lawlor R, Lawrence M, Lazar A, Lazic A, Le X, Lee D, Lee D, Lee E, Lee H, Lee J, Lee J, Lee J, Lee M, Lee-Six H, Lehmann K, Lehrach H, Lenze D, Leonard C, Leongamornlert D, Leshchiner I, Letourneau L, Letunic I, Levine D, Lewis L, Ley T, Li C, Li C, Li H, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang S, Lichter P, Lin P, Lin Z, Linehan W, Lingjærde O, Liu D, Liu E, Liu F, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long G, Lopez-Guillermo A, Lou S, Louis D, Lovat L, Lu Y, Lu Y, Lu Y, Luchini C, Lungu I, Luo X, Luxton H, Lynch A, Lype L, López C, López-Otín C, Z. E, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte D, Maitra A, Majumder P, Malcovati L, Malikic S, Malleo G, Mann G, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis E, Margolin A, Marin M, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra M, Marsden L, Martens J, Martin S, Martin-Subero J, Martincorena I, Martinez-Fundichely A, Maruvka Y, Mashl R, Massie C, Matthew T, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray P, McLellan M, McPherson J, McPherson J, McPherson T, Meier S, Meng A, Meng S, Menzies A, Merrett N, Merson S, Meyerson M, Meyerson W, Mieczkowski P, Mihaiescu G, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller C, Miller D, Miller J, Mills G, Milovanovic A, Minner S, Miotto M, Arnau G, Mirabello L, Mitchell C, Mitchell T, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore M, Moore R, Morganella S, Morris Q, Morrison C, Mose L, Moser C, Muiños F, Mularoni L, Mungall A, Mungall K, Musgrove E, Mustonen V, Mutch D, Muyas F, Muzny D, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial A, Nahal-Bose H, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro F, Neal D, Nettekoven G, Newell F, Newhouse S, Newton Y, Ng A, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen G, Nielsen M, Nik-Zainal S, Noble M, Nones K, Northcott P, Notta F, O’Connor B, O’Donnell P, O’Donovan M, O’Meara S, O’Neill B, O’Neill J, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien K, Ojesina A, Ojima H, Okusaka T, Omberg L, Ong C, Ossowski S, Ott G, Ouellette B, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park J, Park J, Park K, Park K, Park P, Parker J, Parsons S, Pass H, Pasternack D, Pastore A, Patch A, Pauporté I, Pea A, Pearson J, Pedamallu C, Pedersen J, Pederzoli P, Peifer M, Pennell N, Perou C, Perry M, Petersen G, Peto M, Petrelli N, Petryszak R, Pfister S, Phillips M, Pich O, Pickett H, Pihl T, Pillay N, Pinder S, Pinese M, Pinho A, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston S, Prinz M, Pritchard A, Prokopec S, Provenzano E, Puente X, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo G, Purdie C, Quinn M, Rabionet R, Rader J, Radlwimmer B, Radovic P, Raeder B, Raine K, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael B, Rathmell W, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna M, Reynolds S, Rheinbay E, Riazalhosseini Y, Richardson A, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts L, Roberts N, Roberts S, Robertson A, Robertson A, Rodriguez J, Rodriguez-Martin B, Rodríguez-González F, Roehrl M, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel P, Rosenwald A, Rowe E, Royo R, Rozen S, Rubanova Y, Rubin M, Rubio-Perez C, Rudneva V, Rusev B, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova V, Sadeghi S, Sahinalp S, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra J, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw R, Scardoni M, Scarlett C, Scarpa A, Scelo G, Schadendorf D, Schein J, Schilhabel M, Schlesner M, Schlomm T, Schmidt H, Schramm S, Schreiber S, Schultz N, Schumacher S, Schwarz R, Scolyer R, Scott D, Scully R, Seethala R, Segre A, Selander I, Semple C, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi D, Shackleton M, Shah N, Shahabi S, Shang C, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah Y, Shibata T, Shih J, Shimizu E, Shimizu K, Shin S, Shiraishi Y, Shmaya T, Shmulevich I, Shorser S, Short C, Shrestha R, Shringarpure S, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts A, Sieverling L, Signoretti S, Sikora K, Simbolo M, Simon R, Simons J, Simpson J, Simpson P, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly T, Smid M, Smith J, Smith-McCune K, Socci N, Sofia H, Soloway M, Song L, Sood A, Sothi S, Sotiriou C, Soulette C, Span P, Spellman P, Sperandio N, Spillane A, Spiro O, Spring J, Staaf J, Stadler P, Staib P, Stark S, Stebbings L, Stefánsson Ó, Stegle O, Stein L, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe M, Stratton M, Stretch J, Struck A, Stuart J, Stunnenberg H, Su H, Su X, Sun R, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan B, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen T, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk M, Tatsuno K, Tavaré S, Taylor D, Taylor-Weiner A, Teague J, Teh B, Tembe V, Temes J, Thai K, Thayer S, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson A, Thompson J, Thompson R, Thorne H, Thorne L, Thorogood A, Tiao G, Tijanic N, Timms L, Tirabosco R, Tojo M, Tommasi S, Toon C, Toprak U, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta J, Trümper L, Tsao M, Tsunoda T, Tubio J, Tucker O, Turkington R, Turner D, Tutt A, Ueno M, Ueno N, Umbricht C, Umer H, Underwood T, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg D, Van Laere S, Van Loo P, Van Meir E, Van den Eynden G, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke L, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain R, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell N, Waddell N, Wadelius C, Wadi L, Wagener R, Wala J, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring P, Warnatz H, Warrell J, Warren A, Waszak S, Wedge D, Weichenhan D, Weinberger P, Weinstein J, Weischenfeldt J, Weisenberger D, Welch I, Wendl M, Werner J, Whalley J, Wheeler D, Whitaker H, Wigle D, Wilkerson M, Williams A, Wilmott J, Wilson G, Wilson J, Wilson R, Winterhoff B, Wintersinger J, Wiznerowicz M, Wolf S, Wong B, Wong T, Wong W, Woo Y, Wood S, Wouters B, Wright A, Wright D, Wright M, Wu C, Wu D, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi T, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang J, Yang L, Yang L, Yang S, Yang T, Yang Y, Yao X, Yaspo M, Yates L, Yau C, Ye C, Ye K, Yellapantula V, Yoon C, Yoon S, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung C, Zaikova O, Zamora J, Zapatka M, Zenklusen J, Zenz T, Zeps N, Zhang C, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen C, van de Vijver M, Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020, 578: 82-93. PMID: 32025007, PMCID: PMC7025898, DOI: 10.1038/s41586-020-1969-6.Peer-Reviewed Original ResearchMeSH KeywordsCell ProliferationCellular SenescenceChromothripsisCloud ComputingDNA Mutational AnalysisEvolution, MolecularFemaleGenome, HumanGenomicsGerm-Line MutationHigh-Throughput Nucleotide SequencingHumansInformation DisseminationMaleMutagenesisMutationNeoplasmsOncogenesPromoter Regions, GeneticReproducibility of ResultsRNA SplicingTelomeraseTelomereConceptsPan-Cancer Analysis of Whole GenomesInternational Cancer Genome ConsortiumPan-cancer analysisPan-Cancer Analysis of Whole Genomes ConsortiumStructural variantsNon-coding genomic elementsPoint mutationsAnalysis of Whole GenomesSomatic mutationsNon-coding mutationsRare germline variantsAbnormal telomere maintenanceConsequences of somatic mutationsPattern of somatic mutationsSignatures of mutational processesCancer driver discoveryCancer-associated genesSomatic point mutationsGenomic elementsWhole genomeLow replicative activitySmall insertionsCancer Genome ConsortiumBase substitutionsCancer genomes
2019
Abstract 2891: Landscape of infiltrating immune repertoire in pediatric solid tumors
Nabbi A, Jäger N, Sudhaman S, Sun P, Yang S, Zhu K, Kool M, Rathi K, Kalletla K, Raman P, Zhu Y, Paulson J, Jones D, Tabori U, Resnick A, Pfister S, Pugh T. Abstract 2891: Landscape of infiltrating immune repertoire in pediatric solid tumors. Cancer Research 2019, 79: 2891-2891. DOI: 10.1158/1538-7445.am2019-2891.Peer-Reviewed Original ResearchPediatric solid tumorsTumor microenvironmentSolid tumorsConstitutional mismatch repair deficiencyImmune repertoirePediatric cancerExpression profiles of immune cellsCompared to adult counterpartsAssociated with clinical responseImmune checkpoint gene expressionProfile of immune cellsImmune checkpoint blockadeAntigen presentation machineryCheckpoint gene expressionDeterminants of immune responseT cell receptorChildren's Brain Tumor Tissue ConsortiumInternational Cancer Genome ConsortiumCheckpoint blockadeImmunosuppressive environmentPresentation machineryRare malignancyCancer Genome ConsortiumClinical responseMismatch repair deficiency
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