1
|
Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, 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 PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, 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 PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, 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 PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, 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 TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, 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 CHM, van de Vijver MJ, van’t 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] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
Collapse
|
4
|
Kakavand H, Jackett LA, Menzies AM, Gide TN, Carlino MS, Saw RPM, Thompson JF, Wilmott JS, Long GV, Scolyer RA. Negative immune checkpoint regulation by VISTA: a mechanism of acquired resistance to anti-PD-1 therapy in metastatic melanoma patients. Mod Pathol 2017; 30:1666-1676. [PMID: 28776578 DOI: 10.1038/modpathol.2017.89] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/15/2017] [Accepted: 05/15/2017] [Indexed: 12/20/2022]
Abstract
Understanding the mechanisms of acquired resistance to anti-PD-1 will allow development of better treatment strategies for cancer patients. This study evaluated potential mechanisms of acquired resistance to anti-PD-1 in longitudinally collected metastatic melanoma patient biopsies. Thirty-four metastatic melanoma biopsies were collected from 16 patients who had initially responded to either anti-PD-1 (n=13) alone or combination of anti-PD-1 and ipilimumab (n=3) and then progressed. Biopsies were taken prior to treatment (PRE, n=12) and following progression of disease (PROG, n=22). Immunohistochemistry was performed on all biopsies to detect CD8, FOXP3, PD-1 and VISTA expression on T-cells and PTEN, β-catenin, PD-L1, HLA-A, and HLA-DPB1 expression in the tumor. The majority of patients showed significantly increased density of VISTA+ lymphocytes from PRE to PROG (12/18) (P=0.009) and increased expression of tumor PD-L1 from PRE to PROG (11/18). Intratumoral expression of FOXP3+ lymphocytes significantly increased (P=0.018) from PRE to PROG (10/18). Loss of tumor PTEN and downregulation of tumor HLA-A from PRE to PROG were each identified in 5/18 and 4/18 PROG biopsies, respectively. Downregulation of HLA-DPB1 from PRE to PROG was present in 3/18 PROG biopsies, whereas nuclear β-catenin activation was only identified in 2/18 PROG biopsies. Negative immune checkpoint regulation by VISTA represents an important potential mechanism of acquired resistance in melanoma patients treated with anti-PD-1. Downregulation of HLA-associated antigen presentation also occurs with acquired resistance. Augmentation of the VISTA immune checkpoint pathway may hold promise as a therapeutic strategy in metastatic melanoma patients, particularly those failing anti-PD-1 therapy, and warrants assessment in clinical trials.
Collapse
Affiliation(s)
- Hojabr Kakavand
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
| | - Louise A Jackett
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Royal North Shore and Mater Hospitals, St. Leonards, NSW, Australia
| | - Tuba N Gide
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Royal North Shore and Mater Hospitals, St. Leonards, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| |
Collapse
|
5
|
Vilain RE, Menzies AM, Wilmott JS, Kakavand H, Madore J, Guminski A, Liniker E, Kong BY, Cooper AJ, Howle JR, Saw RP, Jakrot V, Lo S, Thompson JF, Carlino MS, Kefford RF, Long GV, Scolyer RA. Dynamic Changes in PD-L1 Expression and Immune Infiltrates Early During Treatment Predict Response to PD-1 Blockade in Melanoma. Clin Cancer Res 2017; 23:5024-5033. [DOI: 10.1158/1078-0432.ccr-16-0698] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 03/13/2017] [Accepted: 05/11/2017] [Indexed: 11/16/2022]
|
6
|
Hayward NK, Wilmott JS, Waddell N, Johansson PA, Field MA, Nones K, Patch AM, Kakavand H, Alexandrov LB, Burke H, Jakrot V, Kazakoff S, Holmes O, Leonard C, Sabarinathan R, Mularoni L, Wood S, Xu Q, Waddell N, Tembe V, Pupo GM, De Paoli-Iseppi R, Vilain RE, Shang P, Lau LMS, Dagg RA, Schramm SJ, Pritchard A, Dutton-Regester K, Newell F, Fitzgerald A, Shang CA, Grimmond SM, Pickett HA, Yang JY, Stretch JR, Behren A, Kefford RF, Hersey P, Long GV, Cebon J, Shackleton M, Spillane AJ, Saw RPM, López-Bigas N, Pearson JV, Thompson JF, Scolyer RA, Mann GJ. Whole-genome landscapes of major melanoma subtypes. Nature 2017; 545:175-180. [PMID: 28467829 DOI: 10.1038/nature22071] [Citation(s) in RCA: 879] [Impact Index Per Article: 125.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 03/15/2017] [Indexed: 12/16/2022]
Abstract
Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. Here we report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. However, acral and mucosal melanomas were dominated by structural changes and mutation signatures of unknown aetiology, not previously identified in melanoma. The number of genes affected by recurrent mutations disrupting non-coding sequences was similar to that affected by recurrent mutations to coding sequences. Significantly mutated genes included BRAF, CDKN2A, NRAS and TP53 in cutaneous melanoma, BRAF, NRAS and NF1 in acral melanoma and SF3B1 in mucosal melanoma. Mutations affecting the TERT promoter were the most frequent of all; however, neither they nor ATRX mutations, which correlate with alternative telomere lengthening, were associated with greater telomere length. Most melanomas had potentially actionable mutations, most in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways. The whole-genome mutation landscape of melanoma reveals diverse carcinogenic processes across its subtypes, some unrelated to sun exposure, and extends potential involvement of the non-coding genome in its pathogenesis.
Collapse
Affiliation(s)
- Nicholas K Hayward
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peter A Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Matthew A Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland 4878, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hojabr Kakavand
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Hazel Burke
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Valerie Jakrot
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Radhakrishnan Sabarinathan
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Loris Mularoni
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nick Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Varsha Tembe
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Gulietta M Pupo
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Ricardo De Paoli-Iseppi
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ricardo E Vilain
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ping Shang
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Loretta M S Lau
- Children's Medical Research Institute, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Rebecca A Dagg
- Children's Hospital at Westmead, The University of Sydney, Westmead, New South Wales Sydney, 2145, Australia
| | - Sarah-Jane Schramm
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Antonia Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Ken Dutton-Regester
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Anna Fitzgerald
- Bioplatforms Australia, North Ryde, Sydney, New South Wales 2109, Australia
| | - Catherine A Shang
- Bioplatforms Australia, North Ryde, Sydney, New South Wales 2109, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Victoria 3052, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Jean Y Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jonathan R Stretch
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, La Trobe University, Austin Health, Heidelberg, Melbourne, Victoria 3084, Australia
| | - Richard F Kefford
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Macquarie University, North Ryde, Sydney, New South Wales 2109, Australia
| | - Peter Hersey
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Centenary Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Department of Medical Oncology, Royal North Shore Hospital, St Leonards, Sydney, New South Wales 2065, Australia
| | - Jonathan Cebon
- Olivia Newton-John Cancer Research Institute, La Trobe University, Austin Health, Heidelberg, Melbourne, Victoria 3084, Australia
| | - Mark Shackleton
- Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Andrew J Spillane
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Núria López-Bigas
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, Sydney, New South Wales 2050, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| |
Collapse
|
7
|
Kakavand H, Walker E, Lum T, Wilmott JS, Selinger CI, Smith E, Saw RPM, Yu B, Cooper WA, Long GV, O'Toole SA, Scolyer RA. BRAF(V600E) and NRAS(Q61L/Q61R) mutation analysis in metastatic melanoma using immunohistochemistry: a study of 754 cases highlighting potential pitfalls and guidelines for interpretation and reporting. Histopathology 2016; 69:680-6. [PMID: 27151331 DOI: 10.1111/his.12992] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/04/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND AIMS BRAF or NRAS mutations occur in approximately 60% of cutaneous melanomas, and the identification of such mutations underpins the appropriate selection of patients who may benefit from BRAF and MEK inhibitor targeted therapies. The utility of immunohistochemistry (IHC) to detect NRAS(Q61L) mutations is currently unknown. This study sought to assess the sensitivity and specificity of anti-BRAF(V600E) (VE1), anti-NRAS(Q61R) (SP174) and anti-NRAS(Q61L) (26193) antibodies for mutation detection in a large series of cases. METHODS AND RESULTS Mutation status was determined using the OncoCarta assay in 754 cutaneous melanomas. IHC with the anti-BRAF(V600E) antibody was performed in all cases, and the anti-NRAS(Q61R) and anti-NRAS(Q61L) antibodies were assessed in a subset of 302 samples utilizing tissue microarrays. The staining with the anti-BRAF(V600E) and anti-NRAS(Q61R) antibodies was diffuse, homogeneous and cytoplasmic. The anti-NRAS(Q61L) antibody displayed variable intensity staining, ranging from weak to strong in NRAS(Q61L) mutant tumours. The sensitivity and specificity for anti-BRAF(V600E) was 100 and 99.3%, anti-NRAS(Q61R) was 100 and 100% and anti-NRAS(Q61L) was 82.6 and 96.2%, respectively. CONCLUSIONS The use of IHC is a fast, efficient and cost-effective method to identify single specific mutations in melanoma patients. BRAF(V600E) and NRAS(Q61R) antibodies have high sensitivity and specificity; however, the NRAS(Q61L) antibody appears less sensitive. IHC can help to facilitate the timely, appropriate selection and treatment of metastatic melanoma patients with targeted therapies. Detection of melanoma-associated mutations by IHC may also provide evidence for a diagnosis of melanoma in metastatic undifferentiated neoplasms lacking expression of melanoma antigens.
Collapse
Affiliation(s)
- Hojabr Kakavand
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Emily Walker
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Trina Lum
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Christina I Selinger
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Elizabeth Smith
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Bing Yu
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Wendy A Cooper
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Melanoma Oncology, Royal North Shore and Mater Hospital, Sydney, NSW, Australia
| | - Sandra A O'Toole
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, North Sydney, NSW, Australia.
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia.
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.
| |
Collapse
|
8
|
Wilmott JS, Field MA, Johansson PA, Kakavand H, Shang P, De Paoli-Iseppi R, Vilain RE, Pupo GM, Tembe V, Jakrot V, Shang CA, Cebon J, Shackleton M, Fitzgerald A, Thompson JF, Hayward NK, Mann GJ, Scolyer RA. Tumour procurement, DNA extraction, coverage analysis and optimisation of mutation-detection algorithms for human melanoma genomes. Pathology 2016; 47:683-93. [PMID: 26517638 DOI: 10.1097/pat.0000000000000324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Whole genome sequencing (WGS) of cancer patients' tumours offers the most comprehensive method of identifying both novel and known clinically-actionable genomic targets. However, the practicalities of performing WGS on clinical samples are poorly defined.This study was designed to test sample preparation, sequencing specifications and bioinformatic algorithms for their effect on accuracy and cost-efficiency in a large WGS analysis of human melanoma samples.WGS was performed on melanoma cell lines (n = 15) and melanoma fresh frozen tumours (n = 222). The appropriate level of coverage and the optimal mutation detection algorithm for the project pipeline were determined.An incremental increase in sequencing coverage from 36X to 132X in melanoma tissue samples and 30X to 103X for cell lines only resulted in a small increase (1-2%) in the number of mutations detected, and the quality scores of the additional mutations indicated a low probability that the mutations were real. The results suggest that 60X coverage for melanoma tissue and 40X for melanoma cell lines empower the detection of 98-99% of informative single nucleotide variants (SNVs), a sensitivity level at which clinical decision making or landscape research projects can be carried out with a high degree of confidence in the results. Likewise the bioinformatic mutation analysis methodology strongly influenced the number and quality of SNVs detected. Detecting mutations in the blood genomes separate to the tumour genomes generated 41% more SNVs than if the blood and melanoma tissue genomes were analysed simultaneously. Therefore, simultaneous analysis should be employed on matched melanoma tissue and blood genomes to reduce errors in mutation detection.This study provided valuable insights into the accuracy of SNV with WGS at various coverage levels in human clinical cancer specimens. Additionally, we investigated the accuracy of the publicly available mutation detection algorithms to detect cancer specific SNVs which will aid researchers and clinicians in study design and implementation of WGS for the identification of somatic mutations in other cancers.
Collapse
Affiliation(s)
- James S Wilmott
- 1Melanoma Institute Australia, North Sydney, NSW 2Sydney Medical School, The University of Sydney, Camperdown, NSW 3Immunogenomics Laboratory, Australian National University, Canberra, ACT 4Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Qld 5Centre for Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, NSW 6Bioplatforms Australia, Macquarie University, North Ryde, NSW 7Ludwig Institute for Cancer Research, Olivia Newton-John Cancer and Wellness Centre, Austin Health, Heidelberg, Vic 8The Cancer Development and Treatment Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Vic 9Departments of Melanoma and Surgical Oncology 10Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; these authors contributed equally
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Welsh SJ, Boyd S, McGuire H, Gonzales M, Menzies AM, Kakavand H, James E, Smith E, Fazekas B, Kefford RF, Guminski A, Scolyer RA, Long GV, Rizos H. Abstract 2650: In depth immune profiling of the response of melanoma to MAPK inhibition. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Melanoma patients with clinically palpable regional lymph node metastases (AJCC Stage III) carry a risk of relapse and death that approaches 70% at 5 years. The NeoCombi study is a pilot phase II study of neoadjuvant dabrafenib plus trametinib in patients with resectable Stage IIIB-C BRAFV600 mutation positive melanoma. Patients receive 12 weeks of combined drug treatment, followed by surgical resection of all disease. Patients then continue combination drug treatment for a further 40 weeks. We aimed to identify host and tumour biomarkers that predict response to MAPK inhibition.
Blood and tumour samples were obtained at baseline, early during treatment (3-7 days on therapy), at completion resection after 12 weeks on therapy, and, if relevant, on progression. Additional blood samples were also collected every 2 weeks up to 12 weeks of therapy. Samples were processed to generate plasma, peripheral blood mononuclear cells (PBMCs), fresh frozen tumour and where possible, tumour-dissociates and cell lines (tumour and immune cells). We have profiled tumour-specific and peripheral immune responses using a combination of flow cytometry, mass cytometry and multiplex cytokine/chemokine arrays. We also profiled circulating tumour-associated DNA (ctDNA) in plasma.
To date, we have accrued 17 patients onto the NeoCombi study. Primary analysis of the first 12 patients has been completed. Decreases in ctDNA and tumour viability, in addition to immunophenotype changes, were seen within 1 week of starting treatment. Changes in immunophenotype continued throughout the first 12 weeks of treatment with conversion of CD8+ and CD4+ naive (CD45RA+) cells to effector cells (CD45RA-) in most patients. We also noted that activation of regulatory T cells (CD4+CD25+CD127-HLA-DR+) increased over the first 12 weeks of treatment in patients with partial pathological responses compared to those with complete pathological responses. Interestingly, the cytokine profile remained relatively stable across treatment within each patient, suggesting that factors already present at baseline may determine response to treatment. A pro-inflammatory cytokine signature has been identified as a potential biomarker of patients likely to relapse and in vitro validation studies are currently underway. Additionally, although ctDNA was only detectable in 42% of patients (compared to over 70% in patients with stage IV disease), high levels of ctDNA identified patients at highest risk of relapse and, if detectable, proved a useful marker to monitor treatment response.
In conclusion, we have identified both host and tumour-specific biomarkers which may be useful to predict (and to monitor) response to MAPK inhibition in melanoma patients.
Citation Format: Sarah J. Welsh, Suzanah Boyd, Helen McGuire, Maria Gonzales, Alexander M. Menzies, Hojabr Kakavand, Elisa James, Elizabeth Smith, Barbara Fazekas, Richard F. Kefford, Alex Guminski, Richard A. Scolyer, Georgina V. Long, Helen Rizos. In depth immune profiling of the response of melanoma to MAPK inhibition. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2650.
Collapse
Affiliation(s)
| | | | - Helen McGuire
- 2Centenary Institute of Cancer Medicine and Cell Biology, Sydney, Australia
| | | | | | | | - Elisa James
- 3Melanoma Institute Australia, Sydney, Australia
| | | | - Barbara Fazekas
- 2Centenary Institute of Cancer Medicine and Cell Biology, Sydney, Australia
| | | | | | | | | | | |
Collapse
|
10
|
De Paoli-Iseppi R, Johansson PA, Menzies AM, Dias KR, Pupo GM, Kakavand H, Wilmott JS, Mann GJ, Hayward NK, Dinger ME, Long GV, Scolyer RA. Comparison of whole-exome sequencing of matched fresh and formalin fixed paraffin embedded melanoma tumours: implications for clinical decision making. Pathology 2016; 48:261-6. [PMID: 27020503 DOI: 10.1016/j.pathol.2016.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 12/22/2015] [Accepted: 01/03/2016] [Indexed: 12/15/2022]
Abstract
The identification of recurrent driver mutations by whole-exome sequencing (WES) of fresh-frozen human cancers and the subsequent development of novel targeted therapies have recently transformed the treatment of many cancers including melanoma. In routine clinical practice, fresh-frozen tissue is rarely available and mutation testing usually needs to be carried out on archival formalin fixed, paraffin embedded (FFPE) tissue, from which DNA is typically fragmented, cross-linked and of lower quality. In this study we aimed to determine whether WES data generated from genomic DNA (gDNA) extracted from FFPE tissues can be produced reliably and of clinically-actionable standard. In this study of ten melanoma patients, we compared WES data produced from analysis of gDNA isolated from FFPE tumour tissue with that isolated from fresh-frozen tumour tissue from the same specimen. FFPE samples were sequenced using both Illumina's Nextera and NimbleGen SeqCap exome capture kits. To examine mutations between the two tissue sources and platforms, somatic mutations in the FFPE exomes were called using the matched fresh tissue sequence as a reference. Of the 10 FFPE DNA samples, seven Nextera and four SeqCap samples passed library preparation. On average, there were 5341 and 2246 variants lost in FFPE compared to matched fresh tissue utilising Nextera and SeqCap kits, respectively. In order to explore the feasibility of future clinical implementation of WES, FFPE variants in 27 genes of important clinical relevance in melanoma were assessed. The average concordance rate was 43.2% over a total of 1299 calls for the chosen genes in the FFPE DNA. For the current clinically most important melanoma mutations, 0/3 BRAF and 6/8 (75%) NRAS FFPE calls were concordant with the fresh tissue result, which was confirmed using a Sequenom OncoCarta Panel. The poor performance of FFPE WES indicates that specialised library construction to account for low quality DNA and further refinements will be necessary before this approach could be used for routine clinical decision making over currently preferred techniques.
Collapse
Affiliation(s)
| | - Peter A Johansson
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia; Department of Medical Oncology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Kerith-Rae Dias
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Gulietta M Pupo
- Centre for Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia
| | - Hojabr Kakavand
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia.
| | - Graham J Mann
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia; Centre for Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia
| | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia; Department of Medical Oncology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Pathology, Sydney Medical School, The University of Sydney, NSW, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| |
Collapse
|
11
|
Kakavand H, Lum T, Wilmott JS, Smith E, O’Toole S, Long GV, Scolyer RA. BRAF (v600e) and NRAS (q61r/q61l) mutation analysis using immunohistochemistry: Implications for routine mutation testing of melanoma samples. Pathology 2016. [DOI: 10.1016/j.pathol.2015.12.349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
12
|
Kakavand H, Wilmott JS, Long GV, Scolyer RA. Targeted therapies and immune checkpoint inhibitors in the treatment of metastatic melanoma patients: a guide and update for pathologists. Pathology 2016; 48:194-202. [PMID: 27020392 DOI: 10.1016/j.pathol.2015.12.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 11/28/2015] [Indexed: 12/19/2022]
Abstract
The previously dismal prospects for patients with advanced stage metastatic melanoma have greatly improved in recent years. Enhanced understanding of both the pathogenesis of melanoma and its molecular drivers, as well as the importance and regulation of anti-tumour immune responses, have provided new therapeutic opportunities for melanoma patients. There are two major distinct categories of systemic treatments with activity for patients with metastatic melanoma: (1) targeted therapies, which act to inhibit the oncogenes that drive the aberrant growth and dissemination of the tumour; and (2) immune checkpoint inhibitor therapies, which act to enhance anti-tumour immune responses by blocking negative regulators of immunity. Pathologists play a critical and expanding role in the selection of the most appropriate treatment for individual metastatic melanoma patients in the modern era of personalised/precision medicine. The molecular pathology testing of melanoma tumour tissue for the presence of targetable oncogenic mutations is already part of routine practice in many institutions. In addition, other potential oncogenic therapeutic targets continue to be identified and pathology testing techniques must readily adapt to this rapidly changing field. Recent research findings suggest that pathological assessment of tumour associated immune cells and immunosuppressive ligand expression of the tumour are likely to be important in identifying patients most likely to benefit from immune checkpoint inhibitors. Similarly, pathological and molecular observations of on-treatment tumour tissue biopsies taken from patients on targeted therapies have provided new insights into the mechanisms of action of targeted molecular therapies, have contributed to the identification of resistance mechanisms to these novel therapies and may be of higher value for selecting patients most likely to benefit from therapies. These data have already provided a rational biological basis for the exciting prospect of combining them to further improve survival rates and this is currently being investigated in clinical trials. Ultimately it may be the responsibility of the pathologist to identify which therapy or combination of therapies is most likely to benefit individual patients.
Collapse
Affiliation(s)
- Hojabr Kakavand
- Melanoma Institute Australia, North Sydney, Australia; The University of Sydney, Sydney, Australia
| | - James S Wilmott
- Melanoma Institute Australia, North Sydney, Australia; The University of Sydney, Sydney, Australia
| | - Georgina V Long
- Melanoma Institute Australia, North Sydney, Australia; The University of Sydney, Sydney, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, North Sydney, Australia; The University of Sydney, Sydney, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.
| |
Collapse
|
13
|
Kakavand H, Vilain RE, Wilmott JS, Burke H, Yearley JH, Thompson JF, Hersey P, Long GV, Scolyer RA. Tumor PD-L1 expression, immune cell correlates and PD-1+ lymphocytes in sentinel lymph node melanoma metastases. Mod Pathol 2015; 28:1535-44. [PMID: 26403784 DOI: 10.1038/modpathol.2015.110] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 08/11/2015] [Accepted: 08/29/2015] [Indexed: 12/22/2022]
Abstract
Melanoma patients with sentinel lymph node metastases have variable 5-year survival rates (39-70%). The prognostic significance of tumor-infiltrating lymphocytes in sentinel lymph node metastases from such patients is currently unknown. Anti-PD-1/PD-L1 inhibitors have significantly improved clinical outcome in unresectable AJCC stage IIIC/IV metastatic melanoma patients, and are being trialed in the adjuvant setting in advanced stage disease, however, their role in early stage (sentinel lymph node positive) metastatic disease remains unclear. The aims of this study were to characterize, in sentinel lymph nodes, the subpopulations of lymphocytes that interact with metastatic melanoma cells and analyze their associations with outcome, and to determine tumor PD-L1 expression as this may provide a rational scientific basis for the administration of adjuvant anti-PD-1/PD-L1 inhibitors in sentinel lymph node positive metastatic melanoma patients. Sentinel lymph nodes containing metastatic melanoma from 60 treatment-naive patients were analyzed for CD3, CD4, CD8, FOXP3, PD-1, and PD-L1 using immunohistochemistry on serial sections. The results were correlated with clinicopathologic features and outcome. Positive correlations between recurrence-free/overall survival with the number of CD3+ tumor-infiltrating lymphocytes (hazard ratio=0.36 (0.17-0.76), P=0.005; hazard ratio=0.29 (0.14-0.61), P=0.0005, respectively), the number of CD4+ tumor-infiltrating lymphocytes (hazard ratio=0.34 (0.15-0.77), P=0.007; hazard ratio=0.32 (0.14-0.74), P=0.005, respectively), and the number of CD8+ tumor-infiltrating lymphocytes (hazard ratio =0.42 (0.21-0.85), P=0.013; hazard ratio =0.32 (0.19-0.78), P=0.006, respectively) were observed. There was also a negative correlation with the number of peritumoral PD-1+ lymphocytes (hazard ratio=2.67 (1.17-6.13), P=0.016; hazard ratio=2.74 (1.14-6.76), P=0.019, respectively). Tumoral PD-L1 expression was present in 26 cases (43%) but did not correlate with outcome. The findings suggest that T-cell subsets in sentinel lymph node metastases can predict melanoma patient outcome. In addition, the relatively high number of PD-L1 positive sentinel lymph node melanoma metastases provides a rationale for anti-PD-1 therapy trials in sentinel lymph node positive melanoma patients, particularly those with peritumoral PD-1+ lymphocytes.
Collapse
Affiliation(s)
- Hojabr Kakavand
- Melanoma Institute Australia, North Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Ricardo E Vilain
- Melanoma Institute Australia, North Sydney, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, North Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Hazel Burke
- Melanoma Institute Australia, North Sydney, NSW, Australia
| | | | - John F Thompson
- Melanoma Institute Australia, North Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Peter Hersey
- Melanoma Institute Australia, North Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Kolling Institute of Medical Research, Royal North Shore Hospital, St. Leonards, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, North Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, North Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| |
Collapse
|
14
|
Shain AH, Garrido M, Botton T, Talevich E, Yeh I, Sanborn JZ, Chung J, Wang NJ, Kakavand H, Mann GJ, Thompson JF, Wiesner T, Roy R, Olshen AB, Gagnon A, Gray JW, Huh N, Hur JS, Busam KJ, Scolyer RA, Cho RJ, Murali R, Bastian BC. Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. Nat Genet 2015; 47:1194-9. [PMID: 26343386 PMCID: PMC4589486 DOI: 10.1038/ng.3382] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/22/2015] [Indexed: 12/16/2022]
Abstract
Desmoplastic melanoma is an uncommon variant of melanoma with sarcomatous histology, distinct clinical behavior and unknown pathogenesis. We performed low-coverage genome and high-coverage exome sequencing of 20 desmoplastic melanomas, followed by targeted sequencing of 293 genes in a validation cohort of 42 cases. A high mutation burden (median of 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers. Mutation patterns strongly implicate ultraviolet radiation as the dominant mutagen, indicating a superficially located cell of origin. Newly identified alterations included recurrent promoter mutations of NFKBIE, encoding NF-κB inhibitor ɛ (IκBɛ), in 14.5% of samples. Common oncogenic mutations in melanomas, in particular in BRAF (encoding p.Val600Glu) and NRAS (encoding p.Gln61Lys or p.Gln61Arg), were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS and PIK3CA, some of which are candidates for targeted therapies.
Collapse
Affiliation(s)
- A Hunter Shain
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Maria Garrido
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Thomas Botton
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Eric Talevich
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Iwei Yeh
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | | | - Jongsuk Chung
- Samsung Advanced Institute of Technology, Seoul, Korea
| | - Nicholas J Wang
- Department of Biomedical Engineering, Oregon Health and Sciences University, Portland, Oregon, USA
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Hojabr Kakavand
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Graham J Mann
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - John F Thompson
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Thomas Wiesner
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Adam B Olshen
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Alexander Gagnon
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health and Sciences University, Portland, Oregon, USA
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Nam Huh
- Samsung Advanced Institute of Technology, Seoul, Korea
| | - Joe S Hur
- Samsung Electronics Headquarters, Seoul, Korea
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Richard A Scolyer
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Boris C Bastian
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| |
Collapse
|
15
|
Vilain R, Kakavand H, Menzies A, Madore J, Wilmott J, Dobney R, Jakrot V, Cooper A, Kong B, Lo S, Liniker E, Saw R, Thompson J, Kefford R, Carlino M, Long G, Scolyer R. 3305 PD1 inhibition-induced changes in melanoma and its associated immune infiltrate. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(15)30063-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
16
|
Shain AH, Garrido M, Botton T, Talevich E, Yeh I, Sanborn Z, Chung J, Wang N, Kakavand H, Mann G, Thompson J, Wiesner T, Roy R, Olshen A, Gagnon A, Gray J, Huh N, Hur J, Busam K, Scolyer R, Cho R, Murali R, Bastian B. Abstract 2968: Exome sequencing of desmoplastic melanoma reveals recurrent NFKBIE promoter mutations and diverse MAPK/PI3K pathway activating mutations. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Desmoplastic melanomas (DMs) comprise 4% of the overall melanoma burden and have a 5-year survival rate of 85%. DMs are dermal tumors characterized by spindled melanocytes situated within abundant desomplastic stroma. These unusual histological features commonly lead to misdiagnosis. Currently, there are no known genetic drivers. A better understanding of the underlying biology of desmoplastic melanoma would provide biomarkers and therapeutic opportunities. Towards this goal, we performed low-coverage genome and high-coverage exome sequencing of 20 DMs in a discovery cohort, followed by targeted sequencing of 293 candidate genes on a validation cohort of 42 cases. Additionally, high-resolution aCGH was performed on samples from both cohorts. A high mutation burden (median 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers sequenced to date. Mutation patterns strongly indicate that UV-radiation is the dominant mutagen and implicate a superficially located cell of origin despite their predominantly intradermal presentation. Novel alterations included recurrent promoter mutations and amplification of NF-kappa B inhibitor epsilon, NFKBIE (IkBϵ) in 14.5% of samples. The promoter mutations typically affect both alleles and occur over a highly conserved DNA region. The mutations are predicted to disrupt a canonical Ets Like Factor 1 (ELF1) binding site. In total, these data imply aberrant NF-kappa B signaling as a pathogenic feature of desmoplastic melanoma. Commonly mutated oncogenes in melanomas, in particular BRAF V600E and NRAS Q61K/R, were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS, and PIK3CA. Rb and p53 pathway alterations occurred respectively in 71% and 66% of tumors, affecting RB1, FBXW7, CDK4, PPP6C, CCND1, CDKN2A, TP53, and MDM2. Finally, TERT promoter mutations or amplifications occurred in 90% of tumors. The consequences of the mutations on protein expression levels was confirmed by immunostaining for NF1, EGFR, Rb, CDK4, CCND1, p16, p53, and Mdm2. Collectively, many of these oncogenic mutations are potentially druggable. In conclusion, desmoplastic melanomas harbor distinct genetic alterations that explain their unique biology, and this study illuminates genetic biomarkers and nominates targets for therapeutic intervention.
Citation Format: Alan H. Shain, Maria Garrido, Thomas Botton, Eric Talevich, Iweh Yeh, Zack Sanborn, Jongsuk Chung, Nicholas Wang, Hojabr Kakavand, Graham Mann, John Thompson, Thomas Wiesner, Ritu Roy, Adam Olshen, Alexander Gagnon, Joe Gray, Nam Huh, Joe Hur, Klaus Busam, Richard Scolyer, Raymond Cho, Rajmohan Murali, Boris Bastian. Exome sequencing of desmoplastic melanoma reveals recurrent NFKBIE promoter mutations and diverse MAPK/PI3K pathway activating mutations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2968. doi:10.1158/1538-7445.AM2015-2968
Collapse
Affiliation(s)
| | | | | | | | | | | | - Jongsuk Chung
- 3Samsung Advanced Institute of Technology, Republic of Korea
| | | | | | | | | | | | | | | | | | - Joe Gray
- 7Oregon Health and Sciences University, OR
| | - Nam Huh
- 3Samsung Advanced Institute of Technology, Republic of Korea
| | - Joe Hur
- 8Samsung Electronics Headquarters, Republic of Korea
| | | | | | | | | | | |
Collapse
|
17
|
Kakavand H, Wilmott JS, Menzies AM, Vilain R, Haydu LE, Yearley JH, Thompson JF, Kefford RF, Hersey P, Long GV, Scolyer RA. PD-L1 Expression and Tumor-Infiltrating Lymphocytes Define Different Subsets of MAPK Inhibitor-Treated Melanoma Patients. Clin Cancer Res 2015; 21:3140-8. [PMID: 25609064 DOI: 10.1158/1078-0432.ccr-14-2023] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 01/13/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE To evaluate the expression of tumor PD-L1 and changes in tumor-infiltrating lymphocyte (TIL) populations in patients with metastatic melanoma treated with targeted MAPK inhibitors. EXPERIMENTAL DESIGN Ninety-three tumors were analyzed from 40 patients treated with a BRAF inhibitor alone (BRAFi; n = 28) or combination of BRAF and MEK inhibitors (Combi; n = 12). Tumors were excised before treatment (PRE), early during treatment (EDT), and at progression (PROG). Immunohistochemical staining was performed for CD4, CD8, CD68, FOXP3, LAG3, PD-1, and PD-L1 and correlated with clinical outcome. RESULTS Patients' tumors that were PD-L1 positive at baseline showed a significant decrease in PD-L1 expression at PROG (P = 0.028), whereas patients' tumors that were PD-L1 negative at baseline showed a significant increase in PD-L1 expression at PROG (P = 0.008) irrespective of treatment with BRAFi or Combi. Overall PD-L1 expression highly correlated with TIL immune markers. BRAFi-treated patients showed significant increases in CD4(+), CD8(+), and PD-1(+) lymphocytes from PRE to EDT (P = 0.001, P = 0.001, P = 0.017, respectively), and Combi-treated patients showed similar increases in CD4(+) and CD8(+) lymphocytes from PRE to EDT (P = 0.017, P = 0.021). CONCLUSIONS The addition of MEKi to BRAFi did not result in significant reduction in immune infiltration in EDT biopsies. This provides support for conducting trials that combine MAPKi with immune checkpoint inhibitors in the hope of improving complete and durable response rates. PD-L1 expression at PROG on MAPK inhibitors varied according to baseline expression suggesting that combining MAPKi with immunotherapies concurrently may be more effective in patients with PD-L1 expression and TILs in baseline melanoma samples.
Collapse
Affiliation(s)
- Hojabr Kakavand
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Sydney Medical School, the University of Sydney, Sydney, New South Wales, Australia
| | - James S Wilmott
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Sydney Medical School, the University of Sydney, Sydney, New South Wales, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Sydney Medical School, the University of Sydney, Sydney, New South Wales, Australia
| | - Ricardo Vilain
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Lauren E Haydu
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Sydney Medical School, the University of Sydney, Sydney, New South Wales, Australia
| | | | - John F Thompson
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Sydney Medical School, the University of Sydney, Sydney, New South Wales, Australia
| | - Richard F Kefford
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, New South Wales, Australia. Australian School of Advanced Medicine, Macquarie University, New South Wales, Australia
| | - Peter Hersey
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Sydney Medical School, the University of Sydney, Sydney, New South Wales, Australia. Kolling Institute of Medical Research, Royal North Shore Hospital, St. Leonards, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Sydney Medical School, the University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, North Sydney, New South Wales, Australia. Sydney Medical School, the University of Sydney, Sydney, New South Wales, Australia. Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia.
| |
Collapse
|
18
|
Wilmott JS, Colebatch AJ, Kakavand H, Shang P, Carlino MS, Thompson JF, Long GV, Scolyer RA, Hersey P. Expression of the class 1 histone deacetylases HDAC8 and 3 are associated with improved survival of patients with metastatic melanoma. Mod Pathol 2015; 28:884-94. [PMID: 25836739 DOI: 10.1038/modpathol.2015.34] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 11/09/2022]
Abstract
Prior studies have shown that combinations of histone deacetylase (HDAC) and BRAF inhibitors (BRAFi) have synergistic effects on BRAFi-resistant melanoma through enhanced apoptosis and inhibition of the cAMP-dependent drug resistance pathway. However, little is known about the expression of various HDACs and their associations with BRAF/NRAS mutation status, clinicopathologic characteristics, and patient outcome. The present study extensively profiled HDAC class 1 and their targets/regulators utilizing immunohistochemistry in human melanoma samples from patients with stage IV melanoma, known BRAF/NRAS mutational status, and detailed clinicopatholgical data. HDAC8 was increased in BRAF-mutated melanoma (P=0.016), however, no association between expression of other HDACs and NRAS/BRAF status was identified. There was also a correlation between HDAC1, HDAC8 expression, and phosphorylated NFκb p65 immunoreactivity (P<0.001). Increased cytoplasmic HDAC8 immunoreactivity was independently associated with an improved survival from both diagnosis of primary melanoma and from first detection of stage IV disease to melanoma death on multivariate analysis (HR 0.992, 95% CI 0.987-0.996; P<0.001 and HR 0.993, 95% CI 0.988-0.998; P=0.009, respectively). These results suggest not only that HDAC8 may be a prognostic biomarker in melanoma, but also provide important data regarding the regulation of HDACs in melanoma and a rational basis for targeting them therapeutically.
Collapse
Affiliation(s)
- James S Wilmott
- 1] Melanoma Institute Australia, Sydney, New South Wales, Australia [2] Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Andrew J Colebatch
- 1] Molecular Oncology Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia [2] Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Hojabr Kakavand
- 1] Melanoma Institute Australia, Sydney, New South Wales, Australia [2] Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Ping Shang
- Melanoma Institute Australia, Sydney, New South Wales, Australia
| | - Matteo S Carlino
- 1] Melanoma Institute Australia, Sydney, New South Wales, Australia [2] Westmead Institute for Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, New South Wales, Australia [3] Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, New South Wales, Australia
| | - John F Thompson
- 1] Melanoma Institute Australia, Sydney, New South Wales, Australia [2] Departments of Melanoma and Surgical Oncology, Camperdown, New South Wales, Australia [3] Mater Hospital, North Sydney, Sydney, New South Wales, Australia [4] Discipline of Surgery, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Georgina V Long
- 1] Melanoma Institute Australia, Sydney, New South Wales, Australia [2] Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- 1] Melanoma Institute Australia, Sydney, New South Wales, Australia [2] Departments of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia [3] Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter Hersey
- 1] Melanoma Institute Australia, Sydney, New South Wales, Australia [2] Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia [3] Kolling Institute, Royal North Shore Hospital, The University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
19
|
Kakavand H, Vilain R, Wilmott JS, Burke H, Yearley J, Thompson JF, Hersey P, Long GV, Scolyer RA. PD-L1 expression, immune cell correlates, and PD-1+ lymphocytes in sentinel lymph node positive melanoma patients: Implications for adjuvant PD-1 clinical trials. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e20011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Ricardo Vilain
- Tissue Pathology and Diagnostic Oncology, Sydney, Australia
| | - James S Wilmott
- Melanoma Institute Australia; Discipline of Pathology, Sydney Medical School, The University of Sydney, Syndey, Australia
| | - Hazel Burke
- Melanoma Institute Australia, North Sydney, Australia
| | | | - John F Thompson
- Melanoma Institute Australia at Royal Prince Alfred Hospital, The University of Sydney, Sydney, Australia
| | - Peter Hersey
- University of Newcastle, Newcastle, NSW, Australia
| | - Georgina V. Long
- Melanoma Institute Australia and The University of Sydney, North Sydney, Australia
| | - Richard A Scolyer
- Royal Prince Alfred Hospital/Melanoma Institute Australia/University of Sydney, Sydney, Australia
| |
Collapse
|
20
|
Madore J, Vilain RE, Menzies AM, Kakavand H, Wilmott JS, Hyman J, Yearley JH, Kefford RF, Thompson JF, Long GV, Hersey P, Scolyer RA. PD-L1 expression in melanoma shows marked heterogeneity within and between patients: implications for anti-PD-1/PD-L1 clinical trials. Pigment Cell Melanoma Res 2014; 28:245-53. [DOI: 10.1111/pcmr.12340] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/02/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Jason Madore
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
| | - Ricardo E. Vilain
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
- Tissue Pathology and Diagnostic Oncology; Royal Prince Alfred Hospital; Sydney NSW Australia
| | - Alexander M. Menzies
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
| | - Hojabr Kakavand
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
| | - James S. Wilmott
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
| | | | | | - Richard F. Kefford
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
| | - John F. Thompson
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
| | - Georgina V. Long
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
| | - Peter Hersey
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
- Tissue Pathology and Diagnostic Oncology; Royal Prince Alfred Hospital; Sydney NSW Australia
| |
Collapse
|
21
|
Hersey P, Kakavand H, Wilmott J, van der Westhuizen A, Gallagher S, Gowrishankar K, Scolyer R. How anti-PD1 treatments are changing the management of melanoma. Melanoma Manag 2014; 1:165-172. [PMID: 30190821 PMCID: PMC6094707 DOI: 10.2217/mmt.14.14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The introduction of immunotherapy based on the blockade of the PD1/PD-L1 checkpoints has been associated with high response rates and durable remissions of disease in patients with metastatic melanoma, to the extent that it is now considered the standard of care for a wide range of patients, irrespective of their BRAF or NRAS mutation status. In addition, more frequent follow-up of patients who are at high risk of recurrence after surgical treatment appears to be justified, as does neoadjuvant treatments in order to render patients treatable by surgery. The limitations of this treatment include failure of some patients to respond, a low rate of complete responses and relapses of the disease during treatment. New initiatives in order to overcome these limitations include the identification of biomarkers for the selection responders and evaluations of treatment combinations that will increase responses and their durability. The latter includes combinations with antibodies against other checkpoints on T cells and cotreatments with inhibitors of resistance pathways in melanoma.
Collapse
Affiliation(s)
- Peter Hersey
- Kolling Institute, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
- Melanoma Institute of Australia, Rocklands Road, North Sydney, NSW, Australia
| | - Hojabr Kakavand
- Melanoma Institute of Australia, Rocklands Road, North Sydney, NSW, Australia
- Department of Anatomical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - James Wilmott
- Melanoma Institute of Australia, Rocklands Road, North Sydney, NSW, Australia
- Department of Anatomical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Stuart Gallagher
- Kolling Institute, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | | | - Richard Scolyer
- Melanoma Institute of Australia, Rocklands Road, North Sydney, NSW, Australia
- Department of Anatomical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| |
Collapse
|
22
|
Carlino MS, Haydu LE, Kakavand H, Menzies AM, Hamilton AL, Yu B, Ng CC, Cooper WA, Thompson JF, Kefford RF, O'Toole SA, Scolyer RA, Long GV. Correlation of BRAF and NRAS mutation status with outcome, site of distant metastasis and response to chemotherapy in metastatic melanoma. Br J Cancer 2014; 111:292-9. [PMID: 24918823 PMCID: PMC4102942 DOI: 10.1038/bjc.2014.287] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/08/2014] [Accepted: 04/30/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The prognostic significance of BRAF and NRAS mutations in metastatic melanoma patients remains uncertain, with several studies reporting conflicting results, often biased by the inclusion of patients treated with BRAF and MEK (MAPK) inhibitors. We therefore interrogated a historical cohort of patients free of the confounding influence of MAPK inhibitor therapy. METHODS Patients with available archival tissue first diagnosed with metastatic melanoma between 2002 and 2006 were analysed. Mutational analysis was performed using the OncoCarta Panel. Patient characteristics, treatment outcome and survival were correlated with BRAF/NRAS mutation status. RESULTS In 193 patients, 92 (48%) melanomas were BRAF-mutant, 39 (20%) were NRAS-mutant and 62 (32%) were wild-type for BRAF/NRAS mutations (wt). There was no difference in response to chemotherapy based on mutation status (35-37%). The distant disease-free interval (DDFI) was significantly shorter in patients with wt melanoma (27.9 months vs 35.1 for BRAF and 49.1 for NRAS) although this was not significant in multivariate analysis. Survival from stage IV melanoma diagnosis was not significantly different based on mutation status. The DDFI was significantly shorter in patients with BRAF(V600K/R) versus BRAF(V600E) melanoma in univariate and multivariate analyses. CONCLUSIONS BRAF and NRAS mutation status does not influence survival in metastatic melanoma.
Collapse
Affiliation(s)
- M S Carlino
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Westmead Institute for Cancer Research, University of Sydney at Westmead Millennium Institute, Westmead, New South Wales, Australia
- Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, New South Wales, Australia
- Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - L E Haydu
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Discipline of Surgery, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - H Kakavand
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - A M Menzies
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - A L Hamilton
- Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Department of Medical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - B Yu
- Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - C C Ng
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - W A Cooper
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- School of Medicine, University of Western Sydney, Sydney, NSW, Australia
| | - J F Thompson
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Discipline of Surgery, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - R F Kefford
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Westmead Institute for Cancer Research, University of Sydney at Westmead Millennium Institute, Westmead, New South Wales, Australia
- Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, New South Wales, Australia
- Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - S A O'Toole
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- The Kinghorn Cancer Centre and Cancer Program Garvan Institute of Medical Research, Victoria Street, Darlinghurst, New South Wales, Australia
| | - R A Scolyer
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - G V Long
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Discipline of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
23
|
Dutton-Regester K, Kakavand H, Aoude LG, Stark MS, Gartside MG, Johansson P, O'Connor L, Lanagan C, Tembe V, Pupo GM, Haydu LE, Schmidt CW, Mann GJ, Thompson JF, Scolyer RA, Hayward NK. Melanomas of unknown primary have a mutation profile consistent with cutaneous sun-exposed melanoma. Pigment Cell Melanoma Res 2013; 26:852-60. [PMID: 23890154 DOI: 10.1111/pcmr.12153] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/19/2013] [Indexed: 11/29/2022]
Abstract
Melanoma of unknown primary (MUP) is an uncommon phenomenon whereby patients present with metastatic disease without an evident primary site. To determine their likely site of origin, we combined exome sequencing from 33 MUPs to assess the total rate of somatic mutations and degree of UV mutagenesis. An independent cohort of 91 archival MUPs was also screened for 46 hot spot mutations highly prevalent in melanoma including BRAF, NRAS, KIT, GNAQ, and GNA11. Results showed that the majority of MUPs exhibited high somatic mutation rates, high ratios of C>T/G>A transitions, and a high rate of BRAF (45 of 101, 45%) and NRAS (32 of 101, 32%) mutations, collectively indicating a mutation profile consistent with cutaneous sun-exposed melanomas. These data suggest that a significant proportion of MUPs arise from regressed or unrecognized primary cutaneous melanomas or arise de novo in lymph nodes from nevus cells that have migrated from the skin.
Collapse
Affiliation(s)
- Ken Dutton-Regester
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Mar VJ, Wong SQ, Li J, Scolyer RA, McLean C, Papenfuss AT, Tothill RW, Kakavand H, Mann GJ, Thompson JF, Behren A, Cebon JS, Wolfe R, Kelly JW, Dobrovic A, McArthur GA. BRAF/NRAS wild-type melanomas have a high mutation load correlating with histologic and molecular signatures of UV damage. Clin Cancer Res 2013; 19:4589-98. [PMID: 23833303 DOI: 10.1158/1078-0432.ccr-13-0398] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The mutation load in melanoma is generally high compared with other tumor types due to extensive UV damage. Translation of exome sequencing data into clinically relevant information is therefore challenging. This study sought to characterize mutations identified in primary cutaneous melanomas and correlate these with clinicopathologic features. EXPERIMENTAL DESIGN DNA was extracted from 34 fresh-frozen primary cutaneous melanomas and matched peripheral blood. Tumor histopathology was reviewed by two dermatopathologists. Exome sequencing was conducted and mutation rates were correlated with age, sex, tumor site, and histopathologic variables. Differences in mutations between categories of solar elastosis, pigmentation, and BRAF/NRAS mutational status were investigated. RESULTS The average mutation rate was 12 per megabase, similar to published results in metastases. The average mutation rate in severely sun damaged (SSD) skin was 21 per Mb compared with 3.8 per Mb in non-SSD skin (P=0.001). BRAF/NRAS wild-type (WT) tumors had a higher average mutation rate compared with BRAF/NRAS-mutant tumors (27 vs. 5.6 mutations per Mb; P=0.0001). Tandem CC>TT/GG>AA mutations comprised 70% of all dinucleotide substitutions and were more common in tumors arising in SSD skin (P=0.0008) and in BRAF/NRAS WT tumors (P=0.0007). Targetable and potentially targetable mutations in WT tumors, including NF1, KIT, and NOTCH1, were spread over various signaling pathways. CONCLUSION Melanomas arising in SSD skin have higher mutation loads and contain a spectrum of molecular subtypes compared with BRAF- and NRAS-mutant tumors indicating multigene screening approaches and combination therapies may be required for management of these patients.
Collapse
Affiliation(s)
- Victoria J Mar
- Molecular Oncology Laboratory, Oncogenic Signaling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Kakavand H, Scolyer RA, Thompson JF, Mann GJ. Identification of new prognostic biomarkers for Stage III metastatic melanoma patients. Oncoimmunology 2013; 2:e25564. [PMID: 24228228 PMCID: PMC3820811 DOI: 10.4161/onci.25564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 06/27/2013] [Indexed: 11/30/2022] Open
Abstract
Accurately predicting disease outcome among patients bearing Stage III metastatic melanoma is complex. However, current advances in personalized medicine call for ever more precise prognostic assessments, as these have a significant impact not only on the design and analysis of clinical trials, but also on therapeutic decision-making.
Collapse
Affiliation(s)
- Hojabr Kakavand
- Melanoma Institute Australia; North Sydney, NSW Australia ; The University of Sydney; Sydney, NSW Australia
| | | | | | | |
Collapse
|
26
|
Lian CG, Xu Y, Ceol C, Wu F, Larson A, Dresser K, Xu W, Tan L, Hu Y, Zhan Q, Lee CW, Hu D, Lian BQ, Kleffel S, Yang Y, Neiswender J, Khorasani AJ, Fang R, Lezcano C, Duncan LM, Scolyer RA, Thompson JF, Kakavand H, Houvras Y, Zon LI, Mihm MC, Kaiser UB, Schatton T, Woda BA, Murphy GF, Shi YG. Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 2012; 150:1135-46. [PMID: 22980977 DOI: 10.1016/j.cell.2012.07.033] [Citation(s) in RCA: 581] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 05/09/2012] [Accepted: 07/03/2012] [Indexed: 12/13/2022]
Abstract
DNA methylation at the 5 position of cytosine (5-mC) is a key epigenetic mark that is critical for various biological and pathological processes. 5-mC can be converted to 5-hydroxymethylcytosine (5-hmC) by the ten-eleven translocation (TET) family of DNA hydroxylases. Here, we report that "loss of 5-hmC" is an epigenetic hallmark of melanoma, with diagnostic and prognostic implications. Genome-wide mapping of 5-hmC reveals loss of the 5-hmC landscape in the melanoma epigenome. We show that downregulation of isocitrate dehydrogenase 2 (IDH2) and TET family enzymes is likely one of the mechanisms underlying 5-hmC loss in melanoma. Rebuilding the 5-hmC landscape in melanoma cells by reintroducing active TET2 or IDH2 suppresses melanoma growth and increases tumor-free survival in animal models. Thus, our study reveals a critical function of 5-hmC in melanoma development and directly links the IDH and TET activity-dependent epigenetic pathway to 5-hmC-mediated suppression of melanoma progression, suggesting a new strategy for epigenetic cancer therapy.
Collapse
Affiliation(s)
- Christine Guo Lian
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|