Publications

 Recent publications

1.    Systematic Evaluation of the Prognostic Impact and Intratumour Heterogeneity of Clear Cell Renal Cell Carcinoma Biomarkers.
Gulati S, Martinez P, Joshi T, Birkbak NJ, Santos CR, Rowan AJ, Pickering L, Gore M, Larkin J, Szallasi Z, Bates PA, Swanton C, Gerlinger M. Eur Urol. 2014 PubMed PMID: 25047176

 

2.    Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Gerlinger M, Horswell S, Larkin J, Rowan AJ, Salm MP, Varela I, Fisher R, McGranahan N, Matthews N, Santos CR, Martinez P, Phillimore B, Begum S, Rabinowitz A, Spencer-Dene B, Gulati S, Bates PA, Stamp G, Pickering L, Gore M, Nicol DL, Hazell S, Futreal PA, Stewart A, Swanton C. Nat Genet. 2014 46(3):225-33. PubMed PMID: 24487277

 

3.    Ultra-deep T cell receptor sequencing reveals the complexity and intratumour heterogeneity of T cell clones in renal cell carcinomas. Gerlinger M, Quezada SA, Peggs KS, Furness AJ, Fisher R, Marafioti T, Shende VH, McGranahan N, Rowan AJ, Hazell S, Hamm D, Robins HS, Pickering L, Gore M, Nicol DL, Larkin J, Swanton C. J Pathol. 2013 Dec;231(4):424-32. PubMed PMID: 24122851

 

4.    Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution.
Fisher R, Horswell S, Rowan A, Salm MP, de Bruin EC, Gulati S, McGranahan N, Stares M, Gerlinger M, Varela I, Crockford A, Favero F, Quidville V, André F, Navas C, Grönroos E, Nicol D, Hazell S, Hrouda D, O Brien T, Matthews N, Phillimore B, Begum S, Rabinowitz A, Biggs J, Bates PA, McDonald NQ, Stamp G, Spencer-Dene B, Hsieh JJ, Xu J, Pickering L, Gore M, Larkin J, Swanton C. Genome Biol. 2014 Aug 27;15(8):433.] PMID: 25159823

 

5.    Multidisciplinary urological engagement in translational renal cancer research.
Stewart GD, Harrison DJ, Swanton C, Lewis R, Bliss J, Larkin J, Nicol DL; A-PREDICT TMG. BJU Int. 2014 Oct;114(4):474-5. doi: 10.1111/bju.12697. Epub 2014 Jul 28. No abstract available. PMID:25146641

 

6.    Gerlinger M, Quezada SA, Peggs KS, Furness AJ, Fisher R, Marafioti T, Shende VH, McGranahan N, Rowan AJ, Hazell S, Hamm D, Robins HS, Pickering L, Gore M, Nicol DL, Larkin J, Swanton C. Ultra-deep T-cell receptor sequencing reveals the complexity and intratumour heterogeneity of T-cell clones in renal cell carcinomas. J Pathol. 2013 Oct 1. doi: 10.1002/path.4284. [Epub ahead of print] PubMed PMID: 24122851.


7.    Martinez P, McGranahan N, Birkbak NJ, Gerlinger M, Swanton C. Computational optimisation of targeted DNA sequencing for cancer detection. Sci Rep. 2013 Dec 3;3:3309. doi: 10.1038/srep03309. PubMed PMID: 24296834.


8.    Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell RA, Rowan AJ, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C. Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol. 2013 Aug;230(4):356-64. doi: 10.1002/path.4214. PubMed PMID: 23716380.


9.    Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, Varela I, Phillimore B, Begum S, McDonald NQ, Butler A, Jones D, Raine K, Latimer C, Santos CR, Nohadani M, Eklund AC, Spencer-Dene B, Clark G, Pickering L, Stamp G, Gore M, Szallasi Z, Downward J, Futreal PA, Swanton C. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012 Mar 8;366(10):883-92. doi:10.1056/NEJMoa1113205.


10.    Gerlinger M, Santos CR, Spencer-Dene B, Martinez P, Endesfelder D, Burrell RA, Vetter M, Jiang M, Saunders RE, Kelly G, Dykema K, Rioux-Leclercq N, Stamp G, Patard JJ, Larkin J, Howell M, Swanton C. Genome-wide RNA interference analysis of renal carcinoma survival regulators identifies MCT4 as a Warburg effect metabolic target. J Pathol. 2012 Jun;227(2):146-56. doi: 10.1002/path.4006. Epub  2012 Apr 18. PubMed PMID: 22362593; PubMed Central PMCID: PMC3504091.


11.    Mihály Z, Sztupinszki Z, Surowiak P, Győrffy B. A comprehensive overview of targeted therapy in metastatic renal cell carcinoma. Curr Cancer Drug Targets. 2012 Sep 1;12(7):857-72.


12.    Győrffy B, Surowiak P, Budczies J, Lánczky A. Online survival analysis software to assess the prognostic value of biomarkers using transcriptomic data in non-small-cell lung cancer. PLoS One. 2013 Dec 18;8(12):e82241. doi: 10.1371/journal.pone.0082241. PubMed PMID: 24367507; PubMed Central PMCID: PMC3867325.


13.    Mihály Zs, Kormos M, Lánczky A, Dank M, Budczies J, Szász AM, Győrffy B. A meta-analysis of gene expression based biomarkers predicting outcome after tamoxifen treatment in breast cancer. Breast Cancer Res Treat, 2013 Jul;140(2):219-32. doi: 10.1007/s10549-013-2622-y.


14.    Mihály Zs, Győrffy B. Improving Pathological Assessment of Breast Cancer by Employing Array-Based Transcriptome Analysis,  Zsuzsanna Mihály, Balázs Győrffy Microarrays 2013, 2(3), 228-242; doi:10.3390/microarrays2030228


15.    Pénzváltó Zs, Tegze B, Szász AM, Sztupinszki Zs, Likó I, Szendrői A, Schäfer R, Győrffy B. Identifying Resistance Mechanisms against five Tyrosine Kinase Inhibitors Targeting the ERBB/RAS Pathway in 45 Cancer Cell Lines. PLoS One, 2013;8(3):e59503. doi: 10.1371/journal.pone.0059503.

 

17.     Zsófia Pénzváltó, András Lánczky, Julianna Lénárt, Nóra Meggyesházi, Tibor Krenács, Norbert Szoboszlai, Carsten Denkert, Imre Pete and Balázs Győrffy. MEK1 is associated with carboplatin resistance and is a prognostic biomarker in epithelial ovarian cancer. BMC Cancer 2014, 14:837.

 

18.     Zsófia Pénzváltó, Pawel Surowiak and Balázs Győrffy. Biomarkers for Systemic Therapy in Ovarian Cancer. Current Cancer Drug Targets, 2014, 14, 259-273.

 

19.     Mihály Z, Győrffy B. HER2-positive breast cancer: available targeted agents and biomarkers of therapy response. Hungarian Oncology 57:147–156, 2013.

 

20.    Balázs Győrffy, Giulia Bottai, Jacqueline Lehmann-Che, György Kéri, László Orfi, Takayuki Iwamoto, Christine Desmedt, Giampaolo Bianchini, Nicholas C Turner, Hugues de Thè, Fabrice André, Christos Sotiriou, Gabriel N Hortobagyi, Angelo Di Leo, Lajos Pusztai, Libero Santarpia. TP53 mutation-correlated genes predict the risk of tumor relapse and identify MPS1 as a potential therapeutic kinase in TP53-mutated breast cancers. Molecular Oncology. Volume 8, Issue 3, May 2014, Pages 508–519

 

21.    Balazs Gyorffy, Thomas Karn, Zsofia Sztupinszki, Boglarka Weltz, Volkmar Muller and Lajos Pusztai. Dynamic classification using case-specific training cohorts outperforms static gene expression signatures in breast cancer. International Journal of Cancer. DOI: 10.1002/ijc.29247.

 

22.    Győrffy B, BottaiG, Lehmann-Che J, Kéri G, Őrfi L, Iwamoto T, Desmedt C, Bianchini G, Turner NC, de Thè´ H, André F, Sotiriou C, Hortobagyi GN, Di Leo A, Pusztai L, Santarpia L. TP53 mutation-modulated genes predict the risk of tumor relapse and identify MPS1 as a potential therapeutic kinase in TP53-mutated breast cancers, Mol Oncol, 2014 (in press)

 

23.    Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol. 2015 Jan;26(1):64-70. doi: 10.1093/annonc/mdu479. Epub 2014 Oct 15.

 

24.    Molnár J, Póti Á, Pipek O, Krzystanek M, Kanu N, Swanton C, Tusnády GE, Szallasi Z, Csabai I, Szüts D. The genome of the chicken DT40 bursal lymphoma cell line. G3 (Bethesda). 2014 Sep 15;4(11):2231-40. doi: 10.1534/g3.114.013482.

 

25.    Kanu N, Grönroos E, Martinez P, Burrell RA, Yi Goh X, Bartkova J, Maya-Mendoza A, Mistrík M, Rowan AJ, Patel H, Rabinowitz A, East P, Wilson G, Santos CR, McGranahan N, Gulati S, Gerlinger M, Birkbak NJ, Joshi T, Alexandrov LB, Stratton MR, Powles T, Matthews N, Bates PA, Stewart A, Szallasi Z, Larkin J, Bartek J, Swanton C. SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair. Oncogene 2015, (1-10). doi:10.1038/onc.2015.24.

 

26.    McGranahan N, Swanton C. Biological and Therapeutic Impact of Intratumor Heterogeneity in Cancer Evolution. Cancer Cell 2015 Jan 12; 27(1):15-26. doi:10.1016/j.ccell.2014.12.001.

 

27.    Kovac M, Navas C, Horswell S, Salm M, Bardella C, Rowan A, Stares M, Castro-Giner F, Fisher R, de Bruin EC, Kovacova M, Gorman M, Makino S, Williams J, Jaeger E, Jones A, Howarth K, Larkin J, Pickering L, Gore M, Nicol DL, Hazell S, Stamp G, O’Brien T, Challacombe B, Matthews N, Phillimore B, Begum S, Rabinowitz A, Varela I, Chandra A, Horsfield C, Polson A, Tran M, Bhatt R, Terracciano L, Eppenberger-Castori S, Protheroe A, Maher E, El Bahrawy M, Fleming S, Ratcliffe P, Heinimann K, Swanton C, Tomlinson I. Recurrent chromosomal gains and heterogeneous driver mutations characterise papillary renal cancer evolution. Nat Commun 2015 March 19; 6(6336). doi:10.1038/ncomms7336.

 

28.    Burrell RA, McClelland SE, Endesfelder D, Groth P, Weller M-C, Shaikh N, Domingo E, Kanu N, Dewhurst SM, Gronroos E, Chew SK, Rowan AJ, Schenk A, Sheffer M, Howell M, Kschischo M, Behrens A, Helleday T, Bartek J, Tomlinson IP, Swanton C. Replication stress links structural and numerical cancer chromosomal instability. Nature 28 February 2013; 494:492–496. doi:10.1038/nature11935.

 

29.    Dewhurst SM, McGranahan N, Burrell RA, Rowan AJ, Grönroos E, Endesfelder D, Joshi T, Mouradov D, Gibbs P, Ward RL, Hawkins NJ, Szallasi Z, Sieber OM, Swanton C. Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. Cancer Discov 2014 Feb;4(2):175-85. doi: 10.1158/2159-8290.CD-13-0285.

 

30.    de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, Jamal-Hanjani M, Shafi S, Murugaesu N, Rowan AJ, Grönroos E, Muhammad MA, Horswell S, Gerlinger M, Varela I, Jones D, Marshall J, Voet T, Van Loo P, Rassl DM, Rintoul RC, Janes SM, Lee S-M, Forster M, Ahmad T, Lawrence D, Falzon M, Capitanio A, Harkins TT, Lee CC, Tom W, Teefe E, Chen S-C, Begum S, Rabinowitz A, Phillimore B, Spencer-Dene B, Stamp G, Szallasi Z, Matthews N, Stewart A, Campbell P, Swanton C. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 10 October 2014; 346(6206):251-256. doi:10.1126/science.1253462.

 

Reviews

1.    Intratumour Heterogeneity in Urologic Cancers: From Molecular Evidence to Clinical Implications. Gerlinger M, Catto JW, Orntoft TF, Real FX, Zwarthoff EC, Swanton C. Eur Urol. 2014 PMID: 24836153

 

2.    Prioritizing targets for precision cancer medicine. Andre F, Mardis E, Salm M, Soria JC, Siu LL, Swanton C. Ann Oncol. 2014 Dec;25(12):2295-2303. Epub 2014 Oct 24. Review. PMID:25344359

 

3.    Cancer: evolution within a lifetime. Gerlinger M, McGranahan N, Dewhurst SM, Burrell RA, Tomlinson I, Swanton C. Annu Rev Genet. 2014 Nov 23;48:215-36. doi: 10.1146/annurev-genet-120213-092314. 2014 Oct 1. PMID:25292359

 

4.    Deciphering intratumor heterogeneity and temporal acquisition of driver events to refine precision medicine. Hiley C, de Bruin EC, McGranahan N, Swanton C. Genome Biol. 2014 Aug 27;15(8):453. PMID:25222836

 

5.    Tumour heterogeneity and the evolution of polyclonal drug resistance. Burrell RA, Swanton C. Mol Oncol. 2014 Sep 12;8(6):1095-111. doi: 10.1016/j.molonc.2014.06.005. 2014 Jul 10. Review. PMID:25087573

 

6.    Chromosomal instability, aneuploidy, and cancer. Bakhoum SF, Swanton C. Front Oncol. 2014 Jun 19;4:161. doi: 10.3389/fonc.2014.00161. eCollection 2014. PMID:24995162

 

7.    Intratumour Heterogeneity in Urologic Cancers: From Molecular Evidence to Clinical Implications. Gerlinger M, Catto JW, Orntoft TF, Real FX, Zwarthoff EC, Swanton C. Eur Urol. 2014 May 2. pii: S0302-2838(14)00395-9. doi: 10.1016/j.eururo.2014.04.014. Review. PMID:24836153

 

8.    Cancer evolution: the final frontier of precision medicine? Swanton C. Ann Oncol. 2014 Mar;25(3):549-51. doi: 10.1093/annonc/mdu005. PMID:24567514