41 results on '"Glodzik, D"'
Search Results
2. Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancers
- Author
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Głodzik, D., Purdie, C., Rye, I.H., Simpson, P.T., Staaf, J., Span, P.N., Russnes, H.G., and Nik-Zainal, S.
- Published
- 2018
- Full Text
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3. CDK12 loss leads to replication stress and sensitivity to combinations of the ATR inhibitor camonsertib (RP-3500) with PARP inhibitors
- Author
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Setton, J., primary, Gallo, D., additional, Glodzik, D., additional, Kaiser, B., additional, Braverman, S., additional, Ubhi, T., additional, Fournier, S., additional, Selenica, P., additional, Laterreur, N., additional, Roulston, A., additional, Brown, G., additional, Morris, S., additional, Reis-Filho, J., additional, and Zimmermann, M., additional
- Published
- 2022
- Full Text
- View/download PDF
4. Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- Author
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Bailey M. H., Meyerson W. U., Dursi L. J., Wang L. -B., Dong G., Liang W. -W., Weerasinghe A., Li S., Li Y., Kelso S., Akbani R., Anur P., Buchanan A., Chiotti K., Covington K., Creason A., Ding L., Ellrott K., Fan Y., Foltz S., Getz G., Hale W., Haussler D., Hess J. M., Hutter C. M., Kandoth C., Kasaian K., Kasapi M., Larson D., Leshchiner I., Letaw J., Ma S., McLellan M. D., Men Y., Mills G. B., Niu B., Peto M., Radenbaugh A., Reynolds S. M., Saksena G., Sofia H., Stewart C., Struck A. J., Stuart J. M., Wang W., Weinstein J. N., Wheeler D. A., Wong C. K., Xi L., Ye K., Bieg M., Boutros P. C., Buchhalter I., Butler A. P., Chen K., Chong Z., Drechsel O., Jonathan Dursi L., Eils R., Espiritu S. M. G., Fulton R. S., Gao S., Gelpi J. L., Gerstein M. B., Gonzalez S., Gut I. G., Hach F., Heinold M. C., Hinton J., Hu T., Huang V., Huang Y., Hutter B., Jones D. R., Jung J., Jager N., Kim H. -L., Kleinheinz K., Kumar S., Kumar Y., Lalansingh C. M., Letunic I., Livitz D., Ma E. Z., Maruvka Y. E., Mashl R. J., Menzies A., Milovanovic A., Nielsen M. M., Ossowski S., Paramasivam N., Pedersen J. S., Perry M. D., Puiggros M., Raine K. M., Rheinbay E., Royo R., Sahinalp S. C., Sarrafi I., Schlesner M., Simpson J. T., Stebbings L., Stobbe M. D., Teague J. W., Tiao G., Torrents D., Wala J. A., Wang J., Waszak S. M., Weischenfeldt J., Wendl M. C., Werner J., Wu Z., Xue H., Yakneen S., Yamaguchi T. N., Yellapantula V. D., Yung C. K., Zhang J., Aaltonen L. A., Abascal F., Abeshouse A., Aburatani H., Adams D. J., Agrawal N., Ahn K. S., Ahn S. -M., Aikata H., Akdemir K. C., Al-Ahmadie H., Al-Sedairy S. T., Al-Shahrour F., Alawi M., Albert M., Aldape K., Alexandrov L. B., Ally A., Alsop K., Alvarez E. G., Amary F., Amin S. B., Aminou B., Ammerpohl O., Anderson M. J., Ang Y., Antonello D., Aparicio S., Appelbaum E. L., Arai Y., Aretz A., Arihiro K., Ariizumi S. -I., Armenia J., Arnould L., Asa S., Assenov Y., Atwal G., Aukema S., Auman J. T., Aure M. R., Awadalla P., Aymerich M., Bader G. D., Baez-Ortega A., Bailey P. J., Balasundaram M., Balu S., Bandopadhayay P., Banks R. E., Barbi S., Barbour A. P., Barenboim J., Barnholtz-Sloan J., Barr H., Barrera E., Bartlett J., Bartolome J., Bassi C., Bathe O. F., Baumhoer D., Bavi P., Baylin S. B., Bazant W., Beardsmore D., Beck T. A., Behjati S., Behren A., Bell C., Beltran S., Benz C., Berchuck A., Bergmann A. K., Bergstrom E. N., Berman B. P., Berney D. M., Bernhart S. H., Beroukhim R., Berrios M., Bersani S., Bertl J., Betancourt M., Bhandari V., Bhosle S. G., Biankin A. V., Bigner D., Binder H., Birney E., Birrer M., Biswas N. K., Bjerkehagen B., Bodenheimer T., Boice L., Bonizzato G., De Bono J. S., Boot A., Bootwalla M. S., Borg A., Borkhardt A., Boroevich K. A., Borozan I., Borst C., Bosenberg M., Bosio M., Boultwood J., Bourque G., Bova G. S., Bowen D. T., Bowlby R., Bowtell D. D. L., Boyault S., Boyce R., Boyd J., Brazma A., Brennan P., Brewer D. S., Brinkman A. B., Bristow R. G., Broaddus R. R., Brock J. E., Brock M., Broeks A., Brooks A. N., Brooks D., Brors B., Brunak S., Bruxner T. J. C., Bruzos A. L., Buchholz C., Bullman S., Burke H., Burkhardt B., Burns K. H., Busanovich J., Bustamante C. D., Butte A. J., Byrne N. J., Borresen-Dale A. -L., Caesar-Johnson S. J., Cafferkey A., Cahill D., Calabrese C., Caldas C., Calvo F., Camacho N., Campbell P. J., Campo E., Cantu C., Cao S., Carey T. E., Carlevaro-Fita J., Carlsen R., Cataldo I., Cazzola M., Cebon J., Cerfolio R., Chadwick D. E., Chakravarty D., Chalmers D., Chan C. W. Y., Chan K., Chan-Seng-Yue M., Chandan V. S., Chang D. K., Chanock S. J., Chantrill L. A., Chateigner A., Chatterjee N., Chayama K., Chen H. -W., Chen J., Chen Y., Chen Z., Cherniack A. D., Chien J., Chiew Y. -E., Chin S. -F., Cho J., Cho S., Choi J. K., Choi W., Chomienne C., Choo S. P., Chou A., Christ A. N., Christie E. L., Chuah E., Cibulskis C., Cibulskis K., Cingarlini S., Clapham P., Claviez A., Cleary S., Cloonan N., Cmero M., Collins C. C., Connor A. A., Cooke S. L., Cooper C. S., Cope L., Corbo V., Cordes M. G., Cordner S. M., Cortes-Ciriano I., Cowin P. A., Craft B., Craft D., Creighton C. J., Cun Y., Curley E., Cutcutache I., Czajka K., Czerniak B., Dagg R. A., Danilova L., Davi M. V., Davidson N. R., Davies H., Davis I. J., Davis-Dusenbery B. N., Dawson K. J., De La Vega F. M., De Paoli-Iseppi R., Defreitas T., Dei Tos A. P., Delaneau O., Demchok J. A., Demeulemeester J., Demidov G. M., Demircioglu D., Dennis N. M., Denroche R. E., Dentro S. C., Desai N., Deshpande V., Deshwar A. G., Desmedt C., Deu-Pons J., Dhalla N., Dhani N. C., Dhingra P., Dhir R., DiBiase A., Diamanti K., Ding S., Dinh H. Q., Dirix L., Doddapaneni H. V., Donmez N., Dow M. T., Drapkin R., Drews R. M., Serge S., Dudderidge T., Dueso-Barroso A., Dunford A. J., Dunn M., Duthie F. R., Dutton-Regester K., Eagles J., Easton D. F., Edmonds S., Edwards P. A., Edwards S. E., Eeles R. A., Ehinger A., Eils J., El-Naggar A., Eldridge M., Erkek S., Escaramis G., Estivill X., Etemadmoghadam D., Eyfjord J. E., Faltas B. M., Fan D., Faquin W. C., Farcas C., Fassan M., Fatima A., Favero F., Fayzullaev N., Felau I., Fereday S., Ferguson M. L., Ferretti V., Feuerbach L., Field M. A., Fink J. L., Finocchiaro G., Fisher C., Fittall M. W., Fitzgerald A., Fitzgerald R. C., Flanagan A. M., Fleshner N. E., Flicek P., Foekens J. A., Fong K. M., Fonseca N. A., Foster C. S., Fox N. S., Fraser M., Frazer S., Frenkel-Morgenstern M., Friedman W., Frigola J., Fronick C. C., Fujimoto A., Fujita M., Fukayama M., Fulton L. A., Furuta M., Futreal P. A., Fullgrabe A., Gabriel S. B., Gallinger S., Gambacorti Passerini C., Gao J., Garraway L., Garred O., Garrison E., Garsed D. W., Gehlenborg N., George J., Gerhard D. S., Gerhauser C., Gershenwald J. E., Gerstung M., Ghori M., Ghossein R., Giama N. H., Gibbs R. A., Gill A. J., Gill P., Giri D. D., Glodzik D., Gnanapragasam V. J., Goebler M. E., Goldman M. J., Gomez C., Gonzalez-Perez A., Gordenin D. A., Gossage J., Gotoh K., Govindan R., Grabau D., Graham J. S., Grant R. C., Green A. R., Green E., Greger L., Grehan N., Grimaldi S., Grimmond S. M., Grossman R. L., Grundhoff A., Gundem G., Guo Q., Gupta M., Gupta S., Gut M., Goke J., Ha G., Haake A., Haan D., Haas S., Haase K., Haber J. E., Habermann N., Haider S., Hama N., Hamdy F. C., Hamilton A., Hamilton M. P., Han L., Hanna G. B., Hansmann M., Haradhvala N. J., Harismendy O., Harliwong I., Harmanci A. O., Harrington E., Hasegawa T., Hawkins S., Hayami S., Hayashi S., Hayes D. N., Hayes S. J., Hayward N. K., Hazell S., He Y., Heath A. P., Heath S. C., Hedley D., Hegde A. M., Heiman D. I., Heins Z., Heisler L. E., Hellstrom-Lindberg E., Helmy M., Heo S. G., Hepperla A. J., Heredia-Genestar J. M., Herrmann C., Hersey P., Hilmarsdottir H., Hirano S., Hiraoka N., Hoadley K. A., Hobolth A., Hodzic E., Hoell J. I., Hoffmann S., Hofmann O., Holbrook A., Holik A. Z., Hollingsworth M. A., Holmes O., Holt R. A., Hong C., Hong E. P., Hong J. H., Hooijer G. K., Hornshoj H., Hosoda F., Hou Y., Hovestadt V., Howat W., Hoyle A. P., Hruban R. H., Hu J., Hua X., Huang K. -L., Huang M., Huang M. N., Huber W., Hudson T. J., Hummel M., Hung J. A., Huntsman D., Hupp T. R., Huse J., Huska M. R., Hubschmann D., Iacobuzio-Donahue C. A., Imbusch C. D., Imielinski M., Imoto S., Isaacs W. B., Isaev K., Ishikawa S., Iskar M., Islam S. M. A., Ittmann M., Ivkovic S., Izarzugaza J. M. G., Jacquemier J., Jakrot V., Jamieson N. B., Jang G. H., Jang S. J., Jayaseelan J. C., Jayasinghe R., Jefferys S. R., Jegalian K., Jennings J. L., Jeon S. -H., Jerman L., Ji Y., Jiao W., Johansson P. A., Johns A. L., Johns J., Johnson R., Johnson T. A., Jolly C., Joly Y., Jonasson J. G., Jones C. D., Jones D. T. W., Jones N., Jones S. J. M., Jonkers J., Ju Y. S., Juhl H., Juul M., Juul R. I., Juul S., Kabbe R., Kahles A., Kahraman A., Kaiser V. B., Kakavand H., Kalimuthu S., von Kalle C., Kang K. J., Karaszi K., Karlan B., Karlic R., Karsch D., Kassahn K. S., Katai H., Kato M., Katoh H., Kawakami Y., Kay J. D., Kazakoff S. H., Kazanov M. D., Keays M., Kebebew E., Kefford R. F., Kellis M., Kench J. G., Kennedy C. J., Kerssemakers J. N. A., Khoo D., Khoo V., Khuntikeo N., Khurana E., Kilpinen H., Kim H. K., Kim H. -Y., Kim H., Kim J., Kim J. K., Kim Y., King T. A., Klapper W., Klimczak L. J., Knappskog S., Kneba M., Knoppers B. M., Koh Y., Jan Komorowski, Komura D., Komura M., Kong G., Kool M., Korbel J. O., 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., Kundra R., Kubler K., Kuppers R., Lagergren J., Lai P. H., Laird P. W., Lakhani S. R., Lalonde E., Lamaze F. C., Lambert A., Lander E., Landgraf P., Landoni L., Langerod A., Lanzos A., Larsimont D., Larsson E., Lathrop M., Lau L. M. S., Lawerenz C., Lawlor R. T., Lawrence M. S., Lazar A. J., Le X., Lee D., Lee E. A., Lee H. J., Lee J. J. -K., Lee J. -Y., Lee J., Lee M. T. M., Lee-Six H., Lehmann K. -V., Lehrach H., Lenze D., Leonard C. R., Leongamornlert D. A., Letourneau L., Levine D. A., Lewis L., Ley T., Li C., Li C. H., Li H. I., Li J., Li L., Li X., Liang H., Liang S. -B., Lichter P., Lin P., Lin Z., Linehan W. M., Lingjaerde O. C., Liu D., Liu E. M., Liu F. -F., Liu F., Liu J., Liu X., Livingstone J., Livni N., Lochovsky L., Loeffler M., Long G. V., Lopez-Guillermo A., Lou S., Louis D. N., Lovat L. B., Lu Y., Lu Y. -J., Luchini C., Lungu I., Luo X., Luxton H. J., Lynch A. G., Lype L., Lopez C., Lopez-Otin C., Ma Y., MacGrogan G., MacRae S., Macintyre G., Madsen T., Maejima K., Mafficini A., Maglinte D. T., Maitra A., Majumder P. P., Malcovati L., Malikic S., Malleo G., Mann G. J., Mantovani-Loffler L., Marchal K., Marchegiani G., Mardis E. R., Margolin A. A., Marin M. G., Markowetz F., Markowski J., Marks J., Marques-Bonet T., Marra M. A., Marsden L., Martens J. W. M., Martin S., Martin-Subero J. I., Martincorena I., Martinez-Fundichely A., Massie C. E., Matthew T. J., Matthews L., Mayer E., Mayes S., Mayo M., Mbabaali F., McCune K., McDermott U., McGillivray P. D., McPherson J. D., McPherson J. R., McPherson T. A., Meier S. R., Meng A., Meng S., Merrett N. D., Merson S., Meyerson M., Mieczkowski P. A., Mihaiescu G. L., Mijalkovic S., Mijalkovic-Lazic A. M., Mikkelsen T., Milella M., Mileshkin L., Miller C. A., Miller D. K., Miller J. K., Minner S., Miotto M., Arnau G. M., Mirabello L., Mitchell C., Mitchell T. J., Miyano S., Miyoshi N., Mizuno S., Molnar-Gabor F., Moore M. J., Moore R. A., Morganella S., Morris Q. D., Morrison C., Mose L. E., Moser C. D., Muinos F., Mularoni L., Mungall A. J., Mungall K., Musgrove E. A., Mustonen V., Mutch D., Muyas F., Muzny D. M., Munoz A., Myers J., Myklebost O., Moller P., Nagae G., Nagrial A. M., Nahal-Bose H. K., Nakagama H., Nakagawa H., Nakamura H., Nakamura T., Nakano K., Nandi T., Nangalia J., Nastic M., Navarro A., Navarro F. C. P., Neal D. E., Nettekoven G., Newell F., Newhouse S. J., Newton Y., Ng A. W. T., Ng A., Nicholson J., Nicol D., Nie Y., Nielsen G. P., Nik-Zainal S., Noble M. S., Nones K., Northcott P. A., Notta F., O'Connor B. D., O'Donnell P., O'Donovan M., O'Meara S., O'Neill B. P., O'Neill J. R., Ocana D., Ochoa A., Oesper L., Ogden C., Ohdan H., Ohi K., Ohno-Machado L., Oien K. A., Ojesina A. I., Ojima H., Okusaka T., Omberg L., Ong C. K., Ott G., Ouellette B. F. F., P'ng C., Paczkowska M., Paiella S., Pairojkul C., Pajic M., Pan-Hammarstrom Q., Papaemmanuil E., Papatheodorou I., Park J. W., Park J. -W., Park K., Park P. J., Parker J. S., Parsons S. L., Pass H., Pasternack D., Pastore A., Patch A. -M., Pauporte I., Pea A., Pearson J. V., Pedamallu C. S., Pederzoli P., Peifer M., Pennell N. A., Perou C. M., Petersen G. M., Petrelli N., Petryszak R., Pfister S. M., Phillips M., Pich O., Pickett H. A., Pihl T. D., Pillay N., Pinder S., Pinese M., Pinho A. V., Pitkanen E., Pivot X., Pineiro-Yanez E., Planko L., Plass C., Polak P., Pons T., Popescu I., Potapova O., Prasad A., Preston S. R., Prinz M., Pritchard A. L., Prokopec S. D., Provenzano E., Puente X. S., Puig S., Pulido-Tamayo S., Pupo G. M., Purdie C. A., Quinn M. C., Rabionet R., Rader J. S., Radlwimmer B., Radovic P., Raeder B., Ramakrishna M., Ramakrishnan K., Ramalingam S., Raphael B. J., Rathmell W. K., Rausch T., Reifenberger G., Reimand J., Reis-Filho J., Reuter V., Reyes-Salazar I., Reyna M. A., Riazalhosseini Y., Richardson A. L., Richter J., Ringel M., Ringner M., Rino Y., Rippe K., Roach J., Roberts L. R., Roberts N. D., Roberts S. A., Robertson A. G., Robertson A. J., Rodriguez J. B., Rodriguez-Martin B., Rodriguez-Gonzalez F. G., Roehrl M. H. A., Rohde M., Rokutan H., Romieu G., Rooman I., Roques T., Rosebrock D., Rosenberg M., Rosenstiel P. C., Rosenwald A., Rowe E. W., Rozen S. G., Rubanova Y., Rubin M. A., Rubio-Perez C., Rudneva V. A., Rusev B. C., Ruzzenente A., Ratsch G., Sabarinathan R., Sabelnykova V. Y., Sadeghi S., Saini N., Saito-Adachi M., Salcedo A., Salgado R., Salichos L., Sallari R., Saller C., Salvia R., Sam M., Samra J. S., Sanchez-Vega F., Sander C., Sanders G., Sarin R., Sasaki-Oku A., Sauer T., Sauter G., Saw R. P. M., Scardoni M., Scarlett C. J., Scarpa A., Scelo G., Schadendorf D., Schein J. E., Schilhabel M. B., Schlomm T., Schmidt H. K., Schramm S. -J., Schreiber S., Schultz N., Schumacher S. E., Schwarz R. F., Scolyer R. A., Scott D., Scully R., Seethala R., Segre A. V., Selander I., Semple C. A., Senbabaoglu Y., Sengupta S., Sereni E., Serra S., Sgroi D. C., Shackleton M., Shah N. C., Shahabi S., Shang C. A., Shang P., Shapira O., Shelton T., Shen C., Shen H., Shepherd R., Shi R., Shi Y., Shiah Y. -J., Shibata T., Shih J., Shimizu E., Shimizu K., Shin S. J., Shiraishi Y., Shmaya T., Shmulevich I., Shorser S. I., Short C., Shrestha R., Shringarpure S. S., Shriver C., Shuai S., Sidiropoulos N., Siebert R., Sieuwerts A. M., Sieverling L., Signoretti S., Sikora K. O., Simbolo M., Simon R., Simons J. V., Singer S., Sinnott-Armstrong N., Sipahimalani P., Skelly T. J., Smid M., Smith J., Smith-McCune K., Socci N. D., Sofia H. J., Soloway M. G., Song L., Sood A. K., Sothi S., Sotiriou C., Soulette C. M., Span P. N., Spellman P. T., Sperandio N., Spillane A. J., Spiro O., Spring J., Staaf J., Stadler P. F., Staib P., Stark S. G., Stefansson O. A., Stegle O., Stein L. D., Stenhouse A., Stilgenbauer S., Stratton M. R., Stretch J. R., Stunnenberg H. G., Su H., Su X., Sun R. X., Sungalee S., Susak H., Suzuki A., Sweep F., Szczepanowski M., Sultmann H., Yugawa T., Tam A., Tamborero D., Tan B. K. T., Tan D., Tan P., Tanaka H., Taniguchi H., Tanskanen T. J., Tarabichi M., Tarnuzzer R., Tarpey P., Taschuk M. L., Tatsuno K., Tavare S., Taylor D. F., Taylor-Weiner A., Teh B. T., Tembe V., Temes J., Thai K., Thayer S. P., Thiessen N., Thomas G., Thomas S., Thompson A., Thompson A. M., Thompson J. F., Thompson R. H., Thorne H., Thorne L. B., Thorogood A., Tijanic N., Timms L. E., Tirabosco R., Tojo M., Tommasi S., Toon C. W., Toprak U. H., Tortora G., Tost J., Totoki Y., Townend D., Traficante N., Treilleux I., Trotta J. -R., Trumper L. H. P., Tsao M., Tsunoda T., Tubio J. M. C., Tucker O., Turkington R., Turner D. J., Tutt A., Ueno M., Ueno N. T., Umbricht C., Umer H. M., Underwood T. J., Urban L., Urushidate T., Ushiku T., Uuskula-Reimand L., Valencia A., Van Den Berg D. J., Van Laere S., Van Loo P., Van Meir E. G., Van den Eynden G. G., Van der Kwast T., Vasudev N., Vazquez M., Vedururu R., Veluvolu U., Vembu S., Verbeke L. P. C., Vermeulen P., Verrill C., Viari A., Vicente D., Vicentini C., Raghavan K. V., Viksna J., Vilain R. E., Villasante I., Vincent-Salomon A., Visakorpi T., Voet D., Vyas P., Vazquez-Garcia I., Waddell N. M., Waddell N., Wadelius C., Wadi L., Wagener R., Wang L., Wang Q., Wang Y., Wang Z., Waring P. M., Warnatz H. -J., Warrell J., Warren A. Y., Wedge D. C., Weichenhan D., Weinberger P., Weisenberger D. J., Welch I., Whalley J. P., Whitaker H. C., Wigle D., Wilkerson M. D., Williams A., Wilmott J. S., Wilson G. W., Wilson J. M., Wilson R. K., Winterhoff B., Wintersinger J. A., Wiznerowicz M., Wolf S., Wong B. H., Wong T., Wong W., Woo Y., Wood S., Wouters B. G., Wright A. J., Wright D. W., Wright M. H., Wu C. -L., Wu D. -Y., Wu G., Wu J., Wu K., Wu Y., Xia T., Xiang Q., Xiao X., Xing R., Xiong H., Xu Q., Xu Y., Yachida S., Yamaguchi R., Yamamoto M., Yamamoto S., Yamaue H., Yang F., Yang H., Yang J. Y., Yang L., Yang S., Yang T. -P., Yang Y., Yao X., Yaspo M. -L., Yates L., Yau C., Ye C., Yoon C. J., Yoon S. -S., Yousif F., Yu J., Yu K., Yu W., Yu Y., Yuan K., Yuan Y., Yuen D., Zaikova O., Zamora J., Zapatka M., Zenklusen J. C., Zenz T., Zeps N., Zhang C. -Z., Zhang F., Zhang H., Zhang X., Zhang Y., Zhang Z., Zhao Z., Zheng L., Zheng X., Zhou W., Zhou Y., Bin Zhu, Zhu H., Zhu J., Zhu S., Zou L., Zou X., deFazio A., van As N., van Deurzen C. H. M., van de Vijver M. J., van't Veer L., von Mering C., Bailey, M, Meyerson, W, Dursi, L, Wang, L, Dong, G, Liang, W, Weerasinghe, A, Li, S, Li, Y, Kelso, S, Akbani, R, Anur, P, Buchanan, A, Chiotti, K, Covington, K, Creason, A, Ding, L, Ellrott, K, Fan, Y, Foltz, S, Getz, G, Hale, W, Haussler, D, Hess, J, Hutter, C, Kandoth, C, Kasaian, K, Kasapi, M, Larson, D, Leshchiner, I, Letaw, J, Ma, S, Mclellan, M, Men, Y, Mills, G, Niu, B, Peto, M, Radenbaugh, A, Reynolds, S, Saksena, G, Sofia, H, Stewart, C, Struck, A, Stuart, J, Wang, W, Weinstein, J, Wheeler, D, Wong, C, Xi, L, Ye, K, Bieg, M, Boutros, P, Buchhalter, I, Butler, A, Chen, K, Chong, Z, Drechsel, O, Jonathan Dursi, L, Eils, R, Espiritu, S, Fulton, R, Gao, S, Gelpi, J, Gerstein, M, Gonzalez, S, Gut, I, Hach, F, Heinold, M, Hinton, J, Hu, T, Huang, V, Huang, Y, Hutter, B, Jones, D, Jung, J, Jager, N, Kim, H, Kleinheinz, K, Kumar, S, Kumar, Y, Lalansingh, C, Letunic, I, Livitz, D, Ma, E, Maruvka, Y, Mashl, R, Menzies, A, Milovanovic, A, Nielsen, M, 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Science ,MEDLINE ,Medizin ,General Physics and Astronomy ,Pain ,610 Medicine & health ,1600 General Chemistry ,Computational biology ,Biology ,10 kHz spinal cord stimulation ,Genome ,responders ,MC3 Working Group ,General Biochemistry, Genetics and Molecular Biology ,whole exome sequencing ,Machine Learning ,1300 General Biochemistry, Genetics and Molecular Biology ,PCAWG novel somatic mutation calling methods working group ,medicine ,cancer ,Genome mutation ,Exome ,Exome sequencing ,Whole genome sequencing ,whole genome sequencing ,Multidisciplinary ,Published Erratum ,Cancer ,PCAWG Consortium ,General Chemistry ,medicine.disease ,3100 General Physics and Astronomy ,oncology ,10032 Clinic for Oncology and Hematology ,Prediction - Abstract
Weitere Nicht-UDE-Autoren sind nicht genannt. Originalpublikation: 10.1038/s41467-020-18151-y. CA extern The original version of this Article omitted from the author list the 9th author Yize Li, who is from the ‘The McDonnell Genome Institute at Washington University, St. Louis, MO 63108, USA and Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA’. This has been corrected in both the PDF and HTML versions of the Article. © 2020, The Author(s).
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- 2020
5. Sex differences in oncogenic mutational processes
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Li C. H., Prokopec S. D., Sun R. X., Yousif F., Schmitz N., Al-Shahrour F., Atwal G., Bailey P. J., Biankin A. V., Boutros P. C., Campbell P. J., Chang D. K., Cooke S. L., Deshpande V., Faltas B. M., Faquin W. C., Garraway L., Getz G., Grimmond S. M., Haider S., Hoadley K. A., Jiao W., Kaiser V. B., Karlic R., Kato M., Kubler K., Lazar A. J., Louis D. N., Margolin A., Martin S., Nahal-Bose H. K., Nielsen G. P., Nik-Zainal S., Omberg L., P'ng C., Perry M. D., Polak P., Rheinbay E., Rubin M. A., Semple C. A., Sgroi D. C., Shibata T., Siebert R., Smith J., Stein L. D., Stobbe M. D., Thai K., Wright D. W., Wu C. -L., Yuan K., Zhang J., Aaltonen L. A., Abascal F., Abeshouse A., Aburatani H., Adams D. J., Agrawal N., Ahn K. S., Ahn S. -M., Aikata H., Akbani R., Akdemir K. C., Al-Ahmadie H., Al-Sedairy S. T., Alawi M., Albert M., Aldape K., Alexandrov L. B., Ally A., Alsop K., Alvarez E. G., Amary F., Amin S. B., Aminou B., Ammerpohl O., Anderson M. J., Ang Y., Antonello D., Anur P., Aparicio S., Appelbaum E. L., Arai Y., Aretz A., Arihiro K., Ariizumi S. -I., Armenia J., Arnould L., Asa S., Assenov Y., Aukema S., Auman J. T., Aure M. R., Awadalla P., Aymerich M., Bader G. D., Baez-Ortega A., Bailey M. H., Balasundaram M., Balu S., Bandopadhayay P., Banks R. E., Barbi S., Barbour A. P., Barenboim J., Barnholtz-Sloan J., Barr H., Barrera E., Bartlett J., Bartolome J., Bassi C., Bathe O. F., Baumhoer D., Bavi P., Baylin S. B., Bazant W., Beardsmore D., Beck T. A., Behjati S., Behren A., Niu B., Bell C., Beltran S., Benz C., Berchuck A., Bergmann A. K., Bergstrom E. N., Berman B. P., Berney D. M., Bernhart S. H., Beroukhim R., Berrios M., Bersani S., Bertl J., Betancourt M., Bhandari V., Bhosle S. G., Bieg M., Bigner D., Binder H., Birney E., Birrer M., Biswas N. K., Bjerkehagen B., Bodenheimer T., Boice L., Bonizzato G., De Bono J. S., Boot A., Bootwalla M. S., Borg A., Borkhardt A., Boroevich K. A., Borozan I., Borst C., Bosenberg M., Bosio M., Boultwood J., Bourque G., Bova G. S., Bowen D. T., Bowlby R., Bowtell D. D. L., Boyault S., Boyce R., Boyd J., Brazma A., Brennan P., Brewer D. S., Brinkman A. B., Bristow R. G., Broaddus R. R., Brock J. E., Brock M., Broeks A., Brooks A. N., Brooks D., Brors B., Brunak S., Bruxner T. J. C., Bruzos A. L., Buchanan A., Buchhalter I., Buchholz C., Bullman S., Burke H., Burkhardt B., Burns K. H., Busanovich J., Bustamante C. D., Butler A. P., Butte A. J., Byrne N. J., Borresen-Dale A. -L., Caesar-Johnson S. J., Cafferkey A., Cahill D., Calabrese C., Caldas C., Calvo F., Camacho N., Campo E., Cantu C., Cao S., Carey T. E., Carlevaro-Fita J., Carlsen R., Cataldo I., Cazzola M., Cebon J., Cerfolio R., Chadwick D. E., Chakravarty D., Chalmers D., Chan C. W. Y., Chan K., Chan-Seng-Yue M., Chandan V. S., Chanock S. J., Chantrill L. A., Chateigner A., Chatterjee N., Chayama K., Chen H. -W., Chen J., Chen K., Chen Y., Chen Z., Cherniack A. D., Chien J., Chiew Y. -E., Chin S. -F., Cho J., Cho S., Choi J. K., Choi W., Chomienne C., Chong Z., Choo S. P., Chou A., Christ A. N., Christie E. L., Chuah E., Cibulskis C., Cibulskis K., Cingarlini S., Clapham P., Claviez A., Cleary S., Cloonan N., Cmero M., Collins C. C., Connor A. A., Cooper C. S., Cope L., Corbo V., Cordes M. G., Cordner S. M., Cortes-Ciriano I., Covington K., Cowin P. A., Craft B., Craft D., Creighton C. J., Cun Y., Curley E., Cutcutache I., Czajka K., Czerniak B., Dagg R. A., Danilova L., Davi M. V., Davidson N. R., Davies H., Davis I. J., Davis-Dusenbery B. N., Dawson K. J., De La Vega F. M., De Paoli-Iseppi R., Defreitas T., Dei Tos A. P., Delaneau O., Demchok J. A., Demeulemeester J., Demidov G. M., Demircioglu D., Dennis N. M., Denroche R. E., Dentro S. C., Desai N., Deshwar A. G., Desmedt C., Deu-Pons J., Dhalla N., Dhani N. C., Dhingra P., Dhir R., DiBiase A., Diamanti K., Ding L., Ding S., Dinh H. Q., Dirix L., Doddapaneni H. V., Donmez N., Dow M. T., Drapkin R., Drechsel O., Drews R. M., Serge S., Dudderidge T., Dueso-Barroso A., Dunford A. J., Dunn M., Dursi L. J., Duthie F. R., Dutton-Regester K., Eagles J., Easton D. F., Edmonds S., Edwards P. A., Edwards S. E., Eeles R. A., Ehinger A., Eils J., Eils R., El-Naggar A., Eldridge M., Ellrott K., Erkek S., Escaramis G., Espiritu S. M. G., Estivill X., Etemadmoghadam D., Eyfjord J. E., Fan D., Fan Y., Farcas C., Fassan M., Fatima A., Favero F., Fayzullaev N., Felau I., Fereday S., Ferguson M. L., Ferretti V., Feuerbach L., Field M. A., Fink J. L., Finocchiaro G., Fisher C., Fittall M. W., Fitzgerald A., Fitzgerald R. C., Flanagan A. M., Fleshner N. E., Flicek P., Foekens J. A., Fong K. M., Fonseca N. A., Foster C. S., Fox N. S., Fraser M., Frazer S., Frenkel-Morgenstern M., Friedman W., Frigola J., Fronick C. C., Fujimoto A., Fujita M., Fukayama M., Fulton L. A., Fulton R. S., Furuta M., Futreal P. A., Fullgrabe A., Gabriel S. B., Gallinger S., Gambacorti Passerini C., Gao J., Gao S., Garred O., Garrison E., Garsed D. W., Gehlenborg N., Gelpi J. L. L., George J., Gerhard D. S., Gerhauser C., Gershenwald J. E., Gerstein M., Gerstung M., Ghori M., Ghossein R., Giama N. H., Gibbs R. A., Gill A. J., Gill P., Giri D. D., Glodzik D., Gnanapragasam V. J., Goebler M. E., Goldman M. J., Gomez C., Gonzalez S., Gonzalez-Perez A., Gordenin D. A., Gossage J., Gotoh K., Govindan R., Grabau D., Graham J. S., Grant R. C., Green A. R., Green E., Greger L., Grehan N., Grimaldi S., Grossman R. L., Grundhoff A., Gundem G., Guo Q., Gupta M., Gupta S., Gut I. G., Gut M., Goke J., Ha G., Haake A., Haan D., Haas S., Haase K., Haber J. E., Habermann N., Hach F., Hama N., Hamdy F. C., Hamilton A., Hamilton M. P., Han L., Hanna G. B., Hansmann M., Haradhvala N. J., Harismendy O., Harliwong I., Harmanci A. O., Harrington E., Hasegawa T., Haussler D., Hawkins S., Hayami S., Hayashi S., Hayes D. N., Hayes S. J., Hayward N. K., Hazell S., He Y., Heath A. P., Heath S. C., Hedley D., Hegde A. M., Heiman D. I., Heinold M. C., Heins Z., Heisler L. E., Hellstrom-Lindberg E., Helmy M., Heo S. G., Hepperla A. J., Heredia-Genestar J. M., Herrmann C., Hersey P., Hess J. M., Hilmarsdottir H., Hinton J., Hirano S., Hiraoka N., Hobolth A., Hodzic E., Hoell J. I., Hoffmann S., Hofmann O., Holbrook A., Holik A. Z., Hollingsworth M. A., Holmes O., Holt R. A., Hong C., Hong E. P., Hong J. H., Hooijer G. K., Hornshoj H., Hosoda F., Hou Y., Hovestadt V., Howat W., Hoyle A. P., Hruban R. H., Hu J., Hu T., Hua X., Huang K. -L., Huang M., Huang M. N., Huang V., Huang Y., Huber W., Hudson T. J., Hummel M., Hung J. A., Huntsman D., Hupp T. R., Huse J., Huska M. R., Hutter B., Hutter C. M., Hubschmann D., Iacobuzio-Donahue C. A., Imbusch C. D., Imielinski M., Imoto S., Isaacs W. B., Isaev K., Ishikawa S., Iskar M., Islam S. M. A., Ittmann M., Ivkovic S., Izarzugaza J. M. G., Jacquemier J., Jakrot V., Jamieson N. B., Jang G. H., Jang S. J., Jayaseelan J. C., Jayasinghe R., Jefferys S. R., Jegalian K., Jennings J. L., Jeon S. -H., Jerman L., Ji Y., Johansson P. A., Johns A. L., Johns J., Johnson R., Johnson T. A., Jolly C., Joly Y., Jonasson J. G., Jones C. D., Jones D. R., Jones D. T. W., Jones N., Jones S. J. M., Jonkers J., Ju Y. S., Juhl H., Jung J., Juul M., Juul R. I., Juul S., Jager N., Kabbe R., Kahles A., Kahraman A., Kakavand H., Kalimuthu S., von Kalle C., Kang K. J., Karaszi K., Karlan B., Karsch D., Kasaian K., Kassahn K. S., Katai H., Katoh H., Kawakami Y., Kay J. D., Kazakoff S. H., Kazanov M. D., Keays M., Kebebew E., Kefford R. F., Kellis M., Kench J. G., Kennedy C. J., Kerssemakers J. N. A., Khoo D., Khoo V., Khuntikeo N., Khurana E., Kilpinen H., Kim H. K., Kim H. -L., Kim H. -Y., Kim H., Kim J., Kim J. K., Kim Y., King T. A., Klapper W., Kleinheinz K., Klimczak L. J., Knappskog S., Kneba M., Knoppers B. M., Koh Y., Komorowski J., Komura D., Komura M., Kong G., Kool M., Korbel J. O., 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., Kuppers R., Lagergren J., Lai P. H., Laird P. W., Lakhani S. R., Lalansingh C. M., Lalonde E., Lamaze F. C., Lambert A., Lander E., Landgraf P., Landoni L., Langerod A., Lanzos A., Larsimont D., Larsson E., Lathrop M., Lau L. M. S., Lawerenz C., Lawlor R. T., Lawrence M. S., Le X., Lee D., Lee E. A., Lee H. J., Lee J. J. -K., Lee J. -Y., Lee J., Lee M. T. M., Lee-Six H., Lehmann K. -V., Lehrach H., Lenze D., Leonard C. R., Leongamornlert D. A., Leshchiner I., Letourneau L., Letunic I., Levine D. A., Lewis L., Ley T., Li C., Li H. I., Li J., Li L., Li S., Li X., Li Y., Liang H., Liang S. -B., Lichter P., Lin P., Lin Z., Linehan W. M., Lingjaerde O. C., Liu D., Liu E. M., Liu F. -F., Liu F., Liu J., Liu X., Livingstone J., Livitz D., Livni N., Lochovsky L., Loeffler M., Long G. V., Lopez-Guillermo A., Lou S., Lovat L. B., Lu Y., Lu Y. -J., Luchini C., Lungu I., Luo X., Luxton H. J., Lynch A. G., Lype L., Lopez C., Lopez-Otin C., Ma E. Z., Ma Y., MacGrogan G., MacRae S., Macintyre G., Madsen T., Maejima K., Mafficini A., Maglinte D. T., Maitra A., Majumder P. P., Malcovati L., Malikic S., Malleo G., Mann G. J., Mantovani-Loffler L., Marchal K., Marchegiani G., Mardis E. R., Margolin A. A., Marin M. G., Markowetz F., Markowski J., Marks J., Marques-Bonet T., Marra M. A., Marsden L., Martens J. W. M., Martin-Subero J. I., Martincorena I., Martinez-Fundichely A., Maruvka Y. E., Mashl R. J., Massie C. E., Matthew T. J., Matthews L., Mayer E., Mayes S., Mayo M., Mbabaali F., McCune K., McDermott U., McGillivray P. D., McLellan M. D., McPherson J. D., McPherson J. R., McPherson T. A., Meier S. R., Meng A., Meng S., Menzies A., Merrett N. D., Merson S., Meyerson M., Meyerson W., Mieczkowski P. A., Mihaiescu G. L., Mijalkovic S., Mijalkovic-Lazic A. M., Mikkelsen T., Milella M., Mileshkin L., Miller C. A., Miller D. K., Miller J. K., Mills G. B., Milovanovic A., Minner S., Miotto M., Arnau G. M., Mirabello L., Mitchell C., Mitchell T. J., Miyano S., Miyoshi N., Mizuno S., Molnar-Gabor F., Moore M. J., Moore R. A., Morganella S., Morris Q. D., Morrison C., Mose L. E., Moser C. D., Muinos F., Mularoni L., Mungall A. J., Mungall K., Musgrove E. A., Mustonen V., Mutch D., Muyas F., Muzny D. M., Munoz A., Myers J., Myklebost O., Moller P., Nagae G., Nagrial A. M., Nakagama H., Nakagawa H., Nakamura H., Nakamura T., Nakano K., Nandi T., Nangalia J., Nastic M., Navarro A., Navarro F. C. P., Neal D. E., Nettekoven G., Newell F., Newhouse S. J., Newton Y., Ng A. W. T., Ng A., Nicholson J., Nicol D., Nie Y., Nielsen M. M., Noble M. S., Nones K., Northcott P. A., Notta F., O'Connor B. D., O'Donnell P., O'Donovan M., O'Meara S., O'Neill B. P., O'Neill J. R., Ocana D., Ochoa A., Oesper L., Ogden C., Ohdan H., Ohi K., Ohno-Machado L., Oien K. A., Ojesina A. I., Ojima H., Okusaka T., Ong C. K., Ossowski S., Ott G., Ouellette B. F. F., Paczkowska M., Paiella S., Pairojkul C., Pajic M., Pan-Hammarstrom Q., Papaemmanuil E., Papatheodorou I., Paramasivam N., Park J. W., Park J. -W., Park K., Park P. J., Parker J. S., Parsons S. L., Pass H., Pasternack D., Pastore A., Patch A. -M., Pauporte I., Pea A., Pearson J. V., Pedamallu C. S., Pedersen J. S., Pederzoli P., Peifer M., Pennell N. A., Perou C. M., Petersen G. M., Peto M., Petrelli N., Petryszak R., Pfister S. M., Phillips M., Pich O., Pickett H. A., Pihl T. D., Pillay N., Pinder S., Pinese M., Pinho A. V., Pitkanen E., Pivot X., Pineiro-Yanez E., Planko L., Plass C., Pons T., Popescu I., Potapova O., Prasad A., Preston S. R., Prinz M., Pritchard A. L., Provenzano E., Puente X. S., Puig S., Puiggros M., Pulido-Tamayo S., Pupo G. M., Purdie C. A., Quinn M. C., Rabionet R., Rader J. S., Radlwimmer B., Radovic P., Raeder B., Raine K. M., Ramakrishna M., Ramakrishnan K., Ramalingam S., Raphael B. J., Rathmell W. K., Rausch T., Reifenberger G., Reimand J., Reis-Filho J., Reuter V., Reyes-Salazar I., Reyna M. A., Reynolds S. M., Riazalhosseini Y., Richardson A. L., Richter J., Ringel M., Ringner M., Rino Y., Rippe K., Roach J., Roberts L. R., Roberts N. D., Roberts S. A., Robertson A. G., Robertson A. J., Rodriguez J. B., Rodriguez-Martin B., Rodriguez-Gonzalez F. G., Roehrl M. H. A., Rohde M., Rokutan H., Romieu G., Rooman I., Roques T., Rosebrock D., Rosenberg M., Rosenstiel P. C., Rosenwald A., Rowe E. W., Royo R., Rozen S. G., Rubanova Y., Rubio-Perez C., Rudneva V. A., Rusev B. C., Ruzzenente A., Ratsch G., Sabarinathan R., Sabelnykova V. Y., Sadeghi S., Sahinalp S. C., Saini N., Saito-Adachi M., Saksena G., Salcedo A., Salgado R., Salichos L., Sallari R., Saller C., Salvia R., Sam M., Samra J. S., Sanchez-Vega F., Sander C., Sanders G., Sarin R., Sarrafi I., Sasaki-Oku A., Sauer T., Sauter G., Saw R. P. M., Scardoni M., Scarlett C. J., Scarpa A., Scelo G., Schadendorf D., Schein J. E., Schilhabel M. B., Schlesner M., Schlomm T., Schmidt H. K., Schramm S. -J., Schreiber S., Schultz N., Schumacher S. E., Schwarz R. F., Scolyer R. A., Scott D., Scully R., Seethala R., Segre A. V., Selander I., Senbabaoglu Y., Sengupta S., Sereni E., Serra S., Shackleton M., Shah N. C., Shahabi S., Shang C. A., Shang P., Shapira O., Shelton T., Shen C., Shen H., Shepherd R., Shi R., Shi Y., Shiah Y. -J., Shih J., Shimizu E., Shimizu K., Shin S. J., Shiraishi Y., Shmaya T., Shmulevich I., Shorser S. I., Short C., Shrestha R., Shringarpure S. S., Shriver C., Shuai S., Sidiropoulos N., Sieuwerts A. M., Sieverling L., Signoretti S., Sikora K. O., Simbolo M., Simon R., Simons J. V., Simpson J. T., Simpson P. T., Singer S., Sinnott-Armstrong N., Sipahimalani P., Skelly T. J., Smid M., Smith-McCune K., Socci N. D., Sofia H. J., Soloway M. G., Song L., Sood A. K., Sothi S., Sotiriou C., Soulette C. M., Span P. N., Spellman P. T., Sperandio N., Spillane A. J., Spiro O., Spring J., Staaf J., Stadler P. F., Staib P., Stark S. G., Stebbings L., Stefansson O. A., Stegle O., Stenhouse A., Stewart C., Stilgenbauer S., Stratton M. R., Stretch J. R., Struck A. J., Stuart J. M., Stunnenberg H. G., Su H., Su X., Sungalee S., Susak H., Suzuki A., Sweep F., Szczepanowski M., Sultmann H., Yugawa T., Tam A., Tamborero D., Tan B. K. T., Tan D., Tan P., Tanaka H., Taniguchi H., Tanskanen T. J., Tarabichi M., Tarnuzzer R., Tarpey P., Taschuk M. L., Tatsuno K., Tavare S., Taylor D. F., Taylor-Weiner A., Teague J. W., Teh B. T., Tembe V., Temes J., Thayer S. P., Thiessen N., Thomas G., Thomas S., Thompson A., Thompson A. M., Thompson J. F., Thompson R. H., Thorne H., Thorne L. B., Thorogood A., Tiao G., Tijanic N., Timms L. E., Tirabosco R., Tojo M., Tommasi S., Toon C. W., Toprak U. H., Torrents D., Tortora G., Tost J., Totoki Y., Townend D., Traficante N., Treilleux I., Trotta J. -R., Trumper L. H. 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D., Williams A., Wilmott J. S., Wilson G. W., Wilson J. M., Wilson R. K., Winterhoff B., Wintersinger J. A., Wiznerowicz M., Wolf S., Wong B. H., Wong T., Wong W., Woo Y., Wood S., Wouters B. G., Wright A. J., Wright M. H., Wu D. -Y., Wu G., Wu J., Wu K., Wu Y., Wu Z., Xi L., Xia T., Xiang Q., Xiao X., Xing R., Xiong H., Xu Q., Xu Y., Xue H., Yachida S., Yakneen S., Yamaguchi R., Yamaguchi T. N., Yamamoto M., Yamamoto S., Yamaue H., Yang F., Yang H., Yang J. Y., Yang L., Yang S., Yang T. -P., Yang Y., Yao X., Yaspo M. -L., Yates L., Yau C., Ye C., Ye K., Yellapantula V. D., Yoon C. J., Yoon S. -S., Yu J., Yu K., Yu W., Yu Y., Yuan Y., Yuen D., Yung C. K., Zaikova O., Zamora J., Zapatka M., Zenklusen J. C., Zenz T., Zeps N., Zhang C. -Z., Zhang F., Zhang H., Zhang X., Zhang Y., Zhang Z., Zhao Z., Zheng L., Zheng X., Zhou W., Zhou Y., Zhu B., Zhu H., Zhu J., Zhu S., Zou L., Zou X., deFazio A., van As N., van Deurzen C. H. M., van de Vijver M. J., Veer L., von Mering C., Lauri Antti Aaltonen / Principal Investigator, Genome-Scale Biology (GSB) Research Program, Department of Medical and Clinical Genetics, Organismal and Evolutionary Biology Research Programme, Helsinki Institute for Information Technology, Institute of Biotechnology, Bioinformatics, Department of Computer Science, Faculty of Medicine, HUS Helsinki and Uusimaa Hospital District, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews. Cellular Medicine Division, University of St Andrews. Statistics, University of St Andrews. School of Medicine, Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Háskóli Íslands, University of Iceland, Li, C, Prokopec, S, Sun, R, Yousif, F, Schmitz, N, Al-Shahrour, F, Atwal, G, Bailey, P, Biankin, A, Boutros, P, Campbell, P, Chang, D, Cooke, S, Deshpande, V, Faltas, B, Faquin, W, Garraway, L, Getz, G, Grimmond, S, Haider, S, Hoadley, K, Jiao, W, Kaiser, V, Karlic, R, Kato, M, Kubler, K, Lazar, A, Louis, D, Margolin, A, Martin, S, Nahal-Bose, H, Nielsen, G, Nik-Zainal, S, Omberg, L, P'Ng, C, Perry, M, Polak, P, Rheinbay, E, Rubin, M, Semple, C, Sgroi, D, Shibata, T, Siebert, R, Smith, J, Stein, L, Stobbe, M, Thai, K, Wright, D, Wu, C, Yuan, K, Zhang, J, Aaltonen, L, Abascal, F, Abeshouse, A, Aburatani, H, Adams, D, Agrawal, N, Ahn, K, Ahn, S, Aikata, H, Akbani, R, Akdemir, K, Al-Ahmadie, H, Al-Sedairy, S, Alawi, M, Albert, M, Aldape, K, Alexandrov, L, Ally, A, Alsop, K, Alvarez, E, Amary, F, Amin, S, Aminou, B, Ammerpohl, O, Anderson, M, Ang, Y, Antonello, D, Anur, P, Aparicio, S, Appelbaum, E, Arai, Y, Aretz, A, Arihiro, K, Ariizumi, S, Armenia, J, Arnould, L, Asa, S, Assenov, Y, Aukema, S, Auman, J, Aure, M, Awadalla, P, Aymerich, M, Bader, G, Baez-Ortega, A, Bailey, M, Balasundaram, M, Balu, S, Bandopadhayay, P, Banks, R, Barbi, S, Barbour, A, Barenboim, J, Barnholtz-Sloan, J, Barr, H, Barrera, E, Bartlett, J, Bartolome, J, Bassi, C, Bathe, O, Baumhoer, D, Bavi, P, Baylin, S, Bazant, W, Beardsmore, D, Beck, T, Behjati, S, Behren, A, Niu, B, Bell, C, Beltran, S, Benz, C, Berchuck, A, Bergmann, A, Bergstrom, E, Berman, B, Berney, D, Bernhart, S, Beroukhim, R, Berrios, M, Bersani, S, Bertl, J, Betancourt, M, Bhandari, V, Bhosle, S, Bieg, M, Bigner, D, Binder, H, Birney, E, Birrer, M, Biswas, N, Bjerkehagen, B, Bodenheimer, T, Boice, L, Bonizzato, G, De Bono, J, Boot, A, Bootwalla, M, Borg, A, Borkhardt, A, Boroevich, K, Borozan, I, Borst, C, Bosenberg, M, Bosio, M, Boultwood, J, Bourque, G, Bova, G, Bowen, D, Bowlby, R, Bowtell, D, Boyault, S, Boyce, R, Boyd, J, Brazma, A, Brennan, P, Brewer, D, Brinkman, A, Bristow, R, Broaddus, R, Brock, J, Brock, M, Broeks, A, Brooks, A, Brooks, D, Brors, B, Brunak, S, Bruxner, T, Bruzos, A, Buchanan, A, Buchhalter, I, Buchholz, C, Bullman, S, Burke, H, Burkhardt, B, Burns, K, Busanovich, J, Bustamante, C, Butler, A, Butte, A, Byrne, N, Borresen-Dale, A, Caesar-Johnson, S, Cafferkey, A, Cahill, D, Calabrese, C, Caldas, C, Calvo, F, Camacho, N, Campo, E, Cantu, C, Cao, S, Carey, T, Carlevaro-Fita, J, Carlsen, R, Cataldo, I, Cazzola, M, Cebon, J, Cerfolio, R, Chadwick, D, Chakravarty, D, Chalmers, D, Chan, C, Chan, K, Chan-Seng-Yue, M, Chandan, V, Chanock, S, Chantrill, L, Chateigner, A, Chatterjee, N, Chayama, K, Chen, H, Chen, J, Chen, K, Chen, Y, Chen, Z, Cherniack, A, Chien, J, Chiew, Y, Chin, S, Cho, J, Cho, S, Choi, J, Choi, W, Chomienne, C, Chong, Z, Choo, S, Chou, A, Christ, A, Christie, E, Chuah, E, Cibulskis, C, Cibulskis, K, Cingarlini, S, Clapham, P, Claviez, A, Cleary, S, Cloonan, N, Cmero, M, Collins, C, Connor, A, Cooper, C, Cope, L, Corbo, V, Cordes, M, Cordner, S, Cortes-Ciriano, I, Covington, K, Cowin, P, Craft, B, Craft, D, Creighton, C, Cun, Y, Curley, E, Cutcutache, I, Czajka, K, Czerniak, B, Dagg, R, Danilova, L, Davi, M, Davidson, N, Davies, H, Davis, I, Davis-Dusenbery, B, Dawson, K, De La Vega, F, De Paoli-Iseppi, R, Defreitas, T, Dei Tos, A, Delaneau, O, Demchok, J, Demeulemeester, J, Demidov, G, Demircioglu, D, Dennis, N, Denroche, R, Dentro, S, Desai, N, Deshwar, A, Desmedt, C, Deu-Pons, J, Dhalla, N, Dhani, N, Dhingra, P, Dhir, R, Dibiase, A, Diamanti, K, Ding, L, Ding, S, Dinh, H, Dirix, L, Doddapaneni, H, Donmez, N, Dow, M, Drapkin, R, Drechsel, O, Drews, R, Serge, S, Dudderidge, T, Dueso-Barroso, A, Dunford, A, Dunn, M, Dursi, L, Duthie, F, Dutton-Regester, K, Eagles, J, Easton, D, Edmonds, S, Edwards, P, Edwards, S, Eeles, R, Ehinger, A, Eils, J, Eils, R, El-Naggar, A, Eldridge, M, Ellrott, K, Erkek, S, Escaramis, G, Espiritu, S, Estivill, X, Etemadmoghadam, D, Eyfjord, J, Fan, D, Fan, Y, Farcas, C, Fassan, M, Fatima, A, Favero, F, Fayzullaev, N, Felau, I, Fereday, S, Ferguson, M, Ferretti, V, Feuerbach, L, Field, M, Fink, J, Finocchiaro, G, Fisher, C, Fittall, M, Fitzgerald, A, Fitzgerald, R, Flanagan, A, Fleshner, N, Flicek, P, Foekens, J, Fong, K, Fonseca, N, Foster, C, Fox, N, Fraser, M, Frazer, S, Frenkel-Morgenstern, M, Friedman, W, Frigola, J, Fronick, C, Fujimoto, A, Fujita, M, Fukayama, M, Fulton, L, Fulton, R, Furuta, M, Futreal, P, Fullgrabe, A, Gabriel, S, Gallinger, S, Gambacorti Passerini, C, Gao, J, Gao, S, Garred, O, Garrison, E, Garsed, D, Gehlenborg, N, Gelpi, J, George, J, Gerhard, D, Gerhauser, C, Gershenwald, J, Gerstein, M, Gerstung, M, Ghori, M, Ghossein, R, Giama, N, Gibbs, R, Gill, A, Gill, P, Giri, D, Glodzik, D, Gnanapragasam, V, Goebler, M, Goldman, M, Gomez, C, Gonzalez, S, Gonzalez-Perez, A, Gordenin, D, Gossage, J, Gotoh, K, Govindan, R, Grabau, D, Graham, J, Grant, R, Green, A, Green, E, Greger, L, Grehan, N, Grimaldi, S, Grossman, R, Grundhoff, A, Gundem, G, Guo, Q, Gupta, M, Gupta, S, Gut, I, Gut, M, Goke, J, Ha, G, Haake, A, Haan, D, Haas, S, Haase, K, Haber, J, Habermann, N, Hach, F, Hama, N, Hamdy, F, Hamilton, A, Hamilton, M, Han, L, Hanna, G, Hansmann, M, Haradhvala, N, Harismendy, O, Harliwong, I, Harmanci, A, Harrington, E, Hasegawa, T, Haussler, D, Hawkins, S, Hayami, S, Hayashi, S, Hayes, D, Hayes, S, Hayward, N, Hazell, S, He, Y, Heath, A, Heath, S, Hedley, D, Hegde, A, Heiman, D, Heinold, M, Heins, Z, Heisler, L, Hellstrom-Lindberg, E, Helmy, M, Heo, S, Hepperla, A, Heredia-Genestar, J, Herrmann, C, Hersey, P, Hess, J, Hilmarsdottir, H, Hinton, J, Hirano, S, Hiraoka, N, Hobolth, A, Hodzic, E, Hoell, J, Hoffmann, S, Hofmann, O, Holbrook, A, Holik, A, Hollingsworth, M, Holmes, O, Holt, R, Hong, C, Hong, E, Hong, J, Hooijer, G, Hornshoj, H, Hosoda, F, Hou, Y, Hovestadt, V, Howat, W, Hoyle, A, Hruban, R, Hu, J, Hu, T, Hua, X, Huang, K, Huang, M, Huang, V, Huang, Y, Huber, W, Hudson, T, Hummel, M, Hung, J, Huntsman, D, Hupp, T, Huse, J, Huska, M, Hutter, B, Hutter, C, Hubschmann, D, Iacobuzio-Donahue, C, Imbusch, C, Imielinski, M, Imoto, S, Isaacs, W, Isaev, K, Ishikawa, S, Iskar, M, Islam, S, Ittmann, M, Ivkovic, S, Izarzugaza, J, Jacquemier, J, Jakrot, V, Jamieson, N, Jang, G, Jang, S, Jayaseelan, J, Jayasinghe, R, Jefferys, S, Jegalian, K, Jennings, J, Jeon, S, Jerman, L, Ji, Y, Johansson, P, Johns, A, Johns, J, Johnson, R, Johnson, T, Jolly, C, Joly, Y, Jonasson, J, Jones, C, Jones, D, Jones, N, Jones, S, Jonkers, J, Ju, Y, Juhl, H, Jung, J, Juul, M, Juul, R, Juul, S, Jager, N, Kabbe, R, Kahles, A, Kahraman, A, Kakavand, H, Kalimuthu, S, von Kalle, C, Kang, K, Karaszi, K, Karlan, B, Karsch, D, Kasaian, K, Kassahn, K, Katai, H, Katoh, H, Kawakami, Y, Kay, J, Kazakoff, S, Kazanov, M, Keays, M, Kebebew, E, Kefford, R, Kellis, M, Kench, J, Kennedy, C, Kerssemakers, J, Khoo, D, Khoo, V, Khuntikeo, N, Khurana, E, Kilpinen, H, Kim, H, Kim, J, Kim, Y, King, T, Klapper, W, Kleinheinz, K, Klimczak, L, Knappskog, S, Kneba, M, Knoppers, B, Koh, Y, Komorowski, J, Komura, D, Komura, M, Kong, G, Kool, M, Korbel, J, Korchina, V, Korshunov, A, Koscher, M, Koster, R, Kote-Jarai, Z, Koures, A, Kovacevic, M, Kremeyer, B, Kretzmer, H, Kreuz, M, Krishnamurthy, S, Kube, D, Kumar, K, Kumar, P, Kumar, S, Kumar, Y, Kundra, R, Kuppers, R, Lagergren, J, Lai, P, Laird, P, Lakhani, S, Lalansingh, C, Lalonde, E, Lamaze, F, Lambert, A, Lander, E, Landgraf, P, Landoni, L, Langerod, A, Lanzos, A, Larsimont, D, Larsson, E, Lathrop, M, Lau, L, Lawerenz, C, Lawlor, R, Lawrence, M, Le, X, Lee, D, Lee, E, Lee, H, Lee, J, Lee, M, Lee-Six, H, Lehmann, K, Lehrach, H, Lenze, D, Leonard, C, Leongamornlert, D, Leshchiner, I, Letourneau, L, Letunic, I, Levine, D, Lewis, L, Ley, T, Li, H, Li, J, Li, L, Li, S, Li, X, Li, Y, Liang, H, Liang, S, Lichter, P, Lin, P, Lin, Z, Linehan, W, Lingjaerde, O, Liu, D, Liu, E, Liu, F, Liu, J, Liu, X, Livingstone, J, Livitz, D, Livni, N, Lochovsky, L, Loeffler, M, Long, G, Lopez-Guillermo, A, Lou, S, Lovat, L, Lu, Y, Luchini, C, Lungu, I, Luo, X, Luxton, H, Lynch, A, Lype, L, Lopez, C, Lopez-Otin, C, Ma, E, Ma, Y, Macgrogan, G, Macrae, S, Macintyre, G, Madsen, T, Maejima, K, Mafficini, A, Maglinte, D, Maitra, A, Majumder, P, Malcovati, L, Malikic, S, Malleo, G, Mann, G, Mantovani-Loffler, L, Marchal, K, Marchegiani, G, Mardis, E, Marin, M, Markowetz, F, Markowski, J, Marks, J, Marques-Bonet, T, Marra, M, Marsden, L, Martens, J, Martin-Subero, J, Martincorena, I, Martinez-Fundichely, A, Maruvka, Y, Mashl, R, Massie, C, Matthew, T, Matthews, L, Mayer, E, Mayes, S, Mayo, M, Mbabaali, F, Mccune, K, Mcdermott, U, Mcgillivray, P, Mclellan, M, Mcpherson, J, Mcpherson, T, Meier, S, Meng, A, Meng, S, Menzies, A, Merrett, N, Merson, S, Meyerson, M, Meyerson, W, Mieczkowski, P, Mihaiescu, G, Mijalkovic, S, Mijalkovic-Lazic, A, Mikkelsen, T, Milella, M, Mileshkin, L, Miller, C, Miller, D, Miller, J, Mills, G, Milovanovic, A, Minner, S, Miotto, M, Arnau, G, Mirabello, L, Mitchell, C, Mitchell, T, Miyano, S, Miyoshi, N, Mizuno, S, Molnar-Gabor, F, Moore, M, Moore, R, Morganella, S, Morris, Q, Morrison, C, Mose, L, Moser, C, Muinos, F, Mularoni, L, Mungall, A, Mungall, K, Musgrove, E, Mustonen, V, Mutch, D, Muyas, F, Muzny, D, Munoz, A, Myers, J, Myklebost, O, Moller, P, Nagae, G, Nagrial, A, Nakagama, H, Nakagawa, H, Nakamura, H, Nakamura, T, Nakano, K, Nandi, T, Nangalia, J, Nastic, M, Navarro, A, Navarro, F, Neal, D, Nettekoven, G, Newell, F, Newhouse, S, Newton, Y, Ng, A, Nicholson, J, Nicol, D, Nie, Y, Nielsen, M, Noble, M, Nones, K, Northcott, P, Notta, F, O'Connor, B, O'Donnell, P, O'Donovan, M, O'Meara, S, O'Neill, B, O'Neill, J, Ocana, D, Ochoa, A, Oesper, L, Ogden, C, Ohdan, H, Ohi, K, Ohno-Machado, L, Oien, K, Ojesina, A, Ojima, H, Okusaka, T, Ong, C, Ossowski, S, Ott, G, Ouellette, B, Paczkowska, M, Paiella, S, Pairojkul, C, Pajic, M, Pan-Hammarstrom, Q, Papaemmanuil, E, Papatheodorou, I, Paramasivam, N, Park, J, Park, K, Park, P, Parker, J, Parsons, S, Pass, H, Pasternack, D, Pastore, A, Patch, A, Pauporte, I, Pea, A, Pearson, J, Pedamallu, C, Pedersen, J, Pederzoli, P, Peifer, M, Pennell, N, Perou, C, Petersen, G, Peto, M, Petrelli, N, Petryszak, R, Pfister, S, Phillips, M, Pich, O, Pickett, H, Pihl, T, Pillay, N, Pinder, S, Pinese, M, Pinho, A, Pitkanen, E, Pivot, X, Pineiro-Yanez, E, Planko, L, Plass, C, Pons, T, Popescu, I, Potapova, O, Prasad, A, Preston, S, Prinz, M, Pritchard, A, Provenzano, E, Puente, X, Puig, S, Puiggros, M, Pulido-Tamayo, S, Pupo, G, Purdie, C, Quinn, M, Rabionet, R, Rader, J, Radlwimmer, B, Radovic, P, Raeder, B, Raine, K, Ramakrishna, M, Ramakrishnan, K, Ramalingam, S, Raphael, B, Rathmell, W, Rausch, T, Reifenberger, G, Reimand, J, Reis-Filho, J, Reuter, V, Reyes-Salazar, I, Reyna, M, Reynolds, S, Riazalhosseini, Y, Richardson, A, Richter, J, Ringel, M, Ringner, M, Rino, Y, Rippe, K, Roach, J, Roberts, L, Roberts, N, Roberts, S, Robertson, A, Rodriguez, J, Rodriguez-Martin, B, Rodriguez-Gonzalez, F, Roehrl, M, Rohde, M, Rokutan, H, Romieu, G, Rooman, I, Roques, T, Rosebrock, D, Rosenberg, M, Rosenstiel, P, Rosenwald, A, Rowe, E, Royo, R, Rozen, S, Rubanova, Y, Rubio-Perez, C, Rudneva, V, Rusev, B, Ruzzenente, A, Ratsch, G, Sabarinathan, R, Sabelnykova, V, Sadeghi, S, Sahinalp, S, Saini, N, Saito-Adachi, M, Saksena, G, Salcedo, A, Salgado, R, Salichos, L, Sallari, R, Saller, C, Salvia, R, Sam, M, Samra, J, Sanchez-Vega, F, Sander, C, Sanders, G, Sarin, R, Sarrafi, I, Sasaki-Oku, A, Sauer, T, Sauter, G, Saw, R, Scardoni, M, Scarlett, C, Scarpa, A, Scelo, G, Schadendorf, D, Schein, J, Schilhabel, M, Schlesner, M, Schlomm, T, Schmidt, H, Schramm, S, Schreiber, S, Schultz, N, Schumacher, S, Schwarz, R, Scolyer, R, Scott, D, Scully, R, Seethala, R, Segre, A, Selander, I, Senbabaoglu, Y, Sengupta, S, Sereni, E, Serra, S, Shackleton, M, Shah, N, Shahabi, S, Shang, C, Shang, P, Shapira, O, Shelton, T, Shen, C, Shen, H, Shepherd, R, Shi, R, Shi, Y, Shiah, Y, Shih, J, Shimizu, E, Shimizu, K, Shin, S, Shiraishi, Y, Shmaya, T, Shmulevich, I, Shorser, S, Short, C, Shrestha, R, Shringarpure, S, Shriver, C, Shuai, S, Sidiropoulos, N, Sieuwerts, A, Sieverling, L, Signoretti, S, Sikora, K, Simbolo, M, Simon, R, Simons, J, Simpson, J, Simpson, P, Singer, S, Sinnott-Armstrong, N, Sipahimalani, P, Skelly, T, Smid, M, Smith-McCune, K, Socci, N, Sofia, H, Soloway, M, Song, L, Sood, A, Sothi, S, Sotiriou, C, Soulette, C, Span, P, Spellman, P, Sperandio, N, Spillane, A, Spiro, O, Spring, J, Staaf, J, Stadler, P, Staib, P, Stark, S, Stebbings, L, Stefansson, O, Stegle, O, Stenhouse, A, Stewart, C, Stilgenbauer, S, Stratton, M, Stretch, J, Struck, A, Stuart, J, Stunnenberg, H, Su, H, Su, X, Sungalee, S, Susak, H, Suzuki, A, Sweep, F, Szczepanowski, M, Sultmann, H, Yugawa, T, Tam, A, Tamborero, D, Tan, B, Tan, D, Tan, P, Tanaka, H, Taniguchi, H, Tanskanen, T, Tarabichi, M, Tarnuzzer, R, Tarpey, P, Taschuk, M, Tatsuno, K, Tavare, S, Taylor, D, Taylor-Weiner, A, Teague, J, Teh, B, Tembe, V, Temes, J, Thayer, S, Thiessen, N, Thomas, G, Thomas, S, Thompson, A, Thompson, J, Thompson, R, Thorne, H, Thorne, L, Thorogood, A, Tiao, G, Tijanic, N, Timms, L, Tirabosco, R, Tojo, M, Tommasi, S, Toon, C, Toprak, U, Torrents, D, Tortora, G, Tost, J, Totoki, Y, Townend, D, Traficante, N, Treilleux, I, Trotta, J, Trumper, L, Tsao, M, Tsunoda, T, Tubio, J, Tucker, O, Turkington, R, Turner, D, Tutt, A, Ueno, M, Ueno, N, Umbricht, C, Umer, H, Underwood, T, Urban, L, Urushidate, T, Ushiku, T, Uuskula-Reimand, L, Valencia, A, Van Den Berg, D, Van Laere, S, Van Loo, P, Van Meir, E, Van den Eynden, G, Van der Kwast, T, Vasudev, N, Vazquez, M, Vedururu, R, Veluvolu, U, Vembu, S, Verbeke, L, Vermeulen, P, Verrill, C, Viari, A, Vicente, D, Vicentini, C, Raghavan, K, Viksna, J, Vilain, R, Villasante, I, Vincent-Salomon, A, Visakorpi, T, Voet, D, Vyas, P, Vazquez-Garcia, I, Waddell, N, Wadelius, 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C, Zhang, F, Zhang, H, Zhang, X, Zhang, Y, Zhang, Z, Zhao, Z, Zheng, L, Zheng, X, Zhou, W, Zhou, Y, Zhu, B, Zhu, H, Zhu, J, Zhu, S, Zou, L, Zou, X, Defazio, A, van As, N, van Deurzen, C, van de Vijver, M, Veer, L, von Mering, C, Natural Sciences and Engineering Research Council of Canada, Canadian Institutes of Health Research, Genome Canada, Canada Foundation for Innovation, National Institutes of Health (US), National Cancer Institute (US), Pathology, CCA - Cancer biology and immunology, Graduate School, Laboratory Genetic Metabolic Diseases, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, CCA -Cancer Center Amsterdam, Li, Constance H. [0000-0002-5487-7225], Prokopec, Stephenie D. [0000-0001-7936-8577], Boutros, Paul C. [0000-0003-0553-7520], Apollo - University of Cambridge Repository, Tampere University, BioMediTech, TAYS Cancer Centre, Basic (bio-) Medical Sciences, Li, Constance H [0000-0002-5487-7225], Prokopec, Stephenie D [0000-0001-7936-8577], Boutros, Paul C [0000-0003-0553-7520], and Medical Oncology
- Subjects
sex differences ,Male ,Colorectal cancer ,Kynferði ,02 engineering and technology ,0302 clinical medicine ,DISPARITIES ,Epidemiology of cancer ,Cancer genomics ,lcsh:Science ,Càncer ,Cancer genetics, Genome informatics, Cancer genomics, Oncogenes ,Cancer genetics ,Exome ,Cancer ,0303 health sciences ,Mutation ,Neoplasms -- genetics ,1184 Genetics, developmental biology, physiology ,Neoplasms/genetics ,3. Good health ,030220 oncology & carcinogenesis ,Medical genetics ,0210 nano-technology ,Human ,Sex characteristics ,medicine.medical_specialty ,Science ,Genomic Instability ,General Biochemistry, Genetics and Molecular Biology ,RC0254 ,Càncer -- Epidemiologia ,Open Reading Frames ,03 medical and health sciences ,SDG 3 - Good Health and Well-being ,Chromosomal Instability ,Sex differences ,Genetics ,Humans ,beta Catenin -- genetics ,Sex organ ,SIGNATURES ,45 ,RC0254 Neoplasms. Tumors. Oncology (including Cancer) ,Oncogenes ,medicine.disease ,692/4028/67/69 ,Cancérologie ,Genòmica ,Logistic Models ,030104 developmental biology ,lcsh:Q ,PCAWG Tumour Subtypes and Clinical Translation ,Human genome ,119 ,0301 basic medicine ,Medizin ,General Physics and Astronomy ,medicine.disease_cause ,Bioinformatics ,Genome informatics ,Genome ,Neoplasms ,38/23 ,Medicine and Health Sciences ,Body Size ,beta Catenin ,Sex Characteristics ,318 Medical biotechnology ,Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17] ,Multidisciplinary ,article ,3rd-DAS ,021001 nanoscience & nanotechnology ,humanities ,Women's cancers Radboud Institute for Health Sciences [Radboudumc 17] ,Causality ,oncology ,1181 Ecology, evolutionary biology ,SURVIVAL ,631/114/2785 ,Female ,Càncer -- Tractament ,Oncogenes -- genetics ,beta Catenin/genetics ,3122 Cancers ,610 Medicine & health ,QH426 Genetics ,Biology ,Cancer epidemiology ,Rare Diseases ,631/67/68 ,Krabbameinsrannsóknir ,medicine ,ddc:610 ,Gene ,QH426 ,030304 developmental biology ,Krabbamein ,Oncogenes/genetics ,Genome, Human ,Sex organs ,Human Genome ,PCAWG Consortium ,General Chemistry ,GENE ,Good Health and Well Being ,Estudis de gènere ,oncogenic mutational processes ,692/4028/67/395 ,Diferències entre sexes ,Gender studies ,3111 Biomedicine - Abstract
Publisher's version (útgefin grein), Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research., We thank all the members of the Boutros lab for insightful discussions. This study was conducted with the support of the Ontario Institute for Cancer Research to P.C.B. through funding provided by the Government of Ontario. This work was supported by the Discovery Frontiers: Advancing Big Data Science in Genomics Research program, which is jointly funded by the Natural Sciences and Engineering Research Council (NSERC) of Canada, the Canadian Institutes of Health Research (CIHR), Genome Canada and the Canada Foundation for Innovation (CFI). P.C.B. was supported by a Terry Fox Research Institute New Investigator Award and a CIHR New Investigator Award. This work was supported by an NSERC Discovery grant and by Canadian Institutes of Health Research, grant #SVB-145586, to P.C.B. This work was supported by the NIH/NCI under award number P30CA016042 and an operating grant from the National Cancer Institute Early Detection Research Network (1U01CA214194-01). We acknowledge the contributions of the many clinical networks across ICGC and TCGA who provided samples and data to the PCAWG Consortium, and the contributions of the Technical Working Group and the Germline Working Group of the PCAWG Consortium for collation, realignment and harmonised variant calling of the cancer genomes used in this study. We thank the patients and their families for their participation in the individual ICGC and TCGA projects.
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- 2020
6. 278 (PB058) - CDK12 loss leads to replication stress and sensitivity to combinations of the ATR inhibitor camonsertib (RP-3500) with PARP inhibitors
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Setton, J., Gallo, D., Glodzik, D., Kaiser, B., Braverman, S., Ubhi, T., Fournier, S., Selenica, P., Laterreur, N., Roulston, A., Brown, G., Morris, S., Reis-Filho, J., and Zimmermann, M.
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- 2022
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7. PO-339 Implications of organ-wise extraction of cancer mutational signatures using 2577 whole genomes
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Degasperi, A., primary, Amarante, T. Dias, additional, Zou, X., additional, Morganella, S., additional, Glodzik, D., additional, Davies, H., additional, and Nik-Zainal, S., additional
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- 2018
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8. Utility of Non-rule-based Visual Matching as a Strategy to Allow Novices to Achieve Skin Lesion Diagnosis
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Rees, JL, primary, Aldridge, RB, additional, Glodzik, D, additional, Ballerini, L, additional, and Fisher, RB, additional
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- 2011
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9. A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers
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Glodzik, D, Morganella, S, Davies, H, Simpson, PT, Li, Y, Zou, X, Diez-Perez, J, Staaf, J, Alexandrov, LB, Smid, M, Brinkman, AB, Rye, IH, Russnes, H, Raine, K, Purdie, CA, Lakhani, Thompson, AM, Birney, E, Stunnenberg, HG, Van De Vijver, MJ, Martens, JWM, Børresen-Dale, A-L, Richardson, AL, Kong, G, Viari, A, Easton, D, Evan, G, Campbell, PJ, Stratton, MR, and Nik-Zainal, S
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breast cancer ,genetics research ,genomics ,3. Good health - Abstract
Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous-recombination-repair deficiency. Notably, these tandem-duplication hotspots were enriched in breast cancer germline susceptibility loci (odds ratio (OR) = 4.28) and breast-specific 'super-enhancer' regulatory elements (OR = 3.54). These hotspots may be sites of selective susceptibility to double-strand-break damage due to high transcriptional activity or, through incrementally increasing copy number, may be sites of secondary selective pressure. The transcriptomic consequences ranged from strong individual oncogene effects to weak but quantifiable multigene expression effects. We thus present a somatic-rearrangement mutational process affecting coding sequences and noncoding regulatory elements and contributing a continuum of driver consequences, from modest to strong effects, thereby supporting a polygenic model of cancer development.
10. Landscape of somatic mutations in 560 breast cancer whole-genome sequences
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Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Lb, Alexandrov, Martin S, Dc, Wedge, Van Loo P, Ys, Ju, Smid M, Ab, Brinkman, Morganella S, Aure MR, Oc, Lingjærde, Langerød A, Markus Ringnér, and Sm, Ahn
11. Pan-cancer analysis of whole genomes
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Campbell, P. J. a., Abpemail, Author, Getz, G. b., C, D, Eemail, Author, Korbel, J. O. f., Gemail, Author, Stuart, hEmail Author, J. M., Jennings, J. L. i., Stein, J, L. D. k., Lemail, Author, Perry, M. D. m., Nahal-Bose, N, Ouellette, H. K. n., B. F. F. o., P, C. H. k., Li, Rheinbay, Q, E. b., E, Nielsen, R, Sgroi, G. P. r., D. C. r., Wu, C. -L. r., Faquin, W. C. r., Deshpande, V. r., Boutros, P. C. k., Q, S, Lazar, T, Hoadley, A. J. u., K. A. v., W, Louis, D. N. r., Dursi, L. J. k., Yung, X, Bailey, C. K. n., M. H. y., Z, Saksena, G. b., Raine, Abp, K. M., Buchhalter, Aa, I., Ab, Ac, Kleinheinz, Aa, K., Schlesner, Ac, Aa, M., Zhang, Ad, Wang, J. n., Ae, W., Wheeler, D. A., Af, Ding, Ag, L. y., Z, Simpson, Ah, J. T. k., Ai, O’Connor, B. D. n., Yakneen, Aj, Ellrott, S. g., Ak, K., Miyoshi, Al, N., Butler, Abp, A. P., Royo, Am, R., Shorser, S. I. k., Vazquez, Am, M., Rausch, An, Tiao, T. g., Waszak, G. b., Rodriguez-Martin, S. M. g., Ao, B., Ap, Aq, Shringarpure, Ar, S., D. -Y., As, Demidov, G. M., At, Au, Av, Delaneau, Aw, O., Ax, Ay, Hayashi, Al, S., Imoto, Habermann, N. g., Segre, A. V. b., Garrison, Az, Abp, E., Cafferkey, A. f., Alvarez, E. G., Ao, Heredia-Genestar, J. M., Ba, Muyas, At, F., Drechsel, At, O., Bruzos, Av, A. L., Ao, Temes, Ao, J., Zamora, Ap, Abp, Baez-Ortega, Bb, A., Kim, H. -L., Bc, Mashl, R. J. z., Bd, Ye, Be, K., Dibiase, Bf, Bg, A., Huang, K. -L. z., Letunic, Bh, Bi, I., Mclellan, M. D. y., Z, Ah, Newhouse, S. J. f., Shmaya, As, T., Kumar, Bj, S., Wedge, Bk, D. C., Bl, Abp, Bm, Wright, M. H., Ar, Yellapantula, V. D., Bn, Gerstein, Bo, Bj, M., Bk, Bp, Khurana, Bq, E., Br, Bs, Marques-Bonet, Bt, Bu, T., Bv, Bw, Navarro, Bx, Bu, A., Bustamante, C. D., Ar, Siebert, By, Bz, R., Nakagawa, Ca, Cb, H., Easton, D. F., Cc, Ossowski, Cd, At, S., Tubio, J. M. C., Ao, De La Vega, F. M., Ar, As, By, Estivill, At, X., Yuen, Ce, Mihaiescu, D. k., Omberg, G. L. n., Cf, L., Ferretti, V. n., Sabarinathan, Cg, Ch, R., Ci, Cj, Pich, Ch, O., Gonzalez-Perez, Cj, Ch, A., Taylor-Weiner, Cj, Ck, A., Fittall, M. W., Cl, Demeulemeester, Cl, J., Tarabichi, Cm, Cl, M., Abp, Roberts, Abp, N. D., Van, Loo, Cl, P., Cortés-Ciriano, Cm, Cn, I., Co, Cp, Urban, L. f., Park, G, Co, P., Zhu, Cp, Cq, B., Pitkänen, E. g., Abp, Y., Saini, Cr, N., Klimczak, L. J., Cs, Weischenfeldt, J. g., Ct, Cu, Sidiropoulos, Cu, N., Alexandrov, L. B., Cv, Abp, Rabionet, At, R., Av, Cw, Escaramis, At, G., Cx, Cy, Bosio, At, Av, Holik, A. Z., At, Susak, At, H., Prasad, Av, Av, A., Erkek, S. g., Calabrese, C. f., Raeder, G, Harrington, B. g., Cz, E., Mayes, Da, S., Turner, Da, D., Juul, Cz, S., Roberts, S. A., Db, Song, Cq, L., Koster, Dc, R., Mirabello, Hua, Cq, X., Tanskanen, T. J., Dd, Tojo, Aq, M., Chen, Bk, J., Aaltonen, De, L. A., Df, Rätsch, Dg, G., Dh, Di, Dj, Dk, Schwarz, Dl, R. F. f., Dm, Dn, Do, Butte, A. J., Dp, Brazma, A. f., Chanock, S. J., Cq, Chatterjee, Dq, N., Stegle, Dr, O. f., G, Harismendy, Ds, Dt, O., Bova, G. S., Du, Gordenin, D. A., Cr, Haan, D. h., Sieverling, Dv, L., Feuerbach, Dw, Chalmers, Dx, D., Joly, Dy, Y., Knoppers, Dy, B., Molnár-Gábor, Dz, F., Phillips, Dy, M., Thorogood, Dy, A., Townend, Dy, D., Goldman, Ea, M., Fonseca, N. A. f., Xiang, Eb, Craft, Q. n., Ea, B., Piñeiro-Yáñez, Ec, E., Muñoz, A. f., Petryszak, R. f., Füllgrabe, A. f., Al-Shahrour, Ec, F., Keays, M. f., Haussler, Ea, D., Weinstein, Ed, Ee, J., Huber, Ef, Valencia, W. g., Am, A., Papatheodorou, Bw, Zhu, I. f., Ea, J., Fan, Ae, Y., Torrents, Am, D., Bieg, Bw, Eg, M., Chen, Eh, Ei, K., Chong, Ej, Z., Cibulskis, K. b., Eils, Aa, R., Ac, Ek, Fulton, El, R. S. y., Z, Gelpi, Ah, J. L., Am, Gonzalez, Em, S. f., G, Gut, I. G., Av, Hach, Bu, En, F., Heinold, Eo, Ac, Hu, Ep, T., Huang, V. k., Hutter, Eh, B., Eq, Er, Jäger, Aa, N., Jung, Es, J., Ep, Y., Lalansingh, C. k., Leshchiner, I. b., Livitz, D. b., E. Z., Ep, Maruvka, Y. E. b., R, Et, Milovanovic, Nielsen, M. M., Eu, Paramasivam, Pedersen, Eh, J. S., Eu, Puiggròs, Ev, Sahinalp, S. C., Eo, Ew, Ex, Sarrafi, Eo, I., Stewart, Ex, Stobbe, C. b., M. D., Av, Wala, Bu, J. A. b., E, Wang, Ey, J. z., Be, Wendl, Ez, M. z., Fa, Werner, Fb, Aa, J., Fc, Wu, Ep, Z., Xue, Ep, H., Yamaguchi, T. N. k., Bn, V., Davis-Dusenbery, Bo, B. N., Fd, Grossman, R. L., Fe, Ff, Y., Heinold, Fg, M. C., Aa, Hinton, Ac, Abp, J., Jones, Abp, D. R., Menzies, Abp, A., Stebbings, Abp, L., Hess, J. M. b., Rosenberg, Et, M. b., R, Dunford, A. J. b., Gupta, M. b., Imielinski, Fh, M., Meyerson, Fi, M. b., E, Beroukhim, Ey, R. b., E, Reimand, Fj, J. k., Q, Dhingra, Br, P., Favero, Bt, Fk, F., Dentro, Bl, S., Abp, Cl, Wintersinger, Fl, J., Fm, Fn, Rudneva, V. g., Park, J. W., Fo, Hong, E. P., Fo, Heo, S. G., Fo, Kahles, Dg, A., Lehmann, K. -V., Dg, Di, Dj, Fp, Fq, Soulette, C. M., Aj, Shiraishi, Al, Y., Liu, Fr, F., Fs, He, Fr, Y., Demircioğlu, Ft, D., Davidson, Fu, N. R., Dg, Dl, Fp, Greger, L. f., Fv, S., Liu, Fw, Fv, D., Stark, Fw, S. G., Dj, Fp, Fx, Zhang, Fy, Amin, S. B., Fz, Ga, Gb, Bailey, Gc, P., Chateigner, A. n., Frenkel-Morgenstern, Gd, M., Hou, Fv, Y., Huska, Fw, M. R., Dm, Kilpinen, Ge, H., Lamaze, F. C. k., Fv, C., Fw, Li, Fv, X., Marin, Fw, M. G., Aj, Markowski, Dm, J., Nandi, Gf, T., Ojesina, A. I., Gg, Gh, Gi, Pan-Hammarström, Fv, Q., Park, Gj, P. J., Co, Pedamallu, Cp, C. S. b., E, Fj, Su, Fv, H., Tan, Fw, Gf, P., Gk, Gl, Teh, Gm, B. T., Gk, Gl, Gm, Gn, Go, Wang, Fv, J., Xiong, Fw, Ye, Yung, Fw, Zhang, C. n., Zheng, Fr, L., Zhu, Awadalla, Fw, P. k., L, Creighton, C. J., Gp, Fv, K., Yang, Fw, Göke, Ft, J., Zhang, Gq, Fr, Z., Brooks, Gr, A. N. b., Aj, Fittall, Ey, Martincorena, Abp, I., Rubio-Perez, Ch, C., Cj, Gs, Eu, M., Schumacher, S. b., Shapira, Gt, O. b., Ey, Tamborero, Ch, D., Mularoni, Cj, Ch, L., Hornshøj, Cj, Eu, H., Deu-Pons, Cj, J., Muiños, Gu, Ch, F., Bertl, Cj, Eu, J., Guo, Gv, Ev, Q., Gonzalez-Perez, Cj, Gw, Xiang, Gx, Q., Bazant, W. f., Barrera, E. f., Al-Sedairy, S. T., Gy, Aretz, Gz, A., Bell, Ha, C., Betancourt, Hb, M., Buchholz, Hc, C., Calvo, Hd, F., Chomienne, He, C., Dunn, Hf, M., Edmonds, Hg, S., Green, Hh, E., Gupta, Hi, S., C. M., Hh, Jegalian, Hj, K., Hk, N., Hl, Y., Hm, Hn, Nakagama, Ho, H., Nettekoven, Hp, G., Planko, Hp, L., Scott, Hk, D., Shibata, Hq, T., Shimizu, Hr, Hs, K., Stratton, Abp, M. R., Yugawa, Hs, T., Tortora, Ht, G., Vijayraghavan, Hu, Hi, K., Zenklusen, J. C., Hv, Hw, D., B. M., Dy, Aminou, B. n., Bartolome, Am, J., Boroevich, K. A., Cb, Boyce, Hx, Buchanan, R. f., Ak, A., Byrne, N. J. n., Hy, Z., Cho, Hz, S., Choi, Ia, W., Clapham, Abp, P., Dow, M. T., Hy, Eils, X, Ek, J., Farcas, El, Hy, C., Fayzullaev, N. n., Flicek, P. f., Heath, A. P., Ib, Hofmann, Ic, O., J. H., Id, Hudson, T. J., Ie, Hübschmann, If, Ac, D., Do, Ek, Ig, Ih, Ivkovic, Ii, S., Jeon, S. -H., Ia, Jiao, W. k., Kabbe, Dj, Fq, Kerssemakers, J. N. A., Aa, Ia, H., Ij, J., Koscher, Ik, M., Koures, Hy, A., Kovacevic, Ii, M., Lawerenz, El, C., Il, J., Mijalkovic, Mijalkovic-Lazic, A. M., Ii, Miyano, Nastic, Nicholson, Ocana, D. f., Ohi, Al, K., Ohno-Machado, Hy, L., Pihl, T. D., Im, Prinz, Radovic, Ii, P., Short, C. f., Sofia, H. J., Hh, Spring, Fe, J., Struck, A. J., Ak, Tijanic, Ii, N., Vicente, Hv, Z., Williams, Woo, Ia, Y., Wright, A. J. k., Yang, Hv, L., Hamilton, M. P., In, Johnson, T. A., Hx, Kahraman, Io, A., Ip, Iq, Kellis, M. b., Polak, Ir, P. b., C, Sallari, E, Sinnott-Armstrong, R. b., N. b., Ar, Von, Mering, Iq, C., Beltran, Is, Av, S., Gerhard, Bu, D. S., It, Av, M., Trotta, Bu, J. -R., Bu, Whalley, J. P., Bu, Niu, Iu, B., Espiritu, S. M. G. k., Gao, Ez, Y., Lalansingh, Iv, Teague, C. M. k., Abp, J. W., Wendl, M. C. z., Fa, Fb, Abascal, Abp, F., Bader, G. D. l., Bandopadhayay, P. b., Iw, Ix, Barenboim, J. k., Brunak, Iy, S., Carlevaro-Fita, Iz, Ja, J., Jb, Jc, Chakravarty, Jd, D., Chan, Je, C. W. Y., Aa, Choi, Dw, J. K., Jf, Diamanti, Jg, K., Fink, Frigola, Jh, Gu, J., Gambacorti-Passerini, Ji, C., Garsed, D. W., Jj, Haradhvala, N. J. b., Harmanci, R, A. O., Bk, Helmy, Jk, Fm, M., Herrmann, Aa, C., Ac, Jl, Hobolth, Ev, A., Hodzic, Gv, Ex, E., Dv, C., Isaev, Dw, K. k., Q, Izarzugaza, J. M. G., Iy, Jb, R., Juul, Jm, R. I., Eu, Kim, J. b., J. K., Jn, Jan, Komorowskijg, Lanzós, Jo, Jb, A., Jc, Jm, Larsson, Dg, E., Lee, Bk, D., Bk, S., Bk, X., Lin, Z. b., Liu, Jp, E. M., Br, Bt, Jq, Lochovsky, Bj, L., Bk, Gb, Lou, Madsen, Bk, Eu, T., Marchal, Jr, K., Martinez-Fundichely, Js, Br, A., Bs, Bt, Mcgillivray, P. D., Bj, Meyerson, Bk, W., Paczkowska, Jt, Park, M. k., Ju, K., Park, Jv, Jw, K., Pons, Jx, T., Pulido-Tamayo, Jr, S., Reyes-Salazar, Js, Ch, I., Reyna, M. A., Jy, Rubin, M. A., Jm, Jz, Ka, Kb, Kc, Salichos, Sander, Bk, Dg, C., Ey, Kd, Schumacher, Ke, S. E. b., Gt, Shackleton, Jj, M., Shen, Ke, C., Shrestha, Kf, Eo, R., Shuai, S. k., Tsunoda, L, Hx, T., Kg, Kh, Umer, Ki, H. M., Jg, Uusküla-Reimand, Kj, Kk, L., Verbeke, Kl, L. P. C., Js, Wadelius, Km, Kn, C., Wadi, L. k., Warrell, Bj, J., Bk, Wu, Ko, G., Kp, J., Zhang, Ez, X., Zhang, Kq, Bk, Y., Kr, Ks, Zhao, Kt, Z., Zou, Ku, L., Lawrence, M. S. b., R, Hx, Raphael, B. J., Jy, P. J., Gc, Craft, D. b., Goldman, Kv, M. J., Ea, Aburatani, Kw, H., Binder, Kx, H., Dinh, Ky, H. Q., Kz, S. C., Av, Hoffmann, Bu, Kx, S., Ky, La, Imbusch, Lb, C. D., Dv, Kretzmer, Ky, H., Laird, Lb, P. W., Lc, Martin-Subero, J. I., Bw, Nagae, Ld, Kw, G., Shen, Le, Lf, H., Ik, Q., Weichenhan, Lg, D., Zhou, Lf, W., Berman, B. P., Kz, Lh, Li, Brors, Dv, B., Er, Lj, Plass, Lg, C., Akdemir, K. C., Ei, Bowtell, D. D. L., Jj, Burns, K. H., Lk, Busanovich, Ll, J. b., Lm, Chan, Ln, K., Dueso-Barroso, Edwards, P. A., Lo, Etemadmoghadam, Lp, Jj, D., Haber, J. E., Lq, D. T. W., Lr, Ls, Ju, Y. S., Jf, Abp, Kazanov, M. D., Lt, Lu, Lv, Koh, Lw, Y., Kumar, Lx, Lee, K. b., E. A., Ly, J. J. -K., Co, Lynch, Cp, A. G., Lo, Lp, Lz, Macintyre, Lo, G., Markowetz, Lo, F., Navarro, Lp, F. C. P., Bj, Pearson, J. V., Ma, Rippe, Mb, Do, K., Scully, Mc, R., Villasante, Am, I., Waddell, Ma, N., Yang, Mb, Md, L., Yao, Fh, X., Yoon, Me, S. -S., Lx, C. -Z. b., E, Ey, Bergstrom, E. N., Mf, Boot, Gl, A., Covington, Mg, Ag, K., Fujimoto, Cb, A., M. N., Gl, Islam, Mg, S. M. A., Cv, Mcpherson, J. R., Gl, Morganella, Mg, Abp, S., Mustonen, Mh, V., Mi, Mj, A. W. T., Mk, Prokopec, S. D. k., Vázquez-García, Bn, I., Ml, Mm, Abp, Wu, Gl, Y., Yousif, Mg, F. k., Yu, Mn, W., Rozen, S. G., Gl, Gm, Mg, Rudneva, V. A. g., S. S., Ar, D. J., Da, Xia, Mo, T., Atwal, G. k., L, Fn, Chang, D. K., Gc, Cooke, Mp, S. L., Gc, Faltas, B. M., Dl, Haider, S. k., Kaiser, V. B., Mq, Karlić, Mr, R., Kato, Ms, M., Kübler, K. b., E, R, Margolin, Martin, Mt, S., Abp, Nik-Zainal, Mu, S., Mv, Mw, Abp, P’Ng, Semple, C. k., C. A., Mq, Smith, Ak, J., Sun, R. X. k., Thai, K. n., D. W., Mx, Yuan, My, Lo, K., Mt, Mz, Biankin, A. V., Gc, Mp, Na, Garraway, Nb, Ey, L., Grimmond, S. M., Nc, Adams, Abp, D. J., Anur, Nd, P., Cao, Ae, S., Christie, E. L., Jj, Cmero, Ne, M., Nf, Ng, Cun, Nh, Y., Dawson, Abp, K. J., S. C., Bl, Deshwar, A. G., Ni, Donmez, Eo, N., Drews, Ex, R. M., Lo, Gerstung, M. f., G, Ha, Haase, G. b., Cl, K., Jerman, L. g., Nj, Ji, Nk, Y., Jolly, Nl, Cl, C., Nm, J., Lee-Six, Abp, H., Malikic, Eo, S., Mitchell, Ex, T. J., Lp, Abp, Nn, Morris, Q. D., Fn, Oesper, No, Np, L., Peifer, Nh, M., Peto, Nq, M., Rosebrock, D. b., Rubanova, Ai, Y., Salcedo, Fn, Sengupta, A. k., Nr, S., Shi, No, R., Shin, S. J., Fy, Spiro, O. b., Vembu, No, S., Wintersinger, Ns, J. A., Fl, T. -P., Nh, Nt, K., Nu, H., Spellman, Nv, P. T., Nw, Weinstein, J. N., Ee, Chen, Ef, Fujita, Cb, M., Han, Kq, L., Hasegawa, Al, T., Komura, Al, M., Ae, J., Mizuno, Nx, S., Shimizu, Al, E., Ny, Xu, Nz, Y., Yamaguchi, Al, R., No, F., Kq, Y., Yoon, C. J., Jf, Yuan, Liang, Ae, H., Alawi, Oa, M., Borozan, Ob, Brewer, I. k., D. S., Oc, Cooper, Od, C. S., Od, Oe, Of, Desai, N. n., Grundhoff, Oa, A., Iskar, Og, Oh, M., Oi, X., Zapatka, Lichter, Eq, P., Alsop, Oh, Jj, K., Bruxner, T. J. C., Jh, Christ, A. N., Jh, Cordner, S. M., Oj, Cowin, P. A., Ok, Drapkin, Ol, R., Fereday, Ok, S., George, Gb, J., Ok, A., Holmes, Ma, O., Hung, Mb, J. A., Om, Kassahn, On, K. S., Jh, Kazakoff, Oo, S. H., Ma, Kennedy, Mb, C. J., Op, Leonard, Oq, C. R., Ma, Mileshkin, Mb, Jj, L., Miller, D. K., Jh, Mp, Or, Arnau, G. M., Ok, Mitchell, Ok, C., Newell, Ma, F., Nones, Mb, Ma, K., Patch, Mb, A. -M., Ma, Quinn, Mb, M. C., Ma, Taylor, Mb, D. F., Jh, Thorne, Ok, H., Traficante, Ok, N., Vedururu, Ok, R., N. M., Mb, Waring, P. M., Os, Wood, Ma, S., Mb, Xu, Ma, Q., Defazio, Mb, Ot, A., Ou, Ov, Anderson, M. J., Jh, Antonello, Ow, D., Barbour, A. P., Ox, Bassi, Oy, Ow, C., Bersani, Oz, S., Cataldo, Oz, I., Chantrill, Pa, L. A., Mp, Chiew, Pb, Y. -E., Ot, Chou, Mp, A., Cingarlini, Pc, Ht, S., Cloonan, Pd, N., Corbo, Pa, V., Davi, Pe, M. V., Pf, Duthie, F. R., Gc, Gill, Pg, A. J., Mp, Graham, Pc, J. S., Gc, Harliwong, Ph, Jh, I., Jamieson, N. B., Gc, Nb, Pi, Johns, A. L., Mp, Kench, Or, J. G., Mp, Pc, Pj, Landoni, Ow, L., Lawlor, R. T., Pa, Mafficini, Pa, A., Merrett, N. D., Ow, Miotto, Pk, Ow, M., Musgrove, E. A., Gc, Nagrial, A. M., Mp, Oien, K. A., Os, Pajic, Pl, Mp, M., Pinese, Pm, M., Robertson, A. J., Jh, Rooman, Mp, I., Rusev, B. C., Pa, Samra, J. S., Ow, Scardoni, Pc, Oz, M., Scarlett, C. J., Mp, Scarpa, Pn, Sereni, Ow, E., Sikora, K. O., Pa, Simbolo, Pe, M., Taschuk, M. L. n., Toon, C. W., Mp, Vicentini, Pa, C., Mp, J., Zeps, Po, N., Behren, Pp, Pq, A., Burke, Pr, H., Cebon, Pq, J., Dagg, R. A., Ps, Paoli-Iseppi, De, Pt, R., Dutton-Regester, Field, M. A., Pu, Fitzgerald, Pv, A., Hersey, Pr, P., Jakrot, Pr, V., Johansson, P. A., Ma, Kakavand, Pt, H., Kefford, R. F., Pw, Lau, L. M. S., Px, Long, G. V., Py, Pickett, H. A., Px, Pritchard, A. L., Ma, Pupo, G. M., Pz, Saw, R. P. M., Py, Schramm, S. -J., Qa, Shang, C. A., Pv, Py, P., Spillane, A. J., Py, Stretch, J. R., Py, Tembe, Ot, V., Thompson, Qa, J. F., Py, Vilain, R. E., Qb, Wilmott, J. S., Py, J. Y., Qc, Hayward, N. K., Ma, Mann, Pr, G. J., Ot, Scolyer, Qd, R. A., Ou, Py, Qb, Bartlett, Qe, Qf, J., Bavi, Qg, Qh, P., Chadwick, D. E., Qi, Chan-Seng-Yue, Qh, M., Cleary, Qh, S., Connor, Qj, A. A., Qj, Czajka, Qk, If, K., Denroche, R. E., Qh, Dhani, N. C., Ql, Eagles, If, J., Gallinger, Qj, Qk, Grant, R. C., Qh, Hedley, Qk, Ql, D., Hollingsworth, M. A., Qm, Jang, G. H., Qh, Kalimuthu, S. -B., Qn, Lungu, Qh, I., Luo, Qo, Mbabaali, X. k., If, F., T. A., Qk, J. K., If, Moore, M. J., Ql, Notta, Qh, F., Pasternack, Qp, If, D., Petersen, G. M., Qq, Roehrl, M. H. A. q., Qh, Qr, Qs, Qt, Sam, If, M., Selander, Qk, I., Serra, Os, S., Shahabi, Qn, S., Thayer, S. P., Qm, Timms, L. E., If, Wilson, G. W. k., Wilson, Qh, J. M., Qh, Wouters, B. G., Qu, J. D., If, Qh, Qv, Beck, T. A. n., Bhandari, Qw, Collins, V. k., C. C., Eo, Fleshner, N. E., Qx, Fox, N. S. k., Fraser, M. k., Heisler, L. E., Qy, Lalonde, E. k., Livingstone, J. k., Meng, Qz, A., Sabelnykova, V. Y. k., Shiah, Y. -J. k., Van der Kwast, Ra, T., Bristow, R. G. q., Rb, Rc, Rd, Re, Ding, Rf, S., Rg, D., Fv, L., Nie, Rg, Y., Xiao, Rh, Xing, Hm, R., Yang, Ri, Rj, Y., Banks, R. 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C., Sz, Macgrogan, Ta, G., Martens, J. W. M., Si, O’Meara, Pauporté, He, I., Pinder, Tb, S., Pivot, Tc, X., Provenzano, Td, E., Purdie, C. A., Te, Ramakrishna, Abp, M., Ramakrishnan, Abp, K., Reis-Filho, Sm, J., Richardson, A. L., Gt, Ringnér, Rw, M., Rodriguez, J. B., Am, Rodríguez-González, F. G., Iz, Romieu, Tf, G., Salgado, Os, R., Sauer, Sz, T., Shepherd, Abp, R., Sieuwerts, A. M., Si, Simpson, P. T., Sw, Smid, Si, M., Sotiriou, Span, P. N., Tg, Stefánsson, Ó. A., Th, Stenhouse, Ti, A., Stunnenberg, H. G., Fw, Sweep, Tj, Tk, F., Tan, B. K. T., Tl, Thomas, Tm, G., Thompson, A. M., Ti, Tommasi, Tn, S., Treilleux, To, I., Tutt, Tp, Ueno, N. T., Nv, Van, Laere, Sf, S., Van den Eynden, G. G., Sf, Vermeulen, Sf, P., Viari, Vincent-Salomon, Tj, A., Wong, B. H., Tq, Yates, Abp, X., Van, Deurzen, C. H. M., Tr, van de Vijver, M. J., Os, Van’T, Veer, Ts, L., Ammerpohl, Tt, O., Tu, Tv, Aukema, Tu, S., Tv, Tw, Bergmann, A. K., Tx, Bernhart, S. H., Kx, Ky, Lb, Borkhardt, Ty, A., Borst, Tz, C., Burkhardt, Ua, B., Claviez, Ub, A., Goebler, M. E., Uc, Haake, Tt, A., Haas, Tz, S., Hansmann, Ud, M., Hoell, J. I., Ty, Hummel, Ue, M., Karsch, Uf, D., Klapper, Tw, W., Kneba, Uf, M., Kreuz, Ug, M., Kube, Uh, D., Küppers, Ui, R., Lenze, Ue, D., Loeffler, López, Ca, C., Mantovani-Löffler, Tt, Uj, L., Möller, Uk, P., Ott, Ul, G., Radlwimmer, Oh, B., Richter, Tt, J., Rohde, Tw, Um, M., Rosenstiel, P. C., Un, Rosenwald, Uo, A., Schilhabel, M. B., Un, Schreiber, Up, S., Stadler, P. F., Kx, Staib, Uq, P., Stilgenbauer, Ur, S., Sungalee, S. g., Szczepanowski, Tw, M., Toprak, U. H., Ac, Trümper, Us, L. H. P., Uh, Wagener, Ca, R., Zenz, Tt, Er, T., Hovestadt, Oh, V., Von, Kalle, Do, C., Kool, Korshunov, Lr, Ik, A., Landgraf, Ut, P., Lehrach, Uu, Uv, H., Northcott, P. A., Uw, Pfister, S. M., Ik, Lr, Ux, Reifenberger, Uu, G., Warnatz, H. -J., Uv, Wolf, Uy, S., Yaspo, M. -L., Uv, Assenov, Uz, Y., Gerhauser, Minner, Va, S., Schlomm, Ct, T., Simon, Vb, Vc, R., Sauter, Vc, G., Sültmann, Er, H., Biswas, Vd, N. K., Ve, Maitra, Ve, A., Majumder, P. P., Ve, Sarin, Vf, R., Barbi, Pe, S., Bonizzato, Pa, G., Cantù, Dei, Tos, A. 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S., Oe, Cahill, Xo, D., Camacho, Oe, N., Dennis, N. M., Xo, Dudderidge, Xo, T., Edwards, Xp, S. E., Oe, Fisher, Xo, C., Foster, C. S., Xq, Ghori, Xr, Gill, Ws, P., Gnanapragasam, V. J., Nn, Gundem, Xs, Jq, G., Hamdy, F. C., Xt, Hawkins, Hazell, Xo, S., Howat, Nn, W., Isaacs, W. B., Xu, Karaszi, Ws, K., Kay, J. D., Ge, Xo, V., Kote-Jarai, Oe, Z., Kremeyer, Abp, B., Xo, P., Lambert, Ws, A., Leongamornlert, D. A., Oe, Abp, Livni, Xo, N., Y. -J., Xn, Luxton, Xv, H. J., Ge, Marsden, Ws, L., Massie, C. E., Lo, Matthews, Oe, L., Mayer, Xo, E., Mcdermott, Xw, Abp, U., Merson, Oe, S., Neal, D. E., Lo, Nn, Ng, Xx, A., Nicol, Ogden, Rowe, E. W., Xo, Shah, N. C., Nn, Xo, A., Verrill, Ws, C., Visakorpi, Xy, Du, T., Warren, A. Y., Nn, Whitaker, Xz, H. C., Ge, Xv, H., Van, As, Eeles, R. A., Oe, Abeshouse, Xo, Jq, A., Agrawal, Fe, N., Akbani, Mv, R., Al-Ahmadie, Ya, Jq, H., Albert, Qg, M., Aldape, Oi, K., Ally, Yb, Yc, A., Appelbaum, E. L. z., Armenia, Ge, Yd, J., Asa, Xe, S., Auman, Ye, J. T., Yf, Balasundaram, Yc, M., Balu, S. w., Barnholtz-Sloan, Yg, J., Bathe, Yh, O. F., Yi, Baylin, Yj, S. B., Dr, Benz, Xp, Yk, C., Berchuck, Yl, A., Berrios, Ym, M., Bigner, Yn, D., Birrer, M. r., Bodenheimer, T. w., Boice, Xg, L., Bootwalla, M. S., Ym, Bosenberg, Yo, M., Bowlby, Yc, R., Boyd, Yp, J., Broaddus, R. R., Oi, Yq, M., Brooks, Yc, D., Bullman, S. b., Caesar-Johnson, Fj, S. J., Hv, Carey, T. E., Yr, Carlsen, Cerfolio, Ys, R., Chandan, V. S., Yt, H. -W., Wt, Cherniack, Yd, A. D. b., Ey, Chien, Fj, Yu, J., Cho, J. b., Chuah, Yc, E., Cibulskis, C. b., Cope, Yv, L., Cordes, M. G. z., Curley, Xh, Yw, E., Czerniak, Oi, B., Danilova, Xb, Davis, I. J., Yx, Defreitas, T. b., Demchok, J. A., Hv, Dhalla, Yc, N., Dhir, Yy, R., Doddapaneni, H. V., Ag, El-Naggar, Oi, A., Felau, Xb, Hv, I., Ferguson, M. L., Yz, Finocchiaro, Za, G., Fong, K. M., Zb, Frazer, S. b., Friedman, Zc, W., Fronick, C. C. z., Fulton, Xh, Gabriel, L. A. z., Gao, S. B. b., Gehlenborg, N. b., Gershenwald, Zd, J. E., Ze, Ghossein, Zf, Sm, R., Giama, N. H., Zg, Gibbs, R. A., Ag, Gomez, Zh, C., Govindan, R. y., Hayes, D. N. w., Zi, Zj, Hegde, A. M., Ee, Heiman, Ef, Heins, D. I. b., Jq, Z., Hepperla, A. J. w., Holbrook, Ym, A., Holt, R. A., Yc, Hoyle, A. P. w., Hruban, R. H., Yv, Ag, J., Xg, M., Huntsman, Zk, D., Huse, Jq, J., Iacobuzio-Donahue, C. A., Sm, Ittmann, Zl, M., Jayaseelan, Zm, J. C., Ag, Jefferys, S. R. w., C. D., Zn, S. J. M., Zo, Juhl, Zp, H., Kang, K. J., Zq, Karlan, Zr, B., Kasaian, Zo, K., Kebebew, Zs, E., Kim, Zt, H. K., Zu, Korchina, Ag, V., Kundra, Wt, R., Lai, Yd, P. H., Ym, Lander, E. b., Zv, X., Levine, D. A., Jq, Lewis, Zw, Ag, L., Ley, Zx, T., H. I., Yc, Lin, P. b., Linehan, W. M., Zy, F. F., No, Ef, Y., Lype, Zz, L., Yc, Y., Maglinte, D. T., Ym, Aaa, Mardis, E. R. z., Yp, Aab, Marks, Ow, J., Aac, Marra, M. A., Yc, Matthew, T. J., Aj, Mayo, Mccune, Aad, K., Meier, S. R. b., Meng, S. w., Mieczkowski, P. A. v., Mikkelsen, Aae, T., Miller, C. A. z., Mills, Aaf, G. B., Morrison, Aag, Mose, Moser, L. E. w., C. D., Zg, Mungall, A. J., Yc, Yc, K., Mutch, Aah, D., Muzny, Aai, D. M., Myers, Aaj, J., Newton, Aj, Y., Noble, M. S. b., O’Donnell, Aak, P., Aal, B. P., Ochoa, Aam, J. -W., Parker, Aan, J. S., Pass, Aao, H., Pastore, Pennell, Aap, N. A., Perou, Aaq, C. M., Petrelli, Aar, N., Potapova, Aas, O., Rader, Aat, J. S., Ramalingam, Aau, S., Rathmell, Aav, W. K., Reuter, Sm, V., Reynolds, S. M., Zz, Ringel, Aaw, M., Roach, Aax, J., L. R., Zg, A. G., Yc, Sadeghi, Yc, S., Saller, Aay, C., Sanchez-Vega, Wt, F., Schadendorf, Yd, Eq, D., Aaz, Schein, J. E., Yc, Schmidt, H. K. z., Schultz, Yd, N., Seethala, Aba, R., Senbabaoglu, Dg, Y., Shelton, Yw, T., Shi, Y. w., Shih, J. b., Shmulevich, Fj, Zz, I., Shriver, Abb, C., Signoretti, Fj, S., Abc, Jb, Simons, J. V. w., Singer, Abd, Sipahimalani, Yc, P., Skelly, T. J. v., Smith-McCune, Socci, N. D., Dg, Soloway, Aan, M. G., Sood, Abe, A. K., Tam, Tan, D. v., Tarnuzzer, Hv, R., Thiessen, Abf, R. H., L. B., Xg, Tsao, Xe, M., Umbricht, Ye, Lk, C., Abg, Wv, Van Den Berg, D. J., Ym, Van, Meir, Abh, E. G., Veluvolu, U. v., Voet, D. b., Weinberger, Abi, P., Weisenberger, Wigle, Abj, D., Wilkerson, M. D. v., Wilson, R. K. z., Abk, Winterhoff, Abl, B., Wiznerowicz, Abm, M., Abn, Wong, T. z., Yc, Abo, W., Yau, Zhang, H. b., Yd, H., Hv, J., The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium View Correspondence (jump link), Medical Oncology, Pathology, IBM, Pharmacyclics, Novartis, Celgene, AstraZeneca, Bayer, Janssen Biotech, University of Chicago, Ipsen, Pfizer, Ono Pharmaceutical, Ariad Pharmaceuticals, Gilead Sciences, Bristol-Myers Squibb, University of St Andrews. School of Medicine, University of St Andrews. Statistics, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews. Cellular Medicine Division, RS: CAPHRI - R4 - Health Inequities and Societal Participation, Metamedica, Háskóli Íslands, University of Iceland, Faculty of Medicine, University of Helsinki, Department of Medical and Clinical Genetics, Research Programs Unit, Lauri Antti Aaltonen / Principal Investigator, ATG - Applied Tumor Genomics, Helsinki Institute of Life Science HiLIFE, Organismal and Evolutionary Biology Research Programme, Helsinki Institute for Information Technology, Institute of Biotechnology, Bioinformatics, Department of Computer Science, STEMM - Stem Cells and Metabolism Research Program, Centre of Excellence in Stem Cell Metabolism, Genome-Scale Biology (GSB) Research Program, Department of Physics, HUS Helsinki and Uusimaa Hospital District, University of Zurich, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Apollo - University of Cambridge Repository, Graduate School, Laboratory Genetic Metabolic Diseases, AGEM - Endocrinology, metabolism and nutrition, 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Weisenberger, D, Wigle, D, Wilkerson, M, Wilson, R, Winterhoff, B, Wiznerowicz, M, Wong, T, Wong, W, Xi, L, Yau, C, Consortium, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes, Demeulemeester, Jonas, Desmedt, Christine, Van Loo, Peter, Barcelona Supercomputing Center, Imperial College Healthcare NHS Trust- BRC Funding, Cancer Research UK, Basic (bio-) Medical Sciences, and Laboratory for Medical and Molecular Oncology
- Subjects
Male ,tert promoter mutations ,Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2] ,DNA Mutational Analysis ,Normal tissue ,systematic analysis ,Germline ,Transcriptome ,0302 clinical medicine ,Aetiology ,Càncer ,Cellular Senescence ,Cancer ,0303 health sciences ,dna-damage ,Massive parallel sequencing ,Pan cancer ,REARRANGEMENTS ,High-Throughput Nucleotide Sequencing ,Genomics ,Sciences bio-médicales et agricoles ,Telomere ,COMPREHENSIVE ,3. Good health ,TERT PROMOTER MUTATIONS ,signatures ,030220 oncology & carcinogenesis ,Science & Technology - Other Topics ,Erfðarannsóknir ,Human ,Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC] ,Evolution ,RNA Splicing ,Article ,Evolution, Molecular ,Structural variation ,RC0254 ,03 medical and health sciences ,SDG 3 - Good Health and Well-being ,Genetic ,genomics ,SYSTEMATIC ANALYSIS ,Genetics ,Genomics--Databases ,Humans ,Genetic Testing ,Molecular Biology ,SIGNATURES ,Whole genome sequencing ,1000 Multidisciplinary ,Chromothripsis ,Science & Technology ,RC0254 Neoplasms. Tumors. Oncology (including Cancer) ,Information Dissemination ,ResearchInstitutes_Networks_Beacons/mcrc ,Prevention ,Biology and Life Sciences ,Molecular ,Oncogenes ,Cloud Computing ,medicine.disease ,Genòmica ,Compute clouds ,Mutation ,570 Life sciences ,biology ,COMPREHENSIVE CHARACTERIZATION ,Genètica ,Whole Genome Sequencing--methods ,Background information ,Genetic / genetics ,Genome ,Germ-Line Mutation / genetics ,Human / genetics ,ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium ,Medizin ,Whole-genome ,Genome mapping ,Neoplasms ,2.1 Biological and endogenous factors ,Promoter Regions, Genetic ,Càncer -- Aspectes genètics ,Telomerase ,Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17] ,Multidisciplinary ,Manchester Cancer Research Centre ,genomics, cancer, profiling ,3rd-DAS ,10124 Institute of Molecular Life Sciences ,Women's cancers Radboud Institute for Health Sciences [Radboudumc 17] ,Multidisciplinary Sciences ,Parallel sequencing ,Female ,profiling ,Medical Genetics ,Engineering sciences. Technology ,Biotechnology ,General Science & Technology ,The Cancer Genome Atlas ,610 Medicine & health ,Computational biology ,QH426 Genetics ,Biology ,Consortium of the International Cancer Genome Consortium ,Promoter Regions ,Germline mutation ,Pan-cancer analysis ,Krabbameinsrannsóknir ,medicine ,cancer ,ddc:610 ,QH426 ,Germ-Line Mutation ,Medicinsk genetik ,Krabbamein ,030304 developmental biology ,Cell Proliferation ,LANDSCAPE ,Genome, Human ,comprehensive characterization ,Pan-cancer analysis of whole genomes ,Point mutation ,Human Genome ,Reproducibility of Results ,SOMATIC MUTATIONS ,EVOLUTION ,Cancer, sequencing, Chromothripsis, telomere ,DNA-DAMAGE ,Mutagenesis ,PATTERNS ,3111 Biomedicine ,CHARACTERIZATION - Abstract
Publisher's version (útgefin grein), Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. 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 genomes8,10,11,12,13,14,15,16,17,18., Competing interests Gad Getz receives research funds from IBM and Pharmacyclics and is an inventor on patent applications related to MuTect, ABSOLUTE, MutSig, MSMuTect, MSMutSig and POLYSOLVER. Hikmat Al-Ahmadie is consultant for AstraZeneca and Bristol-Myers Squibb. Samuel Aparicio is a founder and shareholder of Contextual Genomics. Pratiti Bandopadhayay receives grant funding from Novartis for an unrelated project. Rameen Beroukhim owns equity in Ampressa Therapeutics. Andrew Biankin receives grant funding from Celgene, AstraZeneca and is a consultant for or on advisory boards of AstraZeneca, Celgene, Elstar Therapeutics, Clovis Oncology and Roche. Ewan Birney is a consultant for Oxford Nanopore, Dovetail and GSK. Marcus Bosenberg is a consultant for Eli Lilly. Atul Butte is a cofounder of and consultant for Personalis, NuMedii, a consultant for Samsung, Geisinger Health, Mango Tree Corporation, Regenstrief Institute and in the recent past a consultant for 10x Genomics and Helix, a shareholder in Personalis, a minor shareholder in Apple, Twitter, Facebook, Google, Microsoft, Sarepta, 10x Genomics, Amazon, Biogen, CVS, Illumina, Snap and Sutro and has received honoraria and travel reimbursement for invited talks from Genentech, Roche, Pfizer, Optum, AbbVie and many academic institutions and health systems. Carlos Caldas has served on the Scientific Advisory Board of Illumina. Lorraine Chantrill acted on an advisory board for AMGEN Australia in the past 2 years. Andrew D. Cherniack receives research funding from Bayer. Helen Davies is an inventor on a number of patent applications that encompass the use of mutational signatures. Francisco De La Vega was employed at Annai Systems during part of the project. Ronny Drapkin serves on the scientific advisory board of Repare Therapeutics and Siamab Therapeutics. Rosalind Eeles has received an honorarium for the GU-ASCO meeting in San Francisco in January 2016 as a speaker, a honorarium and support from Janssen for the RMH FR meeting in November 2017 as a speaker (title: genetics and prostate cancer), a honorarium for an University of Chicago invited talk in May 2018 as speaker and an educational honorarium paid by Bayer & Ipsen to attend GU Connect ‘Treatment sequencing for mCRPC patients within the changing landscape of mHSPC’ at a venue at ESMO, Barcelona, on 28 September 2019. Paul Flicek is a member of the scientific advisory boards of Fabric Genomics and Eagle Genomics. Ronald Ghossein is a consultant for Veracyte. Dominik Glodzik is an inventor on a number of patent applications that encompass the use of mutational signatures. Eoghan Harrington is a full-time employee of Oxford Nanopore Technologies and is a stock holder. Yann Joly is responsible for the Data Access Compliance Office (DACO) of ICGC 2009-2018. Sissel Juul is a full-time employee of Oxford Nanopore Technologies and is a stock holder. Vincent Khoo has received personal fees and non-financial support from Accuray, Astellas, Bayer, Boston Scientific and Janssen. Stian Knappskog is a coprincipal investigator on a clinical trial that receives research funding from AstraZeneca and Pfizer. Ignaty Leshchiner is a consultant for PACT Pharma. Carlos López-Otín has ownership interest (including stock and patents) in DREAMgenics. Matthew Meyerson is a scientific advisory board chair of, and consultant for, OrigiMed, has obtained research funding from Bayer and Ono Pharma and receives patent royalties from LabCorp. Serena Nik-Zainal is an inventor on a number of patent applications that encompass the use of mutational signatures. Nathan Pennell has done consulting work with Merck, Astrazeneca, Eli Lilly and Bristol-Myers Squibb. Xose S. Puente has ownership interest (including stock and patents in DREAMgenics. Benjamin J. Raphael is a consultant for and has ownership interest (including stock and patents) in Medley Genomics. Jorge Reis-Filho is a consultant for Goldman Sachs and REPARE Therapeutics, member of the scientific advisory board of Volition RX and Paige.AI and an ad hoc member of the scientific advisory board of Ventana Medical Systems, Roche Tissue Diagnostics, InVicro, Roche, Genentech and Novartis. Lewis R. Roberts has received grant support from ARIAD Pharmaceuticals, Bayer, BTG International, Exact Sciences, Gilead Sciences, Glycotest, RedHill Biopharma, Target PharmaSolutions and Wako Diagnostics and has provided advisory services to Bayer, Exact Sciences, Gilead Sciences, GRAIL, QED Therapeutics and TAVEC Pharmaceuticals. Richard A. Scolyer has received fees for professional services from Merck Sharp & Dohme, GlaxoSmithKline Australia, Bristol-Myers Squibb, Dermpedia, Novartis Pharmaceuticals Australia, Myriad, NeraCare GmbH and Amgen. Tal Shmaya is employed at Annai Systems. Reiner Siebert has received speaker honoraria from Roche and AstraZeneca. Sabina Signoretti is a consultant for Bristol-Myers Squibb, AstraZeneca, Merck, AACR and NCI and has received funding from Bristol-Myers Squibb, AstraZeneca, Exelixis and royalties from Biogenex. Jared Simpson has received research funding and travel support from Oxford Nanopore Technologies. Anil K. Sood is a consultant for Merck and Kiyatec, has received research funding from M-Trap and is a shareholder in BioPath. Simon Tavaré is on the scientific advisory board of Ipsen and a consultant for Kallyope. John F. Thompson has received honoraria and travel support for attending advisory board meetings of GlaxoSmithKline and Provectus and has received honoraria for participation in advisory boards for MSD Australia and BMS Australia. Daniel Turner is a full-time employee of Oxford Nanopore Technologies and is a stock holder. Naveen Vasudev has received speaker honoraria and/or consultancy fees from Bristol-Myers Squibb, Pfizer, EUSA pharma, MSD and Novartis. Jeremiah A. Wala is a consultant for Nference. Daniel J. Weisenberger is a consultant for Zymo Research. Dai-Ying Wu is employed at Annai Systems. Cheng-Zhong Zhang is a cofounder and equity holder of Pillar Biosciences, a for-profit company that specializes in the development of targeted sequencing assays. The other authors declare no competing interests.
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- 2020
12. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
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Bailey, Matthew H, Meyerson, William U, Dursi, Lewis Jonathan, Wang, Liang-Bo, Dong, Guanlan, Liang, Wen-Wei, Weerasinghe, Amila, Shantao, Li, Kelso, Sean, Saksena, Gordon, Ellrott, Kyle, Wendl, Michael C, Wheeler, David A, Getz, Gad, Simpson, Jared T, Gerstein, Mark B, Ding, Lirehan, Akbani, Pavana, Anur, Matthew, H Bailey, Alex, Buchanan, Kami, Chiotti, Kyle, Covington, Allison, Creason, Ding, Li, Kyle, Ellrott, Fan, Yu, Steven, Foltz, Gad, Getz, Walker, Hale, David, Haussler, Julian, M Hess, Carolyn, M Hutter, Cyriac, Kandoth, Katayoon, Kasaian, Melpomeni, Kasapi, Dave, Larson, Ignaty, Leshchiner, John, Letaw, Singer, Ma, Michael, D McLellan, Yifei, Men, Gordon, B Mills, Beifang, Niu, Myron, Peto, Amie, Radenbaugh, Sheila, M Reynolds, Gordon, Saksena, Heidi, Sofia, Chip, Stewart, Adam, J Struck, Joshua, M Stuart, Wenyi, Wang, John, N Weinstein, David, A Wheeler, Christopher, K Wong, Liu, Xi, Kai, Ye, Matthias, Bieg, Paul, C Boutros, Ivo, Buchhalter, Adam, P Butler, Ken, Chen, Zechen, Chong, Oliver, Drechsel, Lewis Jonathan Dursi, Roland, Eils, Shadrielle M, G Espiritu, Robert, S Fulton, Shengjie, Gao, Josep L, L Gelpi, Mark, B Gerstein, Santiago, Gonzalez, Ivo, G Gut, Faraz, Hach, Michael, C Heinold, Jonathan, Hinton, Taobo, Hu, Vincent, Huang, Huang, Yi, Barbara, Hutter, David, R Jones, Jongsun, Jung, Natalie, Jäger, Hyung-Lae, Kim, Kortine, Kleinheinz, Sushant, Kumar, Yogesh, Kumar, Christopher, M Lalansingh, Ivica, Letunic, Dimitri, Livitz, Eric, Z Ma, Yosef, E Maruvka, R Jay Mashl, Andrew, Menzies, Ana, Milovanovic, Morten Muhlig Nielsen, Stephan, Ossowski, Nagarajan, Paramasivam, Jakob Skou Pedersen, Marc, D Perry, Montserrat, Puiggròs, Keiran, M Raine, Esther, Rheinbay, Romina, Royo, S Cenk Sahinalp, Iman, Sarrafi, Matthias, Schlesner, Jared, T Simpson, Lucy, Stebbings, Miranda, D Stobbe, Jon, W Teague, Grace, Tiao, David, Torrents, Jeremiah, A Wala, Jiayin, Wang, Sebastian, M Waszak, Joachim, Weischenfeldt, Michael, C Wendl, Johannes, Werner, Zhenggang, Wu, Hong, Xue, Sergei, Yakneen, Takafumi, N Yamaguchi, Venkata, D Yellapantula, Christina, K Yung, Junjun, Zhang, Lauri, A Aaltonen, Federico, Abascal, Adam, Abeshouse, Hiroyuki, Aburatani, David, J Adams, Nishant, Agrawal, Keun Soo Ahn, Sung-Min, Ahn, Hiroshi, Aikata, Rehan, Akbani, Kadir, C Akdemir, Hikmat, Al-Ahmadie, Sultan, T Al-Sedairy, Fatima, Al-Shahrour, Malik, Alawi, Monique, Albert, Kenneth, Aldape, Ludmil, B Alexandrov, Adrian, Ally, Kathryn, Alsop, Eva, G Alvarez, Fernanda, Amary, Samirkumar, B Amin, Brice, Aminou, Ole, Ammerpohl, Matthew, J Anderson, Yeng, Ang, Davide, Antonello, Samuel, Aparicio, Elizabeth, L Appelbaum, Yasuhito, Arai, Axel, Aretz, Koji, Arihiro, Shun-Ichi, Ariizumi, Joshua, Armenia, Laurent, Arnould, Sylvia, Asa, Yassen, Assenov, Gurnit, Atwal, Sietse, Aukema, J Todd Auman, Miriam, R Aure, Philip, Awadalla, Marta, Aymerich, Gary, D Bader, Adrian, Baez-Ortega, Peter, J Bailey, Miruna, Balasundaram, Saianand, Balu, Pratiti, Bandopadhayay, Rosamonde, E Banks, Stefano, Barbi, Andrew, P Barbour, Jonathan, Barenboim, Jill, Barnholtz-Sloan, Hugh, Barr, Elisabet, Barrera, John, Bartlett, Javier, Bartolome, Bassi, Claudio, Oliver, F Bathe, Daniel, Baumhoer, Prashant, Bavi, Stephen, B Baylin, Wojciech, Bazant, Duncan, Beardsmore, Timothy, A Beck, Sam, Behjati, Andreas, Behren, Cindy, Bell, Sergi, Beltran, Christopher, Benz, Andrew, Berchuck, Anke, K Bergmann, Erik, N Bergstrom, Benjamin, P Berman, Daniel, M Berney, Stephan, H Bernhart, Rameen, Beroukhim, Mario, Berrios, Samantha, Bersani, Johanna, Bertl, Miguel, Betancourt, Vinayak, Bhandari, Shriram, G Bhosle, Andrew, V Biankin, Darell, Bigner, Hans, Binder, Ewan, Birney, Michael, Birrer, Nidhan, K Biswas, Bodil, Bjerkehagen, Tom, Bodenheimer, Lori, Boice, Giada, Bonizzato, Johann, S De Bono, Arnoud, Boot, Moiz, S Bootwalla, Ake, Borg, Arndt, Borkhardt, Keith, A Boroevich, Ivan, Borozan, Christoph, Borst, Marcus, Bosenberg, Mattia, Bosio, Jacqueline, Boultwood, Guillaume, Bourque, G Steven Bova, David, T Bowen, Reanne, Bowlby, David D, L Bowtell, Sandrine, Boyault, Rich, Boyce, Jeffrey, Boyd, Alvis, Brazma, Paul, Brennan, Daniel, S Brewer, Arie, B Brinkman, Robert, G Bristow, Russell, R Broaddus, Jane, E Brock, Malcolm, Brock, Annegien, Broeks, Angela, N Brooks, Denise, Brooks, Benedikt, Brors, Søren, Brunak, Timothy J, C Bruxner, Alicia, L Bruzos, Christiane, Buchholz, Susan, Bullman, Hazel, Burke, Birgit, Burkhardt, Kathleen, H Burns, John, Busanovich, Carlos, D Bustamante, Atul, J Butte, Niall, J Byrne, Anne-Lise, Børresen-Dale, Samantha, J Caesar-Johnson, Andy, Cafferkey, Declan, Cahill, Claudia, Calabrese, Carlos, Caldas, Fabien, Calvo, Niedzica, Camacho, Peter, J Campbell, Elias, Campo, Cinzia, Cantù, Shaolong, Cao, Thomas, E Carey, Joana, Carlevaro-Fita, Rebecca, Carlsen, Ivana, Cataldo, Mario, Cazzola, Jonathan, Cebon, Robert, Cerfolio, Dianne, E Chadwick, Dimple, Chakravarty, Don, Chalmers, Calvin Wing Yiu Chan, Kin, Chan, Michelle, Chan-Seng-Yue, Vishal, S Chandan, David, K Chang, Stephen, J Chanock, Lorraine, A Chantrill, Aurélien, Chateigner, Nilanjan, Chatterjee, Kazuaki, Chayama, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Chen, Andrew, D Cherniack, Jeremy, Chien, Yoke-Eng, Chiew, Suet-Feung, Chin, Juok, Cho, Sunghoon, Cho, Jung Kyoon Choi, Wan, Choi, Christine, Chomienne, Su Pin Choo, Angela, Chou, Angelika, N Christ, Elizabeth, L Christie, Eric, Chuah, Carrie, Cibulskis, Kristian, Cibulskis, Sara, Cingarlini, Peter, Clapham, Alexander, Claviez, Sean, Cleary, Nicole, Cloonan, Marek, Cmero, Colin, C Collins, Ashton, A Connor, Susanna, L Cooke, Colin, S Cooper, Leslie, Cope, Corbo, Vincenzo, Matthew, G Cordes, Stephen, M Cordner, Isidro, Cortés-Ciriano, Prue, A Cowin, Brian, Craft, David, Craft, Chad, J Creighton, Yupeng, Cun, Erin, Curley, Ioana, Cutcutache, Karolina, Czajka, Bogdan, Czerniak, Rebecca, A Dagg, Ludmila, Danilova, Maria Vittoria Davi, Natalie, R Davidson, Helen, Davies, Ian, J Davis, Brandi, N Davis-Dusenbery, Kevin, J Dawson, Francisco, M De La Vega, Ricardo De Paoli-Iseppi, Timothy, Defreitas, Angelo, P Dei Tos, Olivier, Delaneau, John, A Demchok, Jonas, Demeulemeester, German, M Demidov, Deniz, Demircioğlu, Nening, M Dennis, Robert, E Denroche, Stefan, C Dentro, Nikita, Desai, Vikram, Deshpande, Amit, G Deshwar, Christine, Desmedt, Jordi, Deu-Pons, Noreen, Dhalla, Neesha, C Dhani, Priyanka, Dhingra, Rajiv, Dhir, Anthony, Dibiase, Klev, Diamanti, Shuai, Ding, Huy, Q Dinh, Luc, Dirix, Harshavardhan, Doddapaneni, Nilgun, Donmez, Michelle, T Dow, Ronny, Drapkin, Ruben, M Drews, Serge, Serge, Tim, Dudderidge, Ana, Dueso-Barroso, Andrew, J Dunford, Michael, Dunn, Fraser, R Duthie, Ken, Dutton-Regester, Jenna, Eagles, Douglas, F Easton, Stuart, Edmonds, Paul, A Edwards, Sandra, E Edwards, Rosalind, A Eeles, Anna, Ehinger, Juergen, Eils, Adel, El-Naggar, Matthew, Eldridge, Serap, Erkek, Georgia, Escaramis, Xavier, Estivill, Dariush, Etemadmoghadam, Jorunn, E Eyfjord, 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Katoh, Yoshiiku, Kawakami, Jonathan, D Kay, Stephen, H Kazakoff, Marat, D Kazanov, Maria, Keays, Electron, Kebebew, Richard, F Kefford, Manolis, Kellis, James, G Kench, Catherine, J Kennedy, Jules N, A Kerssemakers, David, Khoo, Vincent, Khoo, Narong, Khuntikeo, Ekta, Khurana, Helena, Kilpinen, Hark Kyun Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong, K Kim, Youngwook, Kim, Tari, A King, Wolfram, Klapper, Leszek, J Klimczak, Stian, Knappskog, Michael, Kneba, Bartha, M Knoppers, Youngil, Koh, Jan, Komorowski, Daisuke, Komura, Mitsuhiro, Komura, Kong, Gu, Marcel, Kool, Jan, O Korbel, Viktoriya, Korchina, Andrey, Korshunov, Michael, Koscher, Roelof, Koster, Zsofia, Kote-Jarai, Antonios, Koures, Milena, Kovacevic, Barbara, Kremeyer, Helene, Kretzmer, Markus, Kreuz, Savitri, Krishnamurthy, Dieter, Kube, Kiran, Kumar, Pardeep, Kumar, Ritika, Kundra, Kirsten, Kübler, Ralf, Küppers, Jesper, Lagergren, Phillip, H Lai, Peter, W Laird, Sunil, R Lakhani, Emilie, Lalonde, 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Kumar, P, Kundra, R, Kubler, K, Kuppers, R, Lagergren, J, Lai, P, Laird, P, Lakhani, S, Lalonde, E, Lamaze, F, Lambert, A, Lander, E, Landgraf, P, Landoni, L, Langerod, A, Lanzos, A, Larsimont, D, Larsson, E, Lathrop, M, Lau, L, Lawerenz, C, Lawlor, R, Lawrence, M, Lazar, A, Le, X, Lee, D, Lee, E, Lee, H, Lee, J, Lee, M, Lee-Six, H, Lehmann, K, Lehrach, H, Lenze, D, Leonard, C, Leongamornlert, D, Letourneau, L, Levine, D, Lewis, L, Ley, T, Li, C, Li, H, Li, J, Li, L, Li, X, Li, Y, Liang, H, Liang, S, Lichter, P, Lin, P, Lin, Z, Linehan, W, Lingjaerde, O, Liu, D, Liu, E, Liu, F, Liu, J, Liu, X, Livingstone, J, Livni, N, Lochovsky, L, Loeffler, M, Long, G, Lopez-Guillermo, A, Lou, S, Louis, D, Lovat, L, Lu, Y, Luchini, C, Lungu, I, Luo, X, Luxton, H, Lynch, A, Lype, L, Lopez, C, Lopez-Otin, C, Ma, Y, Macgrogan, G, Macrae, S, Macintyre, G, Madsen, T, Maejima, K, Mafficini, A, Maglinte, D, Maitra, A, Majumder, P, Malcovati, L, Malikic, S, Malleo, G, Mann, G, Mantovani-Loffler, L, Marchal, K, Marchegiani, G, Mardis, E, Margolin, A, Marin, M, Markowetz, F, Markowski, J, Marks, J, Marques-Bonet, T, Marra, M, Marsden, L, Martens, J, Martin, S, Martin-Subero, J, Martincorena, I, Martinez-Fundichely, A, Massie, C, Matthew, T, Matthews, L, Mayer, E, Mayes, S, Mayo, M, Mbabaali, F, Mccune, K, Mcdermott, U, Mcgillivray, P, Mcpherson, J, Mcpherson, T, Meier, S, Meng, A, Meng, S, Merrett, N, Merson, S, Meyerson, M, Mieczkowski, P, Mihaiescu, G, Mijalkovic, S, Mijalkovic-Lazic, A, Mikkelsen, T, Milella, M, Mileshkin, L, Miller, C, Miller, D, Miller, J, Minner, S, Miotto, M, Arnau, G, Mirabello, L, Mitchell, C, Mitchell, T, Miyano, S, Miyoshi, N, Mizuno, S, Molnar-Gabor, F, Moore, M, Moore, R, Morganella, S, Morris, Q, Morrison, C, Mose, L, Moser, C, Muinos, F, Mularoni, L, Mungall, A, Mungall, K, Musgrove, E, Mustonen, V, Mutch, D, Muyas, F, Muzny, D, Munoz, A, Myers, J, Myklebost, O, Moller, P, Nagae, G, Nagrial, A, Nahal-Bose, H, Nakagama, H, Nakagawa, H, Nakamura, H, Nakamura, T, Nakano, K, Nandi, T, Nangalia, J, Nastic, M, Navarro, A, Navarro, F, Neal, D, Nettekoven, G, Newell, F, Newhouse, S, Newton, Y, Ng, A, Nicholson, J, Nicol, D, Nie, Y, Nielsen, G, Nik-Zainal, S, Noble, M, Nones, K, Northcott, P, Notta, F, O'Connor, B, O'Donnell, P, O'Donovan, M, O'Meara, S, O'Neill, B, O'Neill, J, Ocana, D, Ochoa, A, Oesper, L, Ogden, C, Ohdan, H, Ohi, K, Ohno-Machado, L, Oien, K, Ojesina, A, Ojima, H, Okusaka, T, Omberg, L, Ong, C, Ott, G, Ouellette, B, P'Ng, C, Paczkowska, M, Paiella, S, Pairojkul, C, Pajic, M, Pan-Hammarstrom, Q, Papaemmanuil, E, Papatheodorou, I, Park, J, Park, K, Park, P, Parker, J, Parsons, S, Pass, H, Pasternack, D, Pastore, A, Patch, A, Pauporte, I, Pea, A, Pearson, J, Pedamallu, C, Pederzoli, P, Peifer, M, Pennell, N, Perou, C, Petersen, G, Petrelli, N, Petryszak, R, Pfister, S, Phillips, M, Pich, O, Pickett, H, Pihl, T, Pillay, N, Pinder, S, Pinese, M, Pinho, A, Pitkanen, E, Pivot, X, Pineiro-Yanez, E, Planko, L, Plass, C, Polak, P, Pons, T, Popescu, I, Potapova, O, Prasad, A, Preston, S, Prinz, M, Pritchard, A, Prokopec, S, Provenzano, E, Puente, X, Puig, S, Pulido-Tamayo, S, Pupo, G, Purdie, C, Quinn, M, Rabionet, R, Rader, J, Radlwimmer, B, Radovic, P, Raeder, B, Ramakrishna, M, Ramakrishnan, K, Ramalingam, S, Raphael, B, Rathmell, W, Rausch, T, Reifenberger, G, Reimand, J, Reis-Filho, J, Reuter, V, Reyes-Salazar, I, Reyna, M, Riazalhosseini, Y, Richardson, A, Richter, J, Ringel, M, Ringner, M, Rino, Y, Rippe, K, Roach, J, Roberts, L, Roberts, N, Roberts, S, Robertson, A, Rodriguez, J, Rodriguez-Martin, B, Rodriguez-Gonzalez, F, Roehrl, M, Rohde, M, Rokutan, H, Romieu, G, Rooman, I, Roques, T, Rosebrock, D, Rosenberg, M, Rosenstiel, P, Rosenwald, A, Rowe, E, Rozen, S, Rubanova, Y, Rubin, M, Rubio-Perez, C, Rudneva, V, Rusev, B, Ruzzenente, A, Ratsch, G, Sabarinathan, R, Sabelnykova, V, Sadeghi, S, Saini, N, Saito-Adachi, M, Salcedo, A, Salgado, R, Salichos, L, Sallari, R, Saller, C, Salvia, R, Sam, M, Samra, J, Sanchez-Vega, F, Sander, C, Sanders, G, Sarin, R, Sasaki-Oku, A, Sauer, T, Sauter, G, Saw, R, Scardoni, M, Scarlett, C, Scarpa, A, Scelo, G, Schadendorf, D, Schein, J, Schilhabel, M, Schlomm, T, Schmidt, H, Schramm, S, Schreiber, S, Schultz, N, Schumacher, S, Schwarz, R, Scolyer, R, Scott, D, Scully, R, Seethala, R, Segre, A, Selander, I, Semple, C, Senbabaoglu, Y, Sengupta, S, Sereni, E, Serra, S, Sgroi, D, Shackleton, M, Shah, N, Shahabi, S, Shang, C, Shang, P, Shapira, O, Shelton, T, Shen, C, Shen, H, Shepherd, R, Shi, R, Shi, Y, Shiah, Y, Shibata, T, Shih, J, Shimizu, E, Shimizu, K, Shin, S, Shiraishi, Y, Shmaya, T, Shmulevich, I, Shorser, S, Short, C, Shrestha, R, Shringarpure, S, Shriver, C, Shuai, S, Sidiropoulos, N, Siebert, R, Sieuwerts, A, Sieverling, L, Signoretti, S, Sikora, K, Simbolo, M, Simon, R, Simons, J, Simpson, P, Singer, S, Sinnott-Armstrong, N, Sipahimalani, P, Skelly, T, Smid, M, Smith, J, Smith-McCune, K, Socci, N, Soloway, M, Song, L, Sood, A, Sothi, S, Sotiriou, C, Soulette, C, Span, P, Spellman, P, Sperandio, N, Spillane, A, Spiro, O, Spring, J, Staaf, J, Stadler, P, Staib, P, Stark, S, Stefansson, O, Stegle, O, Stein, L, Stenhouse, A, Stilgenbauer, S, Stratton, M, Stretch, J, Stunnenberg, H, Su, H, Su, X, Sun, R, Sungalee, S, Susak, H, Suzuki, A, Sweep, F, Szczepanowski, M, Sultmann, H, Yugawa, T, Tam, A, Tamborero, D, Tan, B, Tan, D, Tan, P, Tanaka, H, Taniguchi, H, Tanskanen, T, Tarabichi, M, Tarnuzzer, R, Tarpey, P, Taschuk, M, Tatsuno, K, Tavare, S, Taylor, D, Taylor-Weiner, A, Teh, B, Tembe, V, Temes, J, Thai, K, Thayer, S, Thiessen, N, Thomas, G, Thomas, S, Thompson, A, Thompson, J, Thompson, R, Thorne, H, Thorne, L, Thorogood, A, Tijanic, N, Timms, L, Tirabosco, R, Tojo, M, Tommasi, S, Toon, C, Toprak, U, Tortora, G, Tost, J, Totoki, Y, Townend, D, Traficante, N, Treilleux, I, Trotta, J, Trumper, L, Tsao, M, Tsunoda, T, Tubio, J, Tucker, O, Turkington, R, Turner, D, Tutt, A, Ueno, M, Ueno, N, Umbricht, C, Umer, H, Underwood, T, Urban, L, Urushidate, T, Ushiku, T, Uuskula-Reimand, L, Valencia, A, Van Den Berg, D, Van Laere, S, Van Loo, P, Van Meir, E, Van den Eynden, G, Van der Kwast, T, Vasudev, N, Vazquez, M, Vedururu, R, Veluvolu, U, Vembu, S, Verbeke, L, Vermeulen, P, Verrill, C, Viari, A, Vicente, D, Vicentini, C, Raghavan, K, Viksna, J, Vilain, R, Villasante, I, Vincent-Salomon, A, Visakorpi, T, Voet, D, Vyas, P, Vazquez-Garcia, I, Waddell, N, Wadelius, C, Wadi, L, Wagener, R, Wang, Q, Wang, Y, Wang, Z, Waring, P, Warnatz, H, Warrell, J, Warren, A, Wedge, D, Weichenhan, D, Weinberger, P, Weisenberger, D, Welch, I, Whalley, J, Whitaker, H, Wigle, D, Wilkerson, M, Williams, A, Wilmott, J, Wilson, G, Wilson, J, Wilson, R, Winterhoff, B, Wintersinger, J, Wiznerowicz, M, Wolf, S, Wong, B, Wong, T, Wong, W, Woo, Y, Wood, S, Wouters, B, Wright, A, Wright, D, Wright, M, Wu, C, Wu, D, Wu, G, Wu, J, Wu, K, Wu, Y, Xia, T, Xiang, Q, Xiao, X, Xing, R, Xiong, H, Xu, Q, Xu, Y, Yachida, S, Yamaguchi, R, Yamamoto, M, Yamamoto, S, Yamaue, H, Yang, F, Yang, H, Yang, J, Yang, L, Yang, S, Yang, T, Yang, Y, Yao, X, Yaspo, M, Yates, L, Yau, C, Ye, C, Yoon, C, Yoon, S, Yousif, F, Yu, J, Yu, K, Yu, W, Yu, Y, Yuan, K, Yuan, Y, Yuen, D, Zaikova, O, Zamora, J, Zapatka, M, Zenklusen, J, Zenz, T, Zeps, N, Zhang, C, Zhang, F, Zhang, H, Zhang, X, Zhang, Y, Zhang, Z, Zhao, Z, Zheng, L, Zheng, X, Zhou, W, Zhou, Y, Bin, Z, Zhu, H, Zhu, J, Zhu, S, Zou, L, Zou, X, Defazio, A, van As, N, van Deurzen, C, van de Vijver, M, van't Veer, L, von Mering, C, Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Háskóli Íslands, University of Iceland, Tampere University, BioMediTech, TAYS Cancer Centre, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews. Cellular Medicine Division, University of St Andrews. Statistics, University of St Andrews. School of Medicine, University of Zurich, Gerstein, Mark B, Ding, Li, Bailey, Matthew H [0000-0003-4526-9727], Wheeler, David A [0000-0002-9056-6299], Gerstein, Mark B [0000-0002-9746-3719], Faculty of Economic and Social Sciences and Solvay Business School, Lauri Antti Aaltonen / Principal Investigator, Genome-Scale Biology (GSB) Research Program, Department of Medical and Clinical Genetics, Organismal and Evolutionary Biology Research Programme, Helsinki Institute for Information Technology, Institute of Biotechnology, Bioinformatics, Department of Computer Science, Faculty of Medicine, and HUS Helsinki and Uusimaa Hospital District
- Subjects
VARIANTS ,0302 clinical medicine ,706/648/697/129/2043 ,Databases, Genetic ,Cancer genomics ,SOMATIC POINT MUTATIONS ,Càncer ,lcsh:Science ,Exome ,Exome sequencing ,Cancer ,Base Composition ,Neoplasms -- genetics ,1184 Genetics, developmental biology, physiology ,3100 General Physics and Astronomy ,3. Good health ,030220 oncology & carcinogenesis ,Science & Technology - Other Topics ,Transformació genètica ,Genetic databases ,Erfðarannsóknir ,Human ,GENES ,Science ,1600 General Chemistry ,General Biochemistry, Genetics and Molecular Biology ,RC0254 ,03 medical and health sciences ,Genetic ,SDG 3 - Good Health and Well-being ,1300 General Biochemistry, Genetics and Molecular Biology ,Exome Sequencing ,Genetics ,Humans ,Author Correction ,Retrospective Studies ,Whole genome sequencing ,Comparative genomics ,Science & Technology ,RC0254 Neoplasms. Tumors. Oncology (including Cancer) ,INSERTIONS ,DNA ,PERFORMANCE ,Human genetics ,Communication and replication ,Cancérologie ,692/4028/67/69 ,Genòmica ,030104 developmental biology ,Mutation ,Genome mutation ,Human genome ,lcsh:Q ,COMPREHENSIVE CHARACTERIZATION ,Genètica ,0301 basic medicine ,Medizin ,General Physics and Astronomy ,Genome ,Whole Exome Sequencing ,Genetic transformation ,International Cancer Genome Consortium ,Neoplasms ,631/114/2399 ,Genamengi ,Medicine and Health Sciences ,Medicine(all) ,Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17] ,Multidisciplinary ,318 Medical biotechnology ,Exome -- genetics ,article ,Exons ,Women's cancers Radboud Institute for Health Sciences [Radboudumc 17] ,Multidisciplinary Sciences ,CAPTURE ,1181 Ecology, evolutionary biology ,oncology ,DNA, Intergenic ,139 ,Medical Genetics ,Biotechnology ,ICGC/TCGA Pan-Cancer Analysis ,3122 Cancers ,610 Medicine & health ,45/23 ,QH426 Genetics ,Biology ,MC3 Working Group ,Databases ,Germline mutation ,PCAWG novel somatic mutation calling methods working group ,Krabbameinsrannsóknir ,Cancer Genome Atlas ,Genome, Human -- genetics ,ddc:610 ,QH426 ,Medicinsk genetik ,Krabbamein ,Intergenic ,Whole Genome Sequencing ,Genome, Human ,Human Genome ,PCAWG Consortium ,DAS ,General Chemistry ,DELETIONS ,Good Health and Well Being ,10032 Clinic for Oncology and Hematology ,3111 Biomedicine ,631/1647/2217/748 - Abstract
MC3 Working Group: Rehan Akbani21, Pavana Anur22, Matthew H. Bailey1,2,3, Alex Buchanan9, Kami Chiotti9, Kyle Covington12,23, Allison Creason9, Li Ding1,2,3,20, Kyle Ellrott9, Yu Fan21, Steven Foltz1,2, Gad Getz8,14,15,16, Walker Hale12, David Haussler24,25, Julian M. Hess8,26, Carolyn M. Hutter27, Cyriac Kandoth28, Katayoon Kasaian29,30, Melpomeni Kasapi27, Dave Larson1 , Ignaty Leshchiner8, John Letaw31, Singer Ma32, Michael D. McLellan1,3,20, Yifei Men32, Gordon B. Mills33,34, Beifang Niu35, Myron Peto22, Amie Radenbaugh24, Sheila M. Reynolds36, Gordon Saksena8, Heidi Sofia27, Chip Stewart8, Adam J. Struck31, Joshua M. Stuart24,37, Wenyi Wang21, John N. Weinstein38, David A. Wheeler12,13, Christopher K. Wong24,39, Liu Xi12 & Kai Ye40,41 21Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. 22Molecular and Medical Genetics, OHSU Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA. 23Castle Biosciences Inc, Friendswood, TX 77546, USA. 24UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 25Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 26Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02114, USA. 27National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20894, USA. 28Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. 29Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada. 30Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada. 31Computational Biology Program, School of Medicine, Oregon Health and Science University, Portland, OR 97239, USA. 32DNAnexus Inc, Mountain View, CA 94040, USA. 33Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA. 34Precision Oncology, OHSU Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA. 35Computer Network Information Center, Chinese Academy of Sciences, Beijing, China. 36Institute for Systems Biology, Seattle, WA 98109, USA. 37Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 38Department of Bioinformatics and Computational Biology and Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. 39Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 40School of Elect, PCAWG novel somatic mutation calling methods working group: Matthew H. Bailey1,2,3, Beifang Niu35, Matthias Bieg42,43, Paul C. Boutros6,44,45,46, Ivo Buchhalter43,47,48, Adam P. Butler49, Ken Chen50, Zechen Chong51, Li Ding1,2,3,20, Oliver Drechsel52,53, Lewis Jonathan Dursi6,7, Roland Eils47,48,54,55, Kyle Ellrott9, Shadrielle M. G. Espiritu6, Yu Fan21, Robert S. Fulton1,3,20, Shengjie Gao56, Josep L. l. Gelpi57,58, Mark B. Gerstein5,18,19, Gad Getz8,14,15,16, Santiago Gonzalez59,60, Ivo G. Gut52,61, Faraz Hach62,63, Michael C. Heinold47,48, Julian M. Hess8,26, Jonathan Hinton49, Taobo Hu64, Vincent Huang6, Yi Huang65,66, Barbara Hutter43,67,68, David R. Jones49, Jongsun Jung69, Natalie Jäger47, Hyung-Lae Kim70, Kortine Kleinheinz47,48, Sushant Kumar5,19, Yogesh Kumar64, Christopher M. Lalansingh6, Ignaty Leshchiner8, Ivica Letunic71, Dimitri Livitz8, Eric Z. Ma64, Yosef E. Maruvka8,26,72, R. Jay Mashl1,2, Michael D. McLellan1,3,20, Andrew Menzies49, Ana Milovanovic57, Morten Muhlig Nielsen73, Stephan Ossowski52,53,74, Nagarajan Paramasivam43,47, Jakob Skou Pedersen73,75, Marc D. Perry76,77, Montserrat Puiggròs57, Keiran M. Raine49, Esther Rheinbay8,14,72, Romina Royo57, S. Cenk Sahinalp62,78,79, Gordon Saksena8, Iman Sarrafi62,78, Matthias Schlesner47,80, Jared T. Simpson6,17, Lucy Stebbings49, Chip Stewart8, Miranda D. Stobbe52,61, Jon W. Teague49, Grace Tiao8, David Torrents57,81, Jeremiah A. Wala8,14,82, Jiayin Wang1,40,66, Wenyi Wang21, Sebastian M. Waszak60, Joachim Weischenfeldt60,83,84, Michael C. Wendl1,10,11, Johannes Werner47,85, Zhenggang Wu64, Hong Xue64, Sergei Yakneen60, Takafumi N. Yamaguchi6, Kai Ye40,41, Venkata D. Yellapantula20,86, Christina K. Yung76 & Junjun Zhang76, PCAWG Consortium: Lauri A. Aaltonen87, Federico Abascal49, Adam Abeshouse88, Hiroyuki Aburatani89, David J. Adams49, Nishant Agrawal90, Keun Soo Ahn91, Sung-Min Ahn92, Hiroshi Aikata93, Rehan Akbani21, Kadir C. Akdemir50, Hikmat Al-Ahmadie88, Sultan T. Al-Sedairy94, Fatima Al-Shahrour95, Malik Alawi96,97, Monique Albert98, Kenneth Aldape99,100, Ludmil B. Alexandrov49,101,102, Adrian Ally30, Kathryn Alsop103, Eva G. Alvarez104,105,106, Fernanda Amary107, Samirkumar B. Amin108,109,110, Brice Aminou76, Ole Ammerpohl111,112, Matthew J. Anderson113, Yeng Ang114, Davide Antonello115, Pavana Anur22, Samuel Aparicio116, Elizabeth L. Appelbaum1,117, Yasuhito Arai118, Axel Aretz119, Koji Arihiro93, Shun-ichi Ariizumi120, Joshua Armenia121, Laurent Arnould122, Sylvia Asa123,124, Yassen Assenov125, Gurnit Atwal6,126,127, Sietse Aukema112,128, J. Todd Auman129, Miriam R. Aure130, Philip Awadalla6,126, Marta Aymerich131, Gary D. Bader126, Adrian Baez-Ortega132, Matthew H. Bailey1,2,3, Peter J. Bailey133, Miruna Balasundaram30, Saianand Balu134, Pratiti Bandopadhayay8,135,136, Rosamonde E. Banks137, Stefano Barbi138, Andrew P. Barbour139,140, Jonathan Barenboim6, Jill Barnholtz-Sloan141,142, Hugh Barr143, Elisabet Barrera59, John Bartlett98,144, Javier Bartolome57, Claudio Bassi115, Oliver F. Bathe145,146, Daniel Baumhoer147, Prashant Bavi148, Stephen B. Baylin149,150, Wojciech Bazant59, Duncan Beardsmore151, Timothy A. Beck152,153, Sam Behjati49, Andreas Behren154, Beifang Niu35, Cindy Bell155, Sergi Beltran52,61, Christopher Benz156, Andrew Berchuck157, Anke K. Bergmann158, Erik N. Bergstrom101,102, Benjamin P. Berman159,160,161, Daniel M. Berney162, Stephan H. Bernhart163,164,165, Rameen Beroukhim8,14,82, Mario Berrios166, Samantha Bersani167, Johanna Bertl73,168, Miguel Betancourt169, Vinayak Bhandari6,44, Shriram G. Bhosle49, Andrew V. Biankin133,170,171,172, Matthias Bieg42,43, Darell Bigner173, Hans Binder163,164, Ewan Birney59, Michael Birrer72, Nidhan K. Biswas174, Bodil Bjerkehagen147,175, Tom Bodenheimer134, Lori Boice176, Giada Bonizzato177, Johann S. De Bono178, Arnoud Boot179,180, Moiz S. Bootwalla166, Ake Borg181, Arndt Borkhardt182, Keith A. Boroevich183,184, Ivan Borozan6, Christoph Borst185, Marcus Bosenberg186, Mattia Bosio52,53,57, Jacqueline Boultwood187, Guillaume Bourque188,189, Paul C. Boutros6,44,45,46, G. Steven Bova190, David T. Bowen49,191, Reanne Bowlby30, David D. L. Bowtell103, Sandrine Boyault192, Rich Boyce59, Jeffrey Boyd193, Alvis Brazma59, Paul Brennan194, Daniel S. Brewer195,196, Arie B. Brinkman197, Robert G. Bristow44,198,199,200,201, Russell R. Broaddus99, Jane E. Brock202, Malcolm Brock203, Annegien Broeks204, Angela N. Brooks8,24,37,82, Denise Brooks30, Benedikt Brors67,205,206, Søren Brunak207,208, Timothy J. C. Bruxner113,209, Alicia L. Bruzos104,105,106, Alex Buchanan9, Ivo Buchhalter43,47,48, Christiane Buchholz210, Susan Bullman8,82, Hazel Burke211, Birgit Burkhardt212, Kathleen H. Burns213,214, John Busanovich8,215, Carlos D. Bustamante216,217, Adam P. Butler49, Atul J. Butte218, Niall J. Byrne76, Anne-Lise Børresen-Dale130,219, Samantha J. Caesar-Johnson220, Andy Cafferkey59, Declan Cahill221, Claudia Calabrese59,60, Carlos Caldas222,223, Fabien Calvo224, Niedzica Camacho178, Peter J. Campbell49,225, Elias Campo226,227, Cinzia Cantù177, Shaolong Cao21, Thomas E. Carey228, Joana Carlevaro-Fita229,230,231, Rebecca Carlsen30, Ivana Cataldo167,177, Mario Cazzola232, Jonathan Cebon154, Robert Cerfolio233, Dianne E. Chadwick234, Dimple Chakravarty235, Don Chalmers236, Calvin Wing Yiu Chan47,237, Kin Chan238, Michelle Chan-Seng-Yue148, Vishal S. Chandan239, David K. Chang133,170, Stephen J. Chanock240, Lorraine A. Chantrill170,241, Aurélien Chateigner76,242, Nilanjan Chatterjee149,243, Kazuaki Chayama93, Hsiao-Wei Chen114,121, Jieming Chen218, Ken Chen50, Yiwen Chen21, Zhaohong Chen244, Andrew D. Cherniack8,82, Jeremy Chien245, Yoke-Eng Chiew246,247, Suet-Feung Chin222,223, Juok Cho8, Sunghoon Cho248, Jung Kyoon Choi249, Wan Choi250, Christine Chomienne251, Zechen Chong51, Su Pin Choo252, Angela Chou170,246, Angelika N. Christ113, Elizabeth L. Christie103, Eric Chuah30, Carrie Cibulskis8, Kristian Cibulskis8, Sara Cingarlini253, Peter Clapham49, Alexander Claviez254, Sean Cleary148,255, Nicole Cloonan256, Marek Cmero257,258,259, Colin C. Collins62, Ashton A. Connor255,260, Susanna L. Cooke133, Colin S. Cooper178,196,261, Leslie Cope149, Vincenzo Corbo138,177, Matthew G. Cordes1,262, Stephen M. Cordner263, Isidro Cortés-Ciriano264,265,266, Kyle Covington12,23, Prue A. Cowin267, Brian Craft24, David Craft8,268, Chad J. Creighton269, Yupeng Cun270, Erin Curley271, Ioana Cutcutache179,180, Karolina Czajka272, Bogdan Czerniak99,273, Rebecca A. Dagg274, Ludmila Danilova149, Maria Vittoria Davi275, Natalie R. Davidson276,277,278,279,280, Helen Davies49,281,282, Ian J. Davis283, Brandi N. Davis-Dusenbery284, Kevin J. Dawson49, Francisco M. De La Vega216,217,285, Ricardo De Paoli-Iseppi211, Timothy Defreitas8, Angelo P. Dei Tos286, Olivier Delaneau287,288,289, John A. Demchok220, Jonas Demeulemeester290,291, German M. Demidov52,53,74, Deniz Demircioğlu292,293, Nening M. Dennis221, Robert E. Denroche148, Stefan C. Dentro49,290,294, Nikita Desai76, Vikram Deshpande72, Amit G. Deshwar295, Christine Desmedt296,297, Jordi Deu-Pons298,299, Noreen Dhalla30, Neesha C. Dhani300, Priyanka Dhingra301,302, Rajiv Dhir303, Anthony DiBiase304, Klev Diamanti305, Li Ding1,2,3,20, Shuai Ding306, Huy Q. Dinh159, Luc Dirix307, HarshaVardhan Doddapaneni12, Nilgun Donmez62,78, Michelle T. Dow244, Ronny Drapkin308, Oliver Drechsel52,53, Ruben M. Drews223, Serge Serge49, Tim Dudderidge150,221, Ana Dueso-Barroso57, Andrew J. Dunford8, Michael Dunn309, Lewis Jonathan Dursi6,7, Fraser R. Duthie133,310, Ken Dutton-Regester311, Jenna Eagles272, Douglas F. Easton312,313, Stuart Edmonds314, Paul A. Edwards223,315, Sandra E. Edwards178, Rosalind A. Eeles178,221, Anna Ehinger316, Juergen Eils54,55, Roland Eils47,48,54,55, Adel El-Naggar99,273, Matthew Eldridge223, Kyle Ellrott9, Serap Erkek60, Georgia Escaramis53,317,318, Shadrielle M. G. Espiritu6, Xavier Estivill53,319, Dariush Etemadmoghadam103, Jorunn E. Eyfjord320, Bishoy M. Faltas280, Daiming Fan321, Yu Fan21, William C. Faquin72, Claudiu Farcas244, Matteo Fassan322, Aquila Fatima323, Francesco Favero324, Nodirjon Fayzullaev76, Ina Felau220, Sian Fereday103, Martin L. Ferguson325, Vincent Ferretti76,326, Lars Feuerbach205, Matthew A. Field327, J. Lynn Fink57,113, Gaetano Finocchiaro328, Cyril Fisher221, Matthew W. Fittall290, Anna Fitzgerald329, Rebecca C. Fitzgerald282, Adrienne M. Flanagan330, Neil E. Fleshner331, Paul Flicek59, John A. Foekens332, Kwun M. Fong333, Nuno A. Fonseca59,334, Christopher S. Foster335,336, Natalie S. Fox6, Michael Fraser6, Scott Frazer8, Milana Frenkel-Morgenstern337, William Friedman338, Joan Frigola298, Catrina C. Fronick1,262, Akihiro Fujimoto184, Masashi Fujita184, Masashi Fukayama339, Lucinda A. Fulton1 , Robert S. Fulton1,3,20, Mayuko Furuta184, P. Andrew Futreal340, Anja Füllgrabe59, Stacey B. Gabriel8, Steven Gallinger148,255,260, Carlo Gambacorti-Passerini341, Jianjiong Gao121, Shengjie Gao56, Levi Garraway82, Øystein Garred342, Erik Garrison49, Dale W. Garsed103, Nils Gehlenborg8,343, Josep L. l. Gelpi57,58, Joshy George110, Daniela S. Gerhard344, Clarissa Gerhauser345, Jeffrey E. Gershenwald346,347, Mark B. Gerstein5,18,19, Moritz Gerstung59,60, Gad Getz8,14,15,16, Mohammed Ghori49, Ronald Ghossein348, Nasra H. Giama349, Richard A. Gibbs12, Anthony J. Gill170,350, Pelvender Gill351, Dilip D. Giri348, Dominik Glodzik49, Vincent J. Gnanapragasam352,353, Maria Elisabeth Goebler354, Mary J. Goldman24, Carmen Gomez355, Santiago Gonzalez59,60, Abel Gonzalez-Perez298,299,356, Dmitry A. Gordenin357, James Gossage358, Kunihito Gotoh359, Ramaswamy Govindan3, Dorthe Grabau360, Janet S. Graham133,361, Robert C. Grant148,260, Anthony R. Green315, Eric Green27, Liliana Greger59, Nicola Grehan282, Sonia Grimaldi177, Sean M. Grimmond362, Robert L. Grossman363, Adam Grundhoff97,364, Gunes Gundem88, Qianyun Guo75, Manaswi Gupta8, Shailja Gupta365, Ivo G. Gut52,61, Marta Gut52,61, Jonathan Göke292,366, Gavin Ha8, Andrea Haake111, David Haan37, Siegfried Haas185, Kerstin Haase290, James E. Haber367, Nina Habermann60, Faraz Hach62,63, Syed Haider6, Natsuko Hama118, Freddie C. Hamdy351, Anne Hamilton267, Mark P. Hamilton368, Leng Han369, George B. Hanna370, Martin Hansmann371, Nicholas J. Haradhvala8,72, Olivier Harismendy102,372, Ivon Harliwong113, Arif O. Harmanci5,373, Eoghan Harrington374, Takanori Hasegawa375, David Haussler24,25, Steve Hawkins223, Shinya Hayami376, Shuto Hayashi375, D. Neil Hayes134,377,378, Stephen J. Hayes379,380, Nicholas K. Hayward211,311, Steven Hazell221, Yao He381, Allison P. Heath382, Simon C. Heath52,61, David Hedley300, Apurva M. Hegde38, David I. Heiman8, Michael C. Heinold47,48, Zachary Heins88, Lawrence E. Heisler152, Eva Hellstrom-Lindberg383, Mohamed Helmy384, Seong Gu Heo385, Austin J. Hepperla134, José María Heredia-Genestar386, Carl Herrmann47,48,387, Peter Hersey211, Julian M. Hess8,26, Holmfridur Hilmarsdottir320, Jonathan Hinton49, Satoshi Hirano388, Nobuyoshi Hiraoka389, Katherine A. Hoadley134,390, Asger Hobolth75,168, Ermin Hodzic78, Jessica I. Hoell182, Steve Hoffmann163,164,165,391, Oliver Hofmann392, Andrea Holbrook166, Aliaksei Z. Holik53, Michael A. Hollingsworth393, Oliver Holmes209,311, Robert A. Holt30, Chen Hong205,237, Eun Pyo Hong385, Jongwhi H. Hong394, Gerrit K. Hooijer395, Henrik Hornshøj73, Fumie Hosoda118, Yong Hou56,396, Volker Hovestadt397, William Howat352, Alan P. Hoyle134, Ralph H. Hruban149, Jianhong Hu12, Taobo Hu64, Xing Hua240, Kuan-lin Huang1,398, Mei Huang176, Mi Ni Huang179,180, Vincent Huang6, Yi Huang65,66, Wolfgang Huber60, Thomas J. Hudson272,399, Michael Hummel400, Jillian A. Hung246,247, David Huntsman401, Ted R. Hupp402, Jason Huse88, Matthew R. Huska403, Barbara Hutter43,67,68, Carolyn M. Hutter27, Daniel Hübschmann48,54,404,405,406, Christine A. Iacobuzio-Donahue348, Charles David Imbusch205, Marcin Imielinski407,408, Seiya Imoto375, William B. Isaacs409, Keren Isaev6,44, Shumpei Ishikawa410, Murat Iskar397, S. M. Ashiqul Islam244, Michael Ittmann411,412,413, Sinisa Ivkovic284, Jose M. G. Izarzugaza414, Jocelyne Jacquemier415, Valerie Jakrot211, Nigel B. Jamieson133,172,416, Gun Ho Jang148, Se Jin Jang417, Joy C. Jayaseelan12, Reyka Jayasinghe1 , Stuart R. Jefferys134, Karine Jegalian418, Jennifer L. Jennings419, Seung-Hyup Jeon250, Lara Jerman60,420, Yuan Ji421,422, Wei Jiao6, Peter A. Johansson311, Amber L. Johns170, Jeremy Johns272, Rory Johnson230,423, Todd A. Johnson183, Clemency Jolly290, Yann Joly424, Jon G. Jonasson320, Corbin D. Jones425, David R. Jones49, David T. W. Jones426,427, Nic Jones428, Steven J. M. Jones30, Jos Jonkers204, Young Seok Ju49,249, Hartmut Juhl429, Jongsun Jung69, Malene Juul73, Randi Istrup Juul73, Sissel Juul374, Natalie Jäger47, Rolf Kabbe47, Andre Kahles276,277,278,279,430, Abdullah Kahraman431,432,433, Vera B. Kaiser434, Hojabr Kakavand211, Sangeetha Kalimuthu148, Christof von Kalle405, Koo Jeong Kang91, Katalin Karaszi351, Beth Karlan435, Rosa Karlić436, Dennis Karsch437, Katayoon Kasaian29,30, Karin S. Kassahn113,438, Hitoshi Katai439, Mamoru Kato440, Hiroto Katoh410, Yoshiiku Kawakami93, Jonathan D. Kay117, Stephen H. Kazakoff209,311, Marat D. Kazanov441,442,443, Maria Keays59, Electron Kebebew444,445, Richard F. Kefford446, Manolis Kellis8,447, James G. Kench170,350,448, Catherine J. Kennedy246,247, Jules N. A. Kerssemakers47, David Khoo273, Vincent Khoo221, Narong Khuntikeo115,449, Ekta Khurana301,302,450,451, Helena Kilpinen117, Hark Kyun Kim452, Hyung-Lae Kim70, Hyung-Yong Kim415, Hyunghwan Kim250, Jaegil Kim8, Jihoon Kim453, Jong K. Kim454, Youngwook Kim455,456, Tari A. King457,458,459, Wolfram Klapper128, Kortine Kleinheinz47,48, Leszek J. Klimczak460, Stian Knappskog49,461, Michael Kneba437, Bartha M. Knoppers424, Youngil Koh462,463, Jan Komorowski305,464, Daisuke Komura410, Mitsuhiro Komura375, Gu Kong415, Marcel Kool426,465, Jan O. Korbel59,60, Viktoriya Korchina12, Andrey Korshunov465, Michael Koscher465, Roelof Koster466, Zsofia Kote-Jarai178, Antonios Koures244, Milena Kovacevic284, Barbara Kremeyer49, Helene Kretzmer164,165, Markus Kreuz467, Savitri Krishnamurthy99,468, Dieter Kube469, Kiran Kumar8, Pardeep Kumar221, Sushant Kumar5,19, Yogesh Kumar64, Ritika Kundra114,121, Kirsten Kübler8,14,72, Ralf Küppers470, Jesper Lagergren383,471, Phillip H. Lai166, Peter W. Laird472, Sunil R. Lakhani473, Christopher M. Lalansingh6, Emilie Lalonde6, Fabien C. Lamaze6, Adam Lambert351, Eric Lander8, Pablo Landgraf474,475, Luca Landoni115, Anita Langerød130, Andrés Lanzós230,231,423, Denis Larsimont476, Erik Larsson477, Mark Lathrop189, Loretta M. S. Lau478, Chris Lawerenz55, Rita T. Lawlor177, Michael S. Lawrence8,72,183, Alexander J. Lazar99,108, Xuan Le479, Darlene Lee30, Donghoon Lee5, Eunjung Alice Lee480, Hee Jin Lee417, Jake June-Koo Lee264,266, Jeong-Yeon Lee481, Juhee Lee482, Ming Ta Michael Lee340, Henry Lee-Six49, Kjong-Van Lehmann276,277,278,279,430, Hans Lehrach483, Dido Lenze400, Conrad R. Leonard209,311, Daniel A. Leongamornlert49,178, Ignaty Leshchiner8, Louis Letourneau484, Ivica Letunic71, Douglas A. Levine88,485, Lora Lewis12, Tim Ley486, Chang Li56,396, Constance H. Li6,44, Haiyan Irene Li30, Jun Li21, Lin Li56, Shantao Li5, Siliang Li56,396, Xiaobo Li56,396, Xiaotong Li5, Xinyue Li56, Yilong Li49, Han Liang21, Sheng-Ben Liang234, Peter Lichter68,397, Pei Lin8, Ziao Lin8,487, W. M. Linehan488, Ole Christian Lingjærde489, Dongbing Liu56,396, Eric Minwei Liu88,301,302, Fei-Fei Liu201,490, Fenglin Liu381,491, Jia Liu492, Xingmin Liu56,396, Julie Livingstone6, Dimitri Livitz8, Naomi Livni221, Lucas Lochovsky5,19,110, Markus Loeffler467, Georgina V. Long211, Armando Lopez-Guillermo493, Shaoke Lou5,19, David N. Louis72, Laurence B. Lovat117, Yiling Lu38, Yong-Jie Lu162,494, Youyong Lu495,496,497, Claudio Luchini167, Ilinca Lungu144,148, Xuemei Luo152, Hayley J. Luxton117, Andy G. Lynch223,315,498, Lisa Lype36, Cristina López111,112, Carlos López-Otín499, Eric Z. Ma64, Yussanne Ma30, Gaetan MacGrogan500, Shona MacRae501, Geoff Macintyre223, Tobias Madsen73, Kazuhiro Maejima184, Andrea Mafficini177, Dennis T. Maglinte166,502, Arindam Maitra174, Partha P. Majumder174, Luca Malcovati232, Salem Malikic62,78, Giuseppe Malleo115, Graham J. Mann211,246,503, Luisa Mantovani-Löffler504, Kathleen Marchal505,506, Giovanni Marchegiani115, Elaine R. Mardis1,193,507, Adam A. Margolin31, Maximillian G. Marin37, Florian Markowetz223,315, Julia Markowski403, Jeffrey Marks508, Tomas Marques-Bonet61,81,386,509, Marco A. Marra30, Luke Marsden351, John W. M. Martens332, Sancha Martin49,510, Jose I. Martin-Subero81,511, Iñigo Martincorena49, Alexander Martinez-Fundichely301,302,451 Yosef E. Maruvka8,26,72, R. Jay Mashl1,2, Charlie E. Massie223, Thomas J. Matthew37, Lucy Matthews178, Erik Mayer221,512, Simon Mayes513, Michael Mayo30, Faridah Mbabaali272, Karen McCune514, Ultan McDermott49, Patrick D. McGillivray19, Michael D. McLellan1,3,20, John D. McPherson148,272,515, John R. McPherson179,180, Treasa A. McPherson260, Samuel R. Meier8, Alice Meng516, Shaowu Meng134, Andrew Menzies49, Neil D. Merrett115,517, Sue Merson178, Matthew Meyerson8,14,82, William U. Meyerson4,5, Piotr A. Mieczkowski518, George L. Mihaiescu76, Sanja Mijalkovic284, Ana Mijalkovic Mijalkovic-Lazic284, Tom Mikkelsen519, Michele Milella253, Linda Mileshkin103, Christopher A. Miller1 , David K. Miller113,170, Jessica K. Miller272, Gordon B. Mills33,34, Ana Milovanovic57, Sarah Minner520, Marco Miotto115, Gisela Mir Arnau267, Lisa Mirabello240, Chris Mitchell103, Thomas J. Mitchell49,315,352, Satoru Miyano375, Naoki Miyoshi375, Shinichi Mizuno521, Fruzsina Molnár-Gábor522, Malcolm J. Moore300, Richard A. Moore30, Sandro Morganella49, Quaid D. Morris127,490, Carl Morrison523,524, Lisle E. Mose134, Catherine D. Moser349, Ferran Muiños298,299, Loris Mularoni298,299, Andrew J. Mungall30, Karen Mungall30, Elizabeth A. Musgrove133, Ville Mustonen525,526,527, David Mutch528, Francesc Muyas52,53,74, Donna M. Muzny12, Alfonso Muñoz59, Jerome Myers529, Ola Myklebost461, Peter Möller530, Genta Nagae89, Adnan M. Nagrial170, Hardeep K. Nahal-Bose76, Hitoshi Nakagama531, Hidewaki Nakagawa184, Hiromi Nakamura118, Toru Nakamura388, Kaoru Nakano184, Tannistha Nandi532, Jyoti Nangalia49, Mia Nastic284, Arcadi Navarro61,81,386, Fabio C. P. Navarro19, David E. Neal223,352, Gerd Nettekoven533, Felicity Newell209,311, Steven J. Newhouse59, Yulia Newton37, Alvin Wei Tian Ng534, Anthony Ng535, Jonathan Nicholson49, David Nicol221, Yongzhan Nie321,536, G. Petur Nielsen72, Morten Muhlig Nielsen73, Serena Nik-Zainal49,281,282,537, Michael S. Noble8, Katia Nones209,311, Paul A. Northcott538, Faiyaz Notta148,539, Brian D. O’Connor76,540, Peter O’Donnell541, Maria O’Donovan282, Sarah O’Meara49, Brian Patrick O’Neill542, J. Robert O’Neill543, David Ocana59, Angelica Ochoa88, Layla Oesper544, Christopher Ogden221, Hideki Ohdan93, Kazuhiro Ohi375, Lucila Ohno-Machado244, Karin A. Oien523,545, Akinyemi I. Ojesina546,547,548, Hidenori Ojima549, Takuji Okusaka550, Larsson Omberg551, Choon Kiat Ong552, Stephan Ossowski52,53,74, German Ott553, B. F. Francis Ouellette76,554, Christine P’ng6, Marta Paczkowska6, Salvatore Paiella115, Chawalit Pairojkul523, Marina Pajic170, Qiang Pan-Hammarström56,555, Elli Papaemmanuil49, Irene Papatheodorou59, Nagarajan Paramasivam43,47, Ji Wan Park385, Joong-Won Park556, Keunchil Park557,558, Kiejung Park559, Peter J. Park264,266, Joel S. Parker518, Simon L. Parsons124, Harvey Pass560, Danielle Pasternack272, Alessandro Pastore276, Ann-Marie Patch209,311, Iris Pauporté251, Antonio Pea115, John V. Pearson209,311, Chandra Sekhar Pedamallu8,14,82, Jakob Skou Pedersen73,75, Paolo Pederzoli115, Martin Peifer270, Nathan A. Pennell561, Charles M. Perou129,518, Marc D. Perry76,77, Gloria M. Petersen562, Myron Peto22, Nicholas Petrelli563, Robert Petryszak59, Stefan M. Pfister426,465,564, Mark Phillips424, Oriol Pich298,299, Hilda A. Pickett478, Todd D. Pihl565, Nischalan Pillay566, Sarah Pinder567, Mark Pinese170, Andreia V. Pinho568, Esa Pitkänen60, Xavier Pivot569, Elena Piñeiro-Yáñez95, Laura Planko533, Christoph Plass345, Paz Polak8,14,15, Tirso Pons570, Irinel Popescu571, Olga Potapova572, Aparna Prasad52, Shaun R. Preston573, Manuel Prinz47, Antonia L. Pritchard311, Stephenie D. Prokopec6, Elena Provenzano574, Xose S. Puente499, Sonia Puig176, Montserrat Puiggròs57, Sergio Pulido-Tamayo505,506, Gulietta M. Pupo246, Colin A. Purdie575, Michael C. Quinn209,311, Raquel Rabionet52,53,576, Janet S. Rader577, Bernhard Radlwimmer397, Petar Radovic284, Benjamin Raeder60, Keiran M. Raine49, Manasa Ramakrishna49, Kamna Ramakrishnan49, Suresh Ramalingam578, Benjamin J. Raphael579, W. Kimryn Rathmell580, Tobias Rausch60, Guido Reifenberger475, Jüri Reimand6,44, Jorge Reis-Filho348, Victor Reuter348, Iker Reyes-Salazar298, Matthew A. Reyna579, Sheila M. Reynolds36, Esther Rheinbay8,14,72, Yasser Riazalhosseini189, Andrea L. Richardson323, Julia Richter111,128, Matthew Ringel581, Markus Ringnér181, Yasushi Rino582, Karsten Rippe405, Jeffrey Roach583, Lewis R. Roberts349, Nicola D. Roberts49, Steven A. Roberts584, A. Gordon Robertson30, Alan J. Robertson113, Javier Bartolomé Rodriguez57, Bernardo Rodriguez-Martin104,105,106, F. Germán Rodríguez-González83,332, Michael H. A. Roehrl44,123,148,234,585,586, Marius Rohde587, Hirofumi Rokutan440, Gilles Romieu588, Ilse Rooman170, Tom Roques262, Daniel Rosebrock8, Mara Rosenberg8,72, Philip C. Rosenstiel589, Andreas Rosenwald590, Edward W. Rowe221,591, Romina Royo57, Steven G. Rozen179,180,592, Yulia Rubanova17,127, Mark A. Rubin423,593,594,595,596, Carlota Rubio-Perez298,299,597, Vasilisa A. Rudneva60, Borislav C. Rusev177, Andrea Ruzzenente598, Gunnar Rätsch276,277,278,279,280,430, Radhakrishnan Sabarinathan298,299,599, Veronica Y. Sabelnykova6, Sara Sadeghi30, S. Cenk Sahinalp62,78,79, Natalie Saini357, Mihoko Saito-Adachi440, Gordon Saksena8, Adriana Salcedo6, Roberto Salgado600, Leonidas Salichos5,19, Richard Sallari8, Charles Saller601, Roberto Salvia115, Michelle Sam272, Jaswinder S. Samra115,602, Francisco Sanchez-Vega114,121, Chris Sander276,603,604, Grant Sanders134, Rajiv Sarin605, Iman Sarrafi62,78, Aya Sasaki-Oku184, Torill Sauer489, Guido Sauter520, Robyn P. M. Saw211, Maria Scardoni167, Christopher J. Scarlett170,606, Aldo Scarpa177, Ghislaine Scelo194, Dirk Schadendorf68,607, Jacqueline E. Schein30, Markus B. Schilhabel589, Matthias Schlesner47,80, Thorsten Schlomm84,608, Heather K. Schmidt1 , Sarah-Jane Schramm246, Stefan Schreiber609, Nikolaus Schultz121, Steven E. Schumacher8,323, Roland F. Schwarz59,403,405,610, Richard A. Scolyer211,448,602, David Scott428, Ralph Scully611, Raja Seethala612, Ayellet V. Segre8,613, Iris Selander260, Colin A. Semple434, Yasin Senbabaoglu276, Subhajit Sengupta614, Elisabetta Sereni115, Stefano Serra585, Dennis C. Sgroi72, Mark Shackleton103, Nimish C. Shah352, Sagedeh Shahabi234, Catherine A. Shang329, Ping Shang211, Ofer Shapira8,323, Troy Shelton271, Ciyue Shen603,604, Hui Shen615, Rebecca Shepherd49, Ruian Shi490, Yan Shi134, Yu-Jia Shiah6, Tatsuhiro Shibata118,616, Juliann Shih8,82, Eigo Shimizu375, Kiyo Shimizu617, Seung Jun Shin618, Yuichi Shiraishi375, Tal Shmaya285, Ilya Shmulevich36, Solomon I. Shorser6, Charles Short59, Raunak Shrestha62, Suyash S. Shringarpure217, Craig Shriver619, Shimin Shuai6,126, Nikos Sidiropoulos83, Reiner Siebert112,620, Anieta M. Sieuwerts332, Lina Sieverling205,237, Sabina Signoretti202,621, Katarzyna O. Sikora177, Michele Simbolo138, Ronald Simon520, Janae V. Simons134, Jared T. Simpson6,17, Peter T. Simpson473, Samuel Singer115,458, Nasa Sinnott-Armstrong8,217, Payal Sipahimalani30, Tara J. Skelly390, Marcel Smid332, Jaclyn Smith622, Karen Smith-McCune514, Nicholas D. Socci276, Heidi J. Sofia27, Matthew G. Soloway134, Lei Song240, Anil K. Sood623,624,625, Sharmila Sothi626, Christos Sotiriou244, Cameron M. Soulette37, Paul N. Span627, Paul T. Spellman22, Nicola Sperandio177, Andrew J. Spillane211, Oliver Spiro8, Jonathan Spring628, Johan Staaf181, Peter F. Stadler163,164,165, Peter Staib629, Stefan G. Stark277,279,618,630, Lucy Stebbings49, Ólafur Andri Stefánsson631, Oliver Stegle59,60,632, Lincoln D. Stein6,126, Alasdair Stenhouse633, Chip Stewart8, Stephan Stilgenbauer634, Miranda D. Stobbe52,61, Michael R. Stratton49, Jonathan R. Stretch211, Adam J. Struck31, Joshua M. Stuart24,37, Henk G. Stunnenberg396,635, Hong Su56,396, Xiaoping Su99, Ren X. Sun6, Stephanie Sungalee60, Hana Susak52,53, Akihiro Suzuki89,636, Fred Sweep637, Monika Szczepanowski128, Holger Sültmann67,638, Takashi Yugawa617, Angela Tam30, David Tamborero298,299, Benita Kiat Tee Tan639, Donghui Tan518, Patrick Tan180,532,592,640, Hiroko Tanaka375, Hirokazu Taniguchi616, Tomas J. Tanskanen641, Maxime Tarabichi49,290, Roy Tarnuzzer220, Patrick Tarpey642, Morgan L. Taschuk152, Kenji Tatsuno89, Simon Tavaré223,643, Darrin F. Taylor113, Amaro Taylor-Weiner8, Jon W. Teague49, Bin Tean Teh180,592,640,644,645, Varsha Tembe246, Javier Temes104,105, Kevin Thai76, Sarah P. Thayer393, Nina Thiessen30, Gilles Thomas646, Sarah Thomas221, Alan Thompson221, Alastair M. Thompson633, John F. Thompson211, R. Houston Thompson647, Heather Thorne103, Leigh B. Thorne176, Adrian Thorogood424, Grace Tiao8, Nebojsa Tijanic284, Lee E. Timms272, Roberto Tirabosco648, Marta Tojo106, Stefania Tommasi649, Christopher W. Toon170, Umut H. Toprak48,650, David Torrents57,81, Giampaolo Tortora651,652, Jörg Tost653, Yasushi Totoki118, David Townend654, Nadia Traficante103, Isabelle Treilleux655,656, Jean-Rémi Trotta61, Lorenz H. P. Trümper469, Ming Tsao124,539, Tatsuhiko Tsunoda183,657,658,659, Jose M. C. Tubio104,105,106, Olga Tucker660, Richard Turkington661, Daniel J. Turner513, Andrew Tutt323, Masaki Ueno376, Naoto T. Ueno662, Christopher Umbricht151,213,663, Husen M. Umer305,664, Timothy J. Underwood665, Lara Urban59,60, Tomoko Urushidate616, Tetsuo Ushiku339, Liis Uusküla-Reimand666,667, Alfonso Valencia57,81, David J. Van Den Berg166, Steven Van Laere307, Peter Van Loo290,291, Erwin G. Van Meir668, Gert G. Van den Eynden307, Theodorus Van der Kwast123, Naveen Vasudev137, Miguel Vazquez57,669, Ravikiran Vedururu267, Umadevi Veluvolu518, Shankar Vembu490,670, Lieven P. C. Verbeke506,671, Peter Vermeulen307, Clare Verrill351,672, Alain Viari177, David Vicente57, Caterina Vicentini177, K. Vijay Raghavan365, Juris Viksna673, Ricardo E. Vilain674, Izar Villasante57, Anne Vincent-Salomon635, Tapio Visakorpi190, Douglas Voet8, Paresh Vyas311,351, Ignacio Vázquez-García49,86,675,676, Nick M. Waddell209, Nicola Waddell209,311, Claes Wadelius677, Lina Wadi6, Rabea Wagener111,112, Jeremiah A. Wala8,14,82, Jian Wang56, Jiayin Wang1,40,66, Linghua Wang12, Qi Wang465, Wenyi Wang21, Yumeng Wang21, Zhining Wang220, Paul M. Waring523, Hans-Jörg Warnatz483, Jonathan Warrell5,19, Anne Y. Warren352,678, Sebastian M. Waszak60, David C. Wedge49,294,679, Dieter Weichenhan345, Paul Weinberger680, John N. Weinstein38, Joachim Weischenfeldt60,83,84, Daniel J. Weisenberger166, Ian Welch681, Michael C. Wendl1,10,11, Johannes Werner47,85, Justin P. Whalley61,682, David A. Wheeler12,13, Hayley C. Whitaker117, Dennis Wigle683, Matthew D. Wilkerson518, Ashley Williams244, James S. Wilmott211, Gavin W. Wilson6,148, Julie M. Wilson148, Richard K. Wilson1,684, Boris Winterhoff685, Jeffrey A. Wintersinger17,127,384, Maciej Wiznerowicz686,687, Stephan Wolf688, Bernice H. Wong689, Tina Wong1,30, Winghing Wong690, Youngchoon Woo250, Scott Wood209,311, Bradly G. Wouters44, Adam J. Wright6, Derek W. Wright133,691, Mark H. Wright217, Chin-Lee Wu72, Dai-Ying Wu285, Guanming Wu692, Jianmin Wu170, Kui Wu56,396, Yang Wu179,180, Zhenggang Wu64, Liu Xi12, Tian Xia693, Qian Xiang76, Xiao Xiao66, Rui Xing497, Heng Xiong56,396, Qinying Xu209,311, Yanxun Xu694, Hong Xue64, Shinichi Yachida118,695, Sergei Yakneen60, Rui Yamaguchi375, Takafumi N. Yamaguchi6, Masakazu Yamamoto120, Shogo Yamamoto89, Hiroki Yamaue376, Fan Yang490, Huanming Yang56, Jean Y. Yang696, Liming Yang220, Lixing Yang697, Shanlin Yang306, Tsun-Po Yang270, Yang Yang369, Xiaotong Yao408,698, Marie-Laure Yaspo483, Lucy Yates49, Christina Yau156, Chen Ye56,396, Kai Ye40,41, Venkata D. Yellapantula20,86, Christopher J. Yoon249, Sung-Soo Yoon463, Fouad Yousif6, Jun Yu699, Kaixian Yu700, Willie Yu701, Yingyan Yu702, Ke Yuan223,510,703, Yuan Yuan21, Denis Yuen6, Takashi Yugawa617, Christina K. Yung76, Olga Zaikova704, Jorge Zamora49,104,105,106, Marc Zapatka397, Jean C. Zenklusen220, Thorsten Zenz67, Nikolajs Zeps705,706, Cheng-Zhong Zhang8,707, Fan Zhang381, Hailei Zhang8, Hongwei Zhang494, Hongxin Zhang121, Jiashan Zhang220, Jing Zhang5, Junjun Zhang76, Xiuqing Zhang56, Xuanping Zhang66,369, Yan Zhang5,708,709, Zemin Zhang381,710, Zhongming Zhao711, Liangtao Zheng381, Xiuqing Zheng381, Wanding Zhou615, Yong Zhou56, Bin Zhu240, Hongtu Zhu700,712, Jingchun Zhu24, Shida Zhu56,396, Lihua Zou713, Xueqing Zou49, Anna deFazio246,247,714, Nicholas van As221, Carolien H. M. van Deurzen715, Marc J. van de Vijver523, L. van’t Veer716 & Christian von Mering433,717, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.
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- 2020
13. Recent Advances in Genomic Approaches for the Detection of Homologous Recombination Deficiency.
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Kim YN, Gulhan DC, Jin H, Glodzik D, and Park PJ
- Abstract
Accurate detection of homologous recombination deficiency (HRD) in cancer patients is paramount in clinical applications, as HRD confers sensitivity to poly (ADP-ribose) polymerase (PARP) inhibitors. With the advances in genome sequencing technology, mutational profiling on a genome-wide scale has become readily accessible, and our knowledge of the genomic consequences of HRD has been greatly expanded and refined. Here, we review the recent advances in HRD detection methods. We examine the copy number and structural alterations that often accompany the genome instability that results from HRD, describe the advantages of mutational signature-based methods that do not rely on specific gene mutations, and review some of the existing algorithms used for HRD detection. We also discuss the choice of sequencing platforms (panel, exome, or whole-genome) and catalog the HRD detection assays used in key PARP inhibitor trials.
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- 2024
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14. Loss of the DNA Repair Gene RNase H2 Identifies a Unique Subset of DDR-Deficient Leiomyosarcomas.
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Nakazawa MS, Silverman IM, Rimkunas V, Veloso A, Glodzik D, Johnson A, Ohsumi TK, Patel SR, Conley AP, Roland CL, Soliman PT, Beird HC, Wu CC, Ingram DR, Lazcano R, Song D, Wani KM, Lazar AJ, Yap TA, Wang WL, and Livingston JA
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- Humans, Female, Biomarkers, Tumor genetics, Male, Prognosis, Middle Aged, Aged, DNA Damage, Ribonuclease H genetics, Leiomyosarcoma genetics, Leiomyosarcoma pathology, Leiomyosarcoma mortality, DNA Repair
- Abstract
Targeting the DNA damage response (DDR) pathway is an emerging therapeutic approach for leiomyosarcoma (LMS), and loss of RNase H2, a DDR pathway member, is a potentially actionable alteration for DDR-targeted treatments. Therefore, we designed a protein- and genomic-based RNase H2 screening assay to determine its prevalence and prognostic significance. Using a selective RNase H2 antibody on a pan-tumor microarray (TMA), RNase H2 loss was more common in LMS (11.5%, 9/78) than across all tumors (3.8%, 32/843). In a separate LMS cohort, RNase H2 deficiency was confirmed in uterine LMS (U-LMS, 21%, 23/108) and soft-tissue LMS (ST-LMS; 30%, 39/102). In the TCGA database, RNASEH2B homozygous deletions (HomDels) were found in 6% (5/80) of LMS cases, with a higher proportion in U-LMS (15%; 4/27) compared with ST-LMS (2%; 1/53). Using the SNiPDx targeted-NGS sequencing assay to detect biallelic loss of function in select DDR-related genes, we found RNASEH2B HomDels in 54% (19/35) of U-LMS cases with RNase H2 loss by IHC, and 7% (3/43) HomDels in RNase H2 intact cases. No RNASEH2B HomDels were detected in ST-LMS. In U-LMS patient cohort (n = 109), no significant overall survival difference was seen in patients with RNase H2 loss versus intact, or RNASEH2B HomDel (n = 12) versus Non-HomDel (n = 37). The overall diagnostic accuracy, sensitivity, and specificity of RNase H2 IHC for detecting RNA-SEH2B HomDels in U-LMS was 76%, 93%, and 71%, respectively, and it is being developed for future predictive biomarker driven clinical trials targeting DDR in U-LMS., (©2024 American Association for Cancer Research.)
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- 2024
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15. Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma.
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Kinnaman MD, Zaccaria S, Makohon-Moore A, Arnold B, Levine MF, Gundem G, Arango Ossa JE, Glodzik D, Rodríguez-Sánchez MI, Bouvier N, Li S, Stockfisch E, Dunigan M, Cobbs C, Bhanot UK, You D, Mullen K, Melchor JP, Ortiz MV, O'Donohue TJ, Slotkin EK, Wexler LH, Dela Cruz FS, Hameed MR, Glade Bender JL, Tap WD, Meyers PA, Papaemmanuil E, Kung AL, and Iacobuzio-Donahue CA
- Subjects
- Humans, Whole Genome Sequencing, Genomics, Recurrence, DNA Copy Number Variations, Mutation, Osteosarcoma genetics, Bone Neoplasms genetics
- Abstract
Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. We conducted longitudinal whole-genome sequencing of 37 tumor samples from 8 patients with relapsed or refractory osteosarcoma. Each patient had at least one sample from a primary site and a metastatic or relapse site. Subclonal copy-number alterations were identified in all patients except one. In 5 patients, subclones from the primary tumor emerged and dominated at subsequent relapses. MYC gain/amplification was enriched in the treatment-resistant clones in 6 of 7 patients with multiple clones. Amplifications in other potential driver genes, such as CCNE1, RAD21, VEGFA, and IGF1R, were also observed in the resistant copy-number clones. A chromosomal duplication timing analysis revealed that complex genomic rearrangements typically occurred prior to diagnosis, supporting a macroevolutionary model of evolution, where a large number of genomic aberrations are acquired over a short period of time followed by clonal selection, as opposed to ongoing evolution. A mutational signature analysis of recurrent tumors revealed that homologous repair deficiency (HRD)-related SBS3 increases at each time point in patients with recurrent disease, suggesting that HRD continues to be an active mutagenic process after diagnosis. Overall, by examining the clonal relationships between temporally and spatially separated samples from patients with relapsed/refractory osteosarcoma, this study sheds light on the intratumor heterogeneity and potential drivers of treatment resistance in this disease., Significance: The chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications., (©2023 The Authors; Published by the American Association for Cancer Research.)
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- 2023
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16. Detection of Biallelic Loss of DNA Repair Genes in Formalin-Fixed, Paraffin-Embedded Tumor Samples Using a Novel Tumor-Only Sequencing Panel.
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Glodzik D, Selenica P, Rogge RA, Silverman IM, Mandelker D, Harris S, Zhao J, Zinda M, Veloso A, Malani N, Riaz N, Koehler M, Daber RD, Johnson V, Rimkunas V, and Reis-Filho JS
- Subjects
- Humans, Paraffin Embedding, Mutation, High-Throughput Nucleotide Sequencing, Formaldehyde, DNA Repair, Neoplasms genetics, Neoplasms diagnosis
- Abstract
Patient selection for synthetic lethal-based cancer therapy may be improved by assessment of gene-specific loss of heterozygosity (LOH) and biallelic loss of function (LOF). This report describes SyNthetic lethal Interactions for Precision Diagnostics (SNiPDx), a targeted next-generation sequencing (NGS) panel for detection of LOH and biallelic LOF alterations in 26 target genes focused on DNA damage response pathways, in tumor-only formalin-fixed, paraffin-embedded (FFPE) samples. NGS was performed across all exons of these 26 genes and encompassed a total of 7632 genome-wide single-nucleotide polymorphisms on genomic DNA from 80 FFPE solid tumor samples. The Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing algorithm was optimized to assess tumor purity and copy number based on heterozygous single-nucleotide polymorphisms. SNiPDx demonstrated high sensitivity (95%) and specificity (91%) for LOH detection compared with whole genome sequencing. Positive agreement with local NGS-based testing in the detection of genetic alterations was 95%. SNiPDx detected 93% of biallelic ATM LOF mutations, 100% of ATM single-nucleotide variants and small insertions/deletions, and 100% of all ATM LOH status events identified by orthogonal NGS-based testing. SNiPDx is a novel, clinically feasible test for analysis of allelic status in FFPE tumor samples, which demonstrated high accuracy when compared with other NGS-based approaches in clinical use., (Copyright © 2023 Association for Molecular Pathology and American Society for Investigative Pathology. All rights reserved.)
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- 2023
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17. Functional patient-derived organoid screenings identify MCLA-158 as a therapeutic EGFR × LGR5 bispecific antibody with efficacy in epithelial tumors.
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Herpers B, Eppink B, James MI, Cortina C, Cañellas-Socias A, Boj SF, Hernando-Momblona X, Glodzik D, Roovers RC, van de Wetering M, Bartelink-Clements C, Zondag-van der Zande V, Mateos JG, Yan K, Salinaro L, Basmeleh A, Fatrai S, Maussang D, Lammerts van Bueren JJ, Chicote I, Serna G, Cabellos L, Ramírez L, Nuciforo P, Salazar R, Santos C, Villanueva A, Stephan-Otto Attolini C, Sancho E, Palmer HG, Tabernero J, Stratton MR, de Kruif J, Logtenberg T, Clevers H, Price LS, Vries RGJ, Batlle E, and Throsby M
- Subjects
- ErbB Receptors metabolism, Humans, Imidazoles, Neoplastic Stem Cells metabolism, Organoids, Pyrazines, Receptors, G-Protein-Coupled metabolism, Antibodies, Bispecific pharmacology, Neoplasms, Glandular and Epithelial metabolism
- Abstract
Patient-derived organoids (PDOs) recapitulate tumor architecture, contain cancer stem cells and have predictive value supporting personalized medicine. Here we describe a large-scale functional screen of dual-targeting bispecific antibodies (bAbs) on a heterogeneous colorectal cancer PDO biobank and paired healthy colonic mucosa samples. More than 500 therapeutic bAbs generated against Wingless-related integration site (WNT) and receptor tyrosine kinase (RTK) targets were functionally evaluated by high-content imaging to capture the complexity of PDO responses. Our drug discovery strategy resulted in the generation of MCLA-158, a bAb that specifically triggers epidermal growth factor receptor degradation in leucine-rich repeat-containing G-protein-coupled receptor 5-positive (LGR5+) cancer stem cells but shows minimal toxicity toward healthy LGR5+ colon stem cells. MCLA-158 exhibits therapeutic properties such as growth inhibition of KRAS-mutant colorectal cancers, blockade of metastasis initiation and suppression of tumor outgrowth in preclinical models for several epithelial cancer types., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2022
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18. Revealing the impact of structural variants in multiple myeloma.
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Rustad EH, Yellapantula VD, Glodzik D, Maclachlan KH, Diamond B, Boyle EM, Ashby C, Blaney P, Gundem G, Hultcrantz M, Leongamornlert D, Angelopoulos N, Agnelli L, Auclair D, Zhang Y, Dogan A, Bolli N, Papaemmanuil E, Anderson KC, Moreau P, Avet-Loiseau H, Munshi NC, Keats JJ, Campbell PJ, Morgan GJ, Landgren O, and Maura F
- Subjects
- Genomics, Humans, Oncogenes genetics, Chromothripsis, Multiple Myeloma genetics, Whole Genome Sequencing methods
- Abstract
The landscape of structural variants (SVs) in multiple myeloma remains poorly understood. Here, we performed comprehensive analysis of SVs in a large cohort of 752 multiple myeloma patients by low coverage long-insert whole genome sequencing. We identified 68 SV hotspots involving 17 new candidate driver genes, including the therapeutic targets BCMA ( TNFRSF17 ), SLAMF and MCL1. Catastrophic complex rearrangements termed chromothripsis were present in 24% of patients and independently associated with poor clinical outcomes. Templated insertions were the second most frequent complex event (19%), mostly involved in super-enhancer hijacking and activation of oncogenes such as CCND1 and MYC . Importantly, in 31% of patients two or more seemingly independent putative driver events were caused by a single structural event, demonstrating that the complex genomic landscape of multiple myeloma can be acquired through few key events during tumor evolutionary history. Overall, this study reveals the critical role of SVs in multiple myeloma pathogenesis., Competing Interests: Conflict of interest statement No conflict of interests to declare.
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- 2020
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19. Cancer therapy shapes the fitness landscape of clonal hematopoiesis.
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Bolton KL, Ptashkin RN, Gao T, Braunstein L, Devlin SM, Kelly D, Patel M, Berthon A, Syed A, Yabe M, Coombs CC, Caltabellotta NM, Walsh M, Offit K, Stadler Z, Mandelker D, Schulman J, Patel A, Philip J, Bernard E, Gundem G, Ossa JEA, Levine M, Martinez JSM, Farnoud N, Glodzik D, Li S, Robson ME, Lee C, Pharoah PDP, Stopsack KH, Spitzer B, Mantha S, Fagin J, Boucai L, Gibson CJ, Ebert BL, Young AL, Druley T, Takahashi K, Gillis N, Ball M, Padron E, Hyman DM, Baselga J, Norton L, Gardos S, Klimek VM, Scher H, Bajorin D, Paraiso E, Benayed R, Arcila ME, Ladanyi M, Solit DB, Berger MF, Tallman M, Garcia-Closas M, Chatterjee N, Diaz LA Jr, Levine RL, Morton LM, Zehir A, and Papaemmanuil E
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Antineoplastic Agents pharmacology, Cell Transformation, Neoplastic drug effects, Cell Transformation, Neoplastic genetics, Cell Transformation, Neoplastic radiation effects, Child, Child, Preschool, Clonal Evolution, Clonal Hematopoiesis drug effects, Cohort Studies, Female, Genetic Fitness, Humans, Infant, Infant, Newborn, Leukemia, Myeloid genetics, Male, Middle Aged, Models, Biological, Mutation, Neoplasms drug therapy, Neoplasms radiotherapy, Selection, Genetic, Young Adult, Clonal Hematopoiesis genetics, Neoplasms, Second Primary genetics
- Abstract
Acquired mutations are pervasive across normal tissues. However, understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMNs). We find that mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response genes (TP53, PPM1D, CHEK2). Sequential sampling provides definitive evidence that DNA damage response clones outcompete other clones when exposed to certain therapies. Among cases in which CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies.
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- 2020
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20. Comprehensive molecular comparison of BRCA1 hypermethylated and BRCA1 mutated triple negative breast cancers.
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Glodzik D, Bosch A, Hartman J, Aine M, Vallon-Christersson J, Reuterswärd C, Karlsson A, Mitra S, Niméus E, Holm K, Häkkinen J, Hegardt C, Saal LH, Larsson C, Malmberg M, Rydén L, Ehinger A, Loman N, Kvist A, Ehrencrona H, Nik-Zainal S, Borg Å, and Staaf J
- Subjects
- Adult, Aged, B7-H1 Antigen genetics, B7-H1 Antigen metabolism, BRCA1 Protein deficiency, Cohort Studies, DNA Methylation genetics, Female, Gene Expression Regulation, Neoplastic, Humans, Middle Aged, Phenotype, Prognosis, Promoter Regions, Genetic, Transcription, Genetic, Treatment Outcome, Triple Negative Breast Neoplasms blood, Triple Negative Breast Neoplasms diagnosis, Triple Negative Breast Neoplasms therapy, BRCA1 Protein genetics, Mutation genetics, Triple Negative Breast Neoplasms genetics
- Abstract
Homologous recombination deficiency (HRD) is a defining characteristic in BRCA-deficient breast tumors caused by genetic or epigenetic alterations in key pathway genes. We investigated the frequency of BRCA1 promoter hypermethylation in 237 triple-negative breast cancers (TNBCs) from a population-based study using reported whole genome and RNA sequencing data, complemented with analyses of genetic, epigenetic, transcriptomic and immune infiltration phenotypes. We demonstrate that BRCA1 promoter hypermethylation is twice as frequent as BRCA1 pathogenic variants in early-stage TNBC and that hypermethylated and mutated cases have similarly improved prognosis after adjuvant chemotherapy. BRCA1 hypermethylation confers an HRD, immune cell type, genome-wide DNA methylation, and transcriptional phenotype similar to TNBC tumors with BRCA1-inactivating variants, and it can be observed in matched peripheral blood of patients with tumor hypermethylation. Hypermethylation may be an early event in tumor development that progress along a common pathway with BRCA1-mutated disease, representing a promising DNA-based biomarker for early-stage TNBC.
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- 2020
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21. 11p15.5 epimutations in children with Wilms tumor and hepatoblastoma detected in peripheral blood.
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Fiala EM, Ortiz MV, Kennedy JA, Glodzik D, Fleischut MH, Duffy KA, Hathaway ER, Heaton T, Gerstle JT, Steinherz P, Shukla N, McNeer N, Tkachuk K, Bouvier N, Cadoo K, Carlo MI, Latham A, Dubard Gault M, Joseph V, Kemel Y, Kentsis A, Stadler Z, La Quaglia M, Papaemmanuil E, Friedman D, Ganguly A, Kung A, Offit K, Kalish JM, and Walsh MF
- Subjects
- Adolescent, Adult, Beckwith-Wiedemann Syndrome genetics, Beckwith-Wiedemann Syndrome pathology, Child, Child, Preschool, Chromosomes, Human, Pair 11 genetics, Female, Genetic Predisposition to Disease, Germ-Line Mutation genetics, Hepatoblastoma genetics, Hepatoblastoma pathology, Humans, Infant, Male, Neoplasm Proteins genetics, Wilms Tumor genetics, Wilms Tumor pathology, Young Adult, Beckwith-Wiedemann Syndrome blood, DNA Methylation genetics, Genomic Imprinting genetics, Hepatoblastoma blood, Wilms Tumor blood
- Abstract
Background: Constitutional or somatic mosaic epimutations are increasingly recognized as a mechanism of gene dysregulation resulting in cancer susceptibility. Beckwith-Wiedemann syndrome is the cancer predisposition syndrome most commonly associated with epimutation and is extremely variable in its phenotypic presentation, which can include isolated tumors. Because to the authors' knowledge large-scale germline DNA sequencing studies have not included methylation analysis, the percentage of pediatric cancer predisposition that is due to epimutations is unknown., Methods: Germline methylation testing at the 11p15.5 locus was performed in blood for 24 consecutive patients presenting with hepatoblastoma (3 patients) or Wilms tumor (21 patients)., Results: Six individuals with Wilms tumor and 1 patient with hepatoblastoma were found to have low-level gain of methylation at imprinting control 1, and a child with hepatoblastoma was found to have loss of methylation at imprinting control 2. The loss of methylation at imprinting control 2 was found to be maternally inherited, despite not being associated with any detectable genomic alteration., Conclusions: Overall, 33% of patients (8 of 24 patients) with Wilms tumor or hepatoblastoma were found to have an epigenetic susceptibility that was detectable in the blood. It is interesting to note that low-level gain of methylation at imprinting control 1 predominantly was detected in females with bilateral Wilms tumors. Further studies in larger cohorts are needed to determine the efficacy of testing all patients with Wilms tumor or hepatoblastoma for 11p15.5 epimutations in the blood as part of DNA analysis because this hallmark of predisposition will not be detected by sequencing-based approaches and detecting a cancer predisposition may modify treatment., (© 2020 American Cancer Society.)
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- 2020
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22. Author Correction: A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies.
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Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G, Momen SE, Georgakopoulos-Soares I, Dias JML, Young J, Memari Y, Davies H, and Nik-Zainal S
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- 2020
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23. A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies.
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Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G, Momen SE, Georgakopoulos-Soares I, Dias JML, Young J, Memari Y, Davies H, and Nik-Zainal S
- Subjects
- Carcinogenesis, Humans, Mutation genetics, Neoplasms genetics
- Abstract
Mutational signatures are patterns of mutations that arise during tumorigenesis. We present an enhanced, practical framework for mutational signature analyses. Applying these methods on 3,107 whole genome sequenced (WGS) primary cancers of 21 organs reveals known signatures and nine previously undescribed rearrangement signatures. We highlight inter-organ variability of signatures and present a way of visualizing that diversity, reinforcing our findings in an independent analysis of 3,096 WGS metastatic cancers. Signatures with a high level of genomic instability are dependent on TP53 dysregulation. We illustrate how uncertainty in mutational signature identification and assignment to samples affects tumor classification, reinforcing that using multiple orthogonal mutational signature data is not only beneficial, it is essential for accurate tumor stratification. Finally, we present a reference web-based tool for cancer and experimentally-generated mutational signatures, called Signal (https://signal.mutationalsignatures.com), that also supports performing mutational signature analyses., Competing Interests: Competing Financial Interests SNZ, DG and HD are inventors on a patent application on HRDetect. All other authors declare no competing interests.
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- 2020
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24. Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study.
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Staaf J, Glodzik D, Bosch A, Vallon-Christersson J, Reuterswärd C, Häkkinen J, Degasperi A, Amarante TD, Saal LH, Hegardt C, Stobart H, Ehinger A, Larsson C, Rydén L, Loman N, Malmberg M, Kvist A, Ehrencrona H, Davies HR, Borg Å, and Nik-Zainal S
- Subjects
- Adult, Aged, Aged, 80 and over, DNA Methylation genetics, Disease-Free Survival, Female, Genetics, Population, Germ-Line Mutation genetics, Humans, Middle Aged, Neoplasm Recurrence, Local epidemiology, Neoplasm Recurrence, Local pathology, Promoter Regions, Genetic, Triple Negative Breast Neoplasms epidemiology, Triple Negative Breast Neoplasms pathology, Neoplasm Recurrence, Local genetics, Prognosis, Triple Negative Breast Neoplasms genetics, Whole Genome Sequencing
- Abstract
Whole-genome sequencing (WGS) brings comprehensive insights to cancer genome interpretation. To explore the clinical value of WGS, we sequenced 254 triple-negative breast cancers (TNBCs) for which associated treatment and outcome data were collected between 2010 and 2015 via the population-based Sweden Cancerome Analysis Network-Breast (SCAN-B) project (ClinicalTrials.gov ID:NCT02306096). Applying the HRDetect mutational-signature-based algorithm to classify tumors, 59% were predicted to have homologous-recombination-repair deficiency (HRDetect-high): 67% explained by germline/somatic mutations of BRCA1/BRCA2, BRCA1 promoter hypermethylation, RAD51C hypermethylation or biallelic loss of PALB2. A novel mechanism of BRCA1 abrogation was discovered via germline SINE-VNTR-Alu retrotransposition. HRDetect provided independent prognostic information, with HRDetect-high patients having better outcome on adjuvant chemotherapy for invasive disease-free survival (hazard ratio (HR) = 0.42; 95% confidence interval (CI) = 0.2-0.87) and distant relapse-free interval (HR = 0.31, CI = 0.13-0.76) compared to HRDetect-low, regardless of whether a genetic/epigenetic cause was identified. HRDetect-intermediate, some possessing potentially targetable biological abnormalities, had the poorest outcomes. HRDetect-low cancers also had inadequate outcomes: ~4.7% were mismatch-repair-deficient (another targetable defect, not typically sought) and they were enriched for (but not restricted to) PIK3CA/AKT1 pathway abnormalities. New treatment options need to be considered for now-discernible HRDetect-intermediate and HRDetect-low categories. This population-based study advocates for WGS of TNBC to better inform trial stratification and improve clinical decision-making.
- Published
- 2019
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25. Genomic landscape and chronological reconstruction of driver events in multiple myeloma.
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Maura F, Bolli N, Angelopoulos N, Dawson KJ, Leongamornlert D, Martincorena I, Mitchell TJ, Fullam A, Gonzalez S, Szalat R, Abascal F, Rodriguez-Martin B, Samur MK, Glodzik D, Roncador M, Fulciniti M, Tai YT, Minvielle S, Magrangeas F, Moreau P, Corradini P, Anderson KC, Tubio JMC, Wedge DC, Gerstung M, Avet-Loiseau H, Munshi N, and Campbell PJ
- Subjects
- Adult, Aged, Bayes Theorem, Bone Marrow pathology, Chromosomes, Human genetics, Chromothripsis, DNA Replication, Female, Genomics, Humans, Male, Middle Aged, Multiple Myeloma pathology, Phylogeny, Point Mutation, Time Factors, Whole Genome Sequencing, Carcinogenesis genetics, Genome, Human genetics, Models, Genetic, Multiple Myeloma genetics
- Abstract
The multiple myeloma (MM) genome is heterogeneous and evolves through preclinical and post-diagnosis phases. Here we report a catalog and hierarchy of driver lesions using sequences from 67 MM genomes serially collected from 30 patients together with public exome datasets. Bayesian clustering defines at least 7 genomic subgroups with distinct sets of co-operating events. Focusing on whole genome sequencing data, complex structural events emerge as major drivers, including chromothripsis and a novel replication-based mechanism of templated insertions, which typically occur early. Hyperdiploidy also occurs early, with individual trisomies often acquired in different chronological windows during evolution, and with a preferred order of acquisition. Conversely, positively selected point mutations, whole genome duplication and chromoplexy events occur in later disease phases. Thus, initiating driver events, drawn from a limited repertoire of structural and numerical chromosomal changes, shape preferred trajectories of evolution that are biologically relevant but heterogeneous across patients.
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- 2019
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26. Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation.
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Brinkman AB, Nik-Zainal S, Simmer F, Rodríguez-González FG, Smid M, Alexandrov LB, Butler A, Martin S, Davies H, Glodzik D, Zou X, Ramakrishna M, Staaf J, Ringnér M, Sieuwerts A, Ferrari A, Morganella S, Fleischer T, Kristensen V, Gut M, van de Vijver MJ, Børresen-Dale AL, Richardson AL, Thomas G, Gut IG, Martens JWM, Foekens JA, Stratton MR, and Stunnenberg HG
- Subjects
- DNA Methylation, Epigenesis, Genetic, Female, Humans, Logistic Models, Breast Neoplasms genetics, CpG Islands
- Abstract
Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. We comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of DNA methylation variation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). Repression effects on tumor suppressor genes are negligible as they are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin and may represent tissue-specific silent regions which tolerate instability at the epigenetic, transcriptomic and genetic level.
- Published
- 2019
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27. Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
- Author
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Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, Van't Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, and Stratton MR
- Abstract
In the Methods section of this Article, 'greater than' should have been 'less than' in the sentence 'Putative regions of clustered rearrangements were identified as having an average inter-rearrangement distance that was at least 10 times greater than the whole-genome average for the individual sample. '. The Article has not been corrected.
- Published
- 2019
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28. Short inverted repeats contribute to localized mutability in human somatic cells.
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Zou X, Morganella S, Glodzik D, Davies H, Li Y, Stratton MR, and Nik-Zainal S
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- Breast Neoplasms genetics, Breast Neoplasms pathology, DNA chemistry, Female, Humans, Nucleic Acid Conformation, DNA genetics, Genome, Human genetics, Inverted Repeat Sequences genetics, Mutation
- Abstract
Selected repetitive sequences termed short inverted repeats (SIRs) have the propensity to form secondary DNA structures called hairpins. SIRs comprise palindromic arm sequences separated by short spacer sequences that form the hairpin stem and loop respectively. Here, we show that SIRs confer an increase in localized mutability in breast cancer, which is domain-dependent with the greatest mutability observed within spacer sequences (∼1.35-fold above background). Mutability is influenced by factors that increase the likelihood of formation of hairpins such as loop lengths (of 4-5 bp) and stem lengths (of 7-15 bp). Increased mutability is an intrinsic property of SIRs as evidenced by how almost all mutational processes demonstrate a higher rate of mutagenesis of spacer sequences. We further identified 88 spacer sequences showing enrichment from 1.8- to 90-fold of local mutability distributed across 283 sites in the genome that intriguingly, can be used to inform the biological status of a tumor., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2017
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29. Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
- Author
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Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, and Nik-Zainal S
- Abstract
This corrects the article DOI: 10.1038/ng.3771.
- Published
- 2017
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30. Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency.
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Davies H, Morganella S, Purdie CA, Jang SJ, Borgen E, Russnes H, Glodzik D, Zou X, Viari A, Richardson AL, Børresen-Dale AL, Thompson A, Eyfjord JE, Kong G, Stratton MR, and Nik-Zainal S
- Subjects
- DNA, Neoplasm analysis, Female, High-Throughput Nucleotide Sequencing methods, Humans, Breast Neoplasms genetics, DNA Mismatch Repair genetics, DNA Repair Enzymes genetics, Genome, Human, Sequence Analysis, DNA methods
- Abstract
Mismatch repair (MMR)-deficient cancers have been discovered to be highly responsive to immune therapies such as PD-1 checkpoint blockade, making their definition in patients, where they may be relatively rare, paramount for treatment decisions. In this study, we utilized patterns of mutagenesis known as mutational signatures, which are imprints of the mutagenic processes associated with MMR deficiency, to identify MMR-deficient breast tumors from a whole-genome sequencing dataset comprising a cohort of 640 patients. We identified 11 of 640 tumors as MMR deficient, but only 2 of 11 exhibited germline mutations in MMR genes or Lynch Syndrome. Two additional tumors had a substantially reduced proportion of mutations attributed to MMR deficiency, where the predominant mutational signatures were related to APOBEC enzymatic activity. Overall, 6 of 11 of the MMR-deficient cases in this cohort were confirmed genetically or epigenetically as having abrogation of MMR genes. However, IHC analysis of MMR-related proteins revealed all but one of 10 samples available for testing as MMR deficient. Thus, the mutational signatures more faithfully reported MMR deficiency than sequencing of MMR genes, because they represent a direct pathophysiologic readout of repair pathway abnormalities. As whole-genome sequencing continues to become more affordable, it could be used to expose individually abnormal tumors in tissue types where MMR deficiency has been rarely detected, but also rarely sought. Cancer Res; 77(18); 4755-62. ©2017 AACR ., (©2017 American Association for Cancer Research.)
- Published
- 2017
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31. HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
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Davies H, Glodzik D, Morganella S, Yates LR, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts AM, Simpson PT, King TA, Raine K, Eyfjord JE, Kong G, Borg Å, Birney E, Stunnenberg HG, van de Vijver MJ, Børresen-Dale AL, Martens JW, Span PN, Lakhani SR, Vincent-Salomon A, Sotiriou C, Tutt A, Thompson AM, Van Laere S, Richardson AL, Viari A, Campbell PJ, Stratton MR, and Nik-Zainal S
- Subjects
- Area Under Curve, BRCA1 Protein deficiency, BRCA2 Protein deficiency, Breast Neoplasms drug therapy, Breast Neoplasms, Male genetics, DNA Mutational Analysis, Female, Humans, Logistic Models, Male, Models, Genetic, Ovarian Neoplasms drug therapy, Pancreatic Neoplasms drug therapy, Poly(ADP-ribose) Polymerase Inhibitors therapeutic use, BRCA1 Protein genetics, BRCA2 Protein genetics, Breast Neoplasms genetics, Mutation, Ovarian Neoplasms genetics, Pancreatic Neoplasms genetics
- Abstract
Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic mutations in BRCA1 and/or BRCA2 (BRCA1/BRCA2) also confer selective sensitivity to PARP inhibitors. Thus, assays to detect BRCA1/BRCA2-deficient tumors have been sought. Recently, somatic substitution, insertion/deletion and rearrangement patterns, or 'mutational signatures', were associated with BRCA1/BRCA2 dysfunction. Herein we used a lasso logistic regression model to identify six distinguishing mutational signatures predictive of BRCA1/BRCA2 deficiency. A weighted model called HRDetect was developed to accurately detect BRCA1/BRCA2-deficient samples. HRDetect identifies BRCA1/BRCA2-deficient tumors with 98.7% sensitivity (area under the curve (AUC) = 0.98). Application of this model in a cohort of 560 individuals with breast cancer, of whom 22 were known to carry a germline BRCA1 or BRCA2 mutation, allowed us to identify an additional 22 tumors with somatic loss of BRCA1 or BRCA2 and 47 tumors with functional BRCA1/BRCA2 deficiency where no mutation was detected. We validated HRDetect on independent cohorts of breast, ovarian and pancreatic cancers and demonstrated its efficacy in alternative sequencing strategies. Integrating all of the classes of mutational signatures thus reveals a larger proportion of individuals with breast cancer harboring BRCA1/BRCA2 deficiency (up to 22%) than hitherto appreciated (∼1-5%) who could have selective therapeutic sensitivity to PARP inhibition.
- Published
- 2017
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32. A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
- Author
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Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, and Nik-Zainal S
- Subjects
- DNA Breaks, Double-Stranded, DNA Repair genetics, Female, Gene Expression genetics, Genome genetics, Humans, Transcriptome genetics, Breast Neoplasms genetics, Genetic Loci genetics, Mutation genetics, Regulatory Sequences, Nucleic Acid genetics
- Abstract
Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous-recombination-repair deficiency. Notably, these tandem-duplication hotspots were enriched in breast cancer germline susceptibility loci (odds ratio (OR) = 4.28) and breast-specific 'super-enhancer' regulatory elements (OR = 3.54). These hotspots may be sites of selective susceptibility to double-strand-break damage due to high transcriptional activity or, through incrementally increasing copy number, may be sites of secondary selective pressure. The transcriptomic consequences ranged from strong individual oncogene effects to weak but quantifiable multigene expression effects. We thus present a somatic-rearrangement mutational process affecting coding sequences and noncoding regulatory elements and contributing a continuum of driver consequences, from modest to strong effects, thereby supporting a polygenic model of cancer development.
- Published
- 2017
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33. Whole-exome sequencing in an isolated population from the Dalmatian island of Vis.
- Author
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Jeroncic A, Memari Y, Ritchie GR, Hendricks AE, Kolb-Kokocinski A, Matchan A, Vitart V, Hayward C, Kolcic I, Glodzik D, Wright AF, Rudan I, Campbell H, Durbin R, Polašek O, Zeggini E, and Boraska Perica V
- Subjects
- Croatia, Evolution, Molecular, Gene Frequency, Humans, Islands, Mutation, Polymorphism, Single Nucleotide, Reproductive Isolation, Exome, Population genetics
- Abstract
We have whole-exome sequenced 176 individuals from the isolated population of the island of Vis in Croatia in order to describe exonic variation architecture. We found 290 577 single nucleotide variants (SNVs), 65% of which are singletons, low frequency or rare variants. A total of 25 430 (9%) SNVs are novel, previously not catalogued in NHLBI GO Exome Sequencing Project, UK10K-Generation Scotland, 1000Genomes Project, ExAC or NCBI Reference Assembly dbSNP. The majority of these variants (76%) are singletons. Comparable to data obtained from UK10K-Generation Scotland that were sequenced and analysed using the same protocols, we detected an enrichment of potentially damaging variants (non-synonymous and loss-of-function) in the low frequency and common variant categories. On average 115 (range 93-140) genotypes with loss-of-function variants, 23 (15-34) of which were homozygous, were identified per person. The landscape of loss-of-function variants across an exome revealed that variants mainly accumulated in genes on the xenobiotic-related pathways, of which majority coded for enzymes. The frequency of loss-of-function variants was additionally increased in Vis runs of homozygosity regions where variants mainly affected signalling pathways. This work confirms the isolate status of Vis population by means of whole-exome sequence and reveals the pattern of loss-of-function mutations, which resembles the trails of adaptive evolution that were found in other species. By cataloguing the exomic variants and describing the allelic structure of the Vis population, this study will serve as a valuable resource for future genetic studies of human diseases, population genetics and evolution in this population.
- Published
- 2016
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34. Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
- Author
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Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, and Stratton MR
- Subjects
- Cohort Studies, DNA Mutational Analysis, DNA Replication genetics, DNA, Neoplasm genetics, Female, Genes, BRCA1, Genes, BRCA2, Genomics, Humans, Male, Mutagenesis, Mutation Rate, Oncogenes genetics, Recombinational DNA Repair genetics, Breast Neoplasms genetics, Genome, Human genetics, Mutation genetics
- Abstract
We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
- Published
- 2016
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35. The topography of mutational processes in breast cancer genomes.
- Author
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Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, and Nik-Zainal S
- Subjects
- Apolipoproteins B metabolism, Breast Neoplasms metabolism, Breast Neoplasms pathology, Chromatin chemistry, Chromatin metabolism, DNA Damage, DNA Replication, Female, Humans, MCF-7 Cells, Mutagenesis, Sequence Analysis, DNA, Transcription, Genetic, Apolipoproteins B genetics, Breast Neoplasms genetics, DNA Repair, Genome, Human, Mutation
- Abstract
Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription, DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Furthermore, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.
- Published
- 2016
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36. The genome as a record of environmental exposure.
- Author
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Nik-Zainal S, Kucab JE, Morganella S, Glodzik D, Alexandrov LB, Arlt VM, Weninger A, Hollstein M, Stratton MR, and Phillips DH
- Subjects
- Animals, Cell Line, Cell Transformation, Neoplastic, DNA Mutational Analysis, DNA Replication, Fibroblasts drug effects, Fibroblasts metabolism, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing, Humans, Mice, Mutagenesis, Mutagens adverse effects, Mutation, Neoplasms etiology, Transcription, Genetic, Environmental Exposure adverse effects, Genome, Genomics methods
- Abstract
Whole genome sequencing of human tumours has revealed distinct patterns of mutation that hint at the causative origins of cancer. Experimental investigations of the mutations and mutation spectra induced by environmental mutagens have traditionally focused on single genes. With the advent of faster cheaper sequencing platforms, it is now possible to assess mutation spectra in experimental models across the whole genome. As a proof of principle, we have examined the whole genome mutation profiles of mouse embryo fibroblasts immortalised following exposure to benzo[a]pyrene (BaP), ultraviolet light (UV) and aristolochic acid (AA). The results reveal that each mutagen induces a characteristic mutation signature: predominantly G→T mutations for BaP, C→T and CC→TT for UV and A→T for AA. The data are not only consistent with existing knowledge but also provide additional information at higher levels of genomic organisation. The approach holds promise for identifying agents responsible for mutations in human tumours and for shedding light on the aetiology of human cancer., (© The Author 2015. Published by Oxford University Press on behalf of the UK Environmental Mutagen Society.)
- Published
- 2015
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37. Subclonal diversification of primary breast cancer revealed by multiregion sequencing.
- Author
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Yates LR, Gerstung M, Knappskog S, Desmedt C, Gundem G, Van Loo P, Aas T, Alexandrov LB, Larsimont D, Davies H, Li Y, Ju YS, Ramakrishna M, Haugland HK, Lilleng PK, Nik-Zainal S, McLaren S, Butler A, Martin S, Glodzik D, Menzies A, Raine K, Hinton J, Jones D, Mudie LJ, Jiang B, Vincent D, Greene-Colozzi A, Adnet PY, Fatima A, Maetens M, Ignatiadis M, Stratton MR, Sotiriou C, Richardson AL, Lønning PE, Wedge DC, and Campbell PJ
- Subjects
- Adult, Aged, Aged, 80 and over, Antineoplastic Agents therapeutic use, Breast Neoplasms drug therapy, Cell Proliferation, Clone Cells, Cohort Studies, DNA Copy Number Variations genetics, Female, Genomics, Humans, Middle Aged, Mutation genetics, Breast Neoplasms genetics, Breast Neoplasms pathology, Genetic Variation, High-Throughput Nucleotide Sequencing methods
- Abstract
The sequencing of cancer genomes may enable tailoring of therapeutics to the underlying biological abnormalities driving a particular patient's tumor. However, sequencing-based strategies rely heavily on representative sampling of tumors. To understand the subclonal structure of primary breast cancer, we applied whole-genome and targeted sequencing to multiple samples from each of 50 patients' tumors (303 samples in total). The extent of subclonal diversification varied among cases and followed spatial patterns. No strict temporal order was evident, with point mutations and rearrangements affecting the most common breast cancer genes, including PIK3CA, TP53, PTEN, BRCA2 and MYC, occurring early in some tumors and late in others. In 13 out of 50 cancers, potentially targetable mutations were subclonal. Landmarks of disease progression, such as resistance to chemotherapy and the acquisition of invasive or metastatic potential, arose within detectable subclones of antecedent lesions. These findings highlight the importance of including analyses of subclonal structure and tumor evolution in clinical trials of primary breast cancer.
- Published
- 2015
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38. Plasma vitamin D concentration influences survival outcome after a diagnosis of colorectal cancer.
- Author
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Zgaga L, Theodoratou E, Farrington SM, Din FV, Ooi LY, Glodzik D, Johnston S, Tenesa A, Campbell H, and Dunlop MG
- Subjects
- Case-Control Studies, Colorectal Neoplasms genetics, Colorectal Neoplasms pathology, Female, Genotype, Humans, Male, Middle Aged, Neoplasm Staging, Polymorphism, Genetic, Prospective Studies, Receptors, Calcitriol genetics, Risk Factors, Scotland epidemiology, Vitamin D blood, Vitamin D metabolism, Colorectal Neoplasms blood, Colorectal Neoplasms mortality, Vitamin D analogs & derivatives
- Abstract
Purpose: We investigated whether the plasma level of 25-hydroxyvitamin D (25-OHD) after a diagnosis of colorectal cancer (CRC) influences survival outcome., Patients and Methods: We prospectively studied 1,598 patients with stage I to III CRC. We sought association between plasma 25-OHD and stage-specific survival and tested for interaction between 25-OHD level and variation at the vitamin D receptor (VDR) gene locus. Blood was sampled postoperatively, and plasma was assayed for 25-OHD by liquid chromatography-tandem mass spectrometry. VDR polymorphisms (rs1544410, rs10735810, rs7975232, rs11568820) were genotyped, and haplotypes were inferred by using BEAGLE software. We tested for association between survival and 25-OHD, VDR genotype/haplotype, and after applying a VDR genotype-25-OHD interaction term. We conducted Kaplan-Meier survival analysis and used Cox proportional hazards models to estimate adjusted hazard ratios (HRs)., Results: We found strong associations between plasma 25-OHD concentration and CRC-specific (P = .008) and all-cause mortality (P = .003). Adjusted HRs were 0.68 (95% CI, 0.50 to 0.90) and 0.70 (95% CI, 0.55 to 0.89), respectively (highest v lowest 25-OHD tertile), particularly in stage II disease (HR, 0.44; P = .004 for CRC-specific mortality). We detected gene-environment interactions between 25-OHD concentration and rs11568820 genotype for CRC-specific (P = .008) and all-cause (P = .022) mortality, number of protective alleles (P = .004 and P = .018, respectively), and GAGC haplotype at the VDR locus for all-cause mortality (P = .008)., Conclusion: In patients with stage I to III CRC, postoperative plasma vitamin D is associated with clinically important differences in survival outcome, higher levels being associated with better outcome. We observed interactions between 25-OHD level and VDR genotype, suggesting a causal relationship between vitamin D and survival. The influence of vitamin D supplementation on CRC outcome will require further investigation., (© 2014 by American Society of Clinical Oncology.)
- Published
- 2014
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39. Inference of identity by descent in population isolates and optimal sequencing studies.
- Author
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Glodzik D, Navarro P, Vitart V, Hayward C, McQuillan R, Wild SH, Dunlop MG, Rudan I, Campbell H, Haley C, Wright AF, Wilson JF, and McKeigue P
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Algorithms, Case-Control Studies, Genetic Loci, Haplotypes, Humans, Islands, Middle Aged, Sensitivity and Specificity, Genetics, Medical methods, Pedigree, Polymorphism, Single Nucleotide, Population genetics, Reproductive Isolation, Sequence Analysis, DNA methods
- Abstract
In an isolated population, individuals are likely to share large genetic regions inherited from common ancestors. Identity by descent (IBD) can be inferred from SNP genotypes, which is useful in a number of applications, including identifying genetic variants influencing complex disease risk, and planning efficient cohort-sequencing strategies. We present ANCHAP--a method for detecting IBD in isolated populations. We compare accuracy of the method against other long-range and local phasing methods, using parent-offspring trios. In our experiments, we show that ANCHAP performs similarly as the other long-range method, but requires an order-of-magnitude less computational resources. A local phasing model is able to achieve similar sensitivity, but only at the cost of higher false discovery rates. In some regions of the genome, the studied individuals share haplotypes particularly often, which hints at the history of the populations studied. We demonstrate the method using SNP genotypes from three isolated island populations, as well as in a cohort of unrelated individuals. In samples from three isolated populations of around 1000 individual each, an average individual shares a haplotype at a genetic locus with 9-12 other individuals, compared with only 1 individual within the non-isolated population. We describe an application of ANCHAP to optimally choose samples in resequencing studies. We find that with sample sizes of 1000 individuals from an isolated population genotyped using a dense SNP array, and with 20% of these individuals sequenced, 65% of sequences of the unsequenced subjects can be partially inferred.
- Published
- 2013
- Full Text
- View/download PDF
40. Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies.
- Author
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Joshi PK, Prendergast J, Fraser RM, Huffman JE, Vitart V, Hayward C, McQuillan R, Glodzik D, Polašek O, Hastie ND, Rudan I, Campbell H, Wright AF, Haley CS, Wilson JF, and Navarro P
- Subjects
- Gene Frequency genetics, Genome, Human genetics, Genotype, Humans, Polymorphism, Single Nucleotide genetics, White People, Exome genetics, Genome-Wide Association Study methods
- Abstract
The analysis of less common variants in genome-wide association studies promises to elucidate complex trait genetics but is hampered by low power to reliably detect association. We show that addition of population-specific exome sequence data to global reference data allows more accurate imputation, particularly of less common SNPs (minor allele frequency 1-10%) in two very different European populations. The imputation improvement corresponds to an increase in effective sample size of 28-38%, for SNPs with a minor allele frequency in the range 1-3%.
- Published
- 2013
- Full Text
- View/download PDF
41. Utility of non-rule-based visual matching as a strategy to allow novices to achieve skin lesion diagnosis.
- Author
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Aldridge RB, Glodzik D, Ballerini L, Fisher RB, and Rees JL
- Subjects
- Adult, Case-Control Studies, Clinical Competence, Databases, Factual, Diagnosis, Differential, Female, Humans, Male, Middle Aged, Predictive Value of Tests, Problem Solving, Scotland, Severity of Illness Index, Skin Diseases pathology, Software, Young Adult, Decision Support Techniques, Dermatology education, Diagnosis, Computer-Assisted, Education, Medical, Undergraduate, Pattern Recognition, Visual, Skin pathology, Skin Diseases diagnosis
- Abstract
Non-analytical reasoning is thought to play a key role in dermatology diagnosis. Considering its potential importance, surprisingly little work has been done to research whether similar identification processes can be supported in non-experts. We describe here a prototype diagnostic support software, which we have used to examine the ability of medical students (at the beginning and end of a dermatology attachment) and lay volunteers, to diagnose 12 images of common skin lesions. Overall, the non-experts using the software had a diagnostic accuracy of 98% (923/936) compared with 33% for the control group (215/648) (Wilcoxon p < 0.0001). We have demonstrated, within the constraints of a simplified clinical model, that novices' diagnostic scores are significantly increased by the use of a structured image database coupled with matching of index and referent images. The novices achieve this high degree of accuracy without any use of explicit definitions of likeness or rule-based strategies.
- Published
- 2011
- Full Text
- View/download PDF
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