Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–74.
Article
CAS
PubMed
Google Scholar
Amado RG, Wolf M, Peeters M, Van Cutsem E, Siena S, Freeman DJ, et al. Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. J Clin Oncol. 2008;26(10):1626–34.
Article
CAS
PubMed
Google Scholar
Flaherty KT, Puzanov I, Kim KB, Ribas A, McArthur GA, Sosman JA, et al. Inhibition of mutated, activated BRAF in metastatic melanoma. N Engl J Med. 2010;363(9):809–19.
Article
PubMed Central
CAS
PubMed
Google Scholar
Prahallad A, Sun C, Huang S, Di Nicolantonio F, Salazar R, Zecchin D, et al. Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR. Nature. 2012;483(7387):100–3.
Article
CAS
PubMed
Google Scholar
Janku F, Wheler JJ, Westin SN, Moulder SL, Naing A, Tsimberidou AM, et al. PI3K/AKT/mTOR inhibitors in patients with breast and gynecologic malignancies harboring PIK3CA mutations. J Clin Oncol. 2012;30(8):777–82.
Article
PubMed Central
CAS
PubMed
Google Scholar
Migliaccio I, Di Leo A, Malorni L. Cyclin-dependent kinase 4/6 inhibitors in breast cancer therapy. Curr Opin Oncol. 2014;26(6):568–75.
Article
CAS
PubMed
Google Scholar
Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012;486(7403):400–4.
PubMed Central
CAS
PubMed
Google Scholar
Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012;486(7403):405–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490(7418):61–70.
Article
Google Scholar
Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012;486(7403):353–60.
PubMed Central
CAS
PubMed
Google Scholar
Desmedt C, Voet T, Sotiriou C, Campbell PJ. Next-generation sequencing in breast cancer: first take home messages. Curr Opin Oncol. 2012;24(6):597–604.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vasan N, Yelensky R, Wang K, Moulder S, Dzimitrowicz H, Avritscher R, et al. A targeted next-generation sequencing assay detects a high frequency of therapeutically targetable alterations in primary and metastatic breast cancers: implications for clinical practice. Oncologist. 2014;19(5):453–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490(7418):61–70.
Article
PubMed Central
Google Scholar
Gyorffy B, Bottai G, Lehmann-Che J, Kéri G, Orfi L, Iwamoto T, et al. TP53 mutation-correlated genes predict the risk of tumor relapse and identify MPS1 as a potential therapeutic kinase in TP53-mutated breast cancers. Mol Oncol. 2014;8(3):508–19.
Article
CAS
PubMed
Google Scholar
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31(3):213–9.
Article
CAS
PubMed
Google Scholar
Keats JJ, Chesi M, Egan JB, Garbitt VM, Palmer SE, Braggio E, et al. Clonal competition with alternating dominance in multiple myeloma. Blood. 2012;120(5):1067–76.
Article
PubMed Central
CAS
PubMed
Google Scholar
Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, et al. COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43(Database issue):D805–11.
Article
PubMed Central
PubMed
Google Scholar
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6(2):80–92.
Article
CAS
Google Scholar
Laddha SV, Ganesan S, Chan CS, White E. Mutational landscape of the essential autophagy gene BECN1 in human cancers. Mol Cancer Res. 2014;12(4):485–90.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wickham H. The split-apply-combine strategy for data analysis. J Stat Softw. 2011;40(1):1–29.
Article
Google Scholar
Gyorffy B, Karn T, Sztupinszki Z, Weltz B, Müller V, Pusztai L. Dynamic classification using case-specific training cohorts outperforms static gene expression signatures in breast cancer. Int J Cancer. 2015;136(9):2091–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gyorffy B, Molnar B, Lage H, Szallasi Z, Eklund AC. Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples. PLoS One. 2009;4:e5645.
Article
PubMed Central
PubMed
Google Scholar
Gyorffy B, Benke Z, Lánczky A, Balázs B, Szállási Z, Timár J, et al. RecurrenceOnline: an online analysis tool to determine breast cancer recurrence and hormone receptor status using microarray data. Breast Cancer Res Treat. 2012;132(3):1025–34.
Article
CAS
PubMed
Google Scholar
Li Q, Birkbak NJ, Gyorffy B, Szallasi Z, Eklund AC. Jetset: selecting the optimal microarray probe set to represent a gene. BMC Bioinformatics. 2011;12:474.
Article
PubMed Central
PubMed
Google Scholar
Hanley JA, McNeil BJ. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology. 1982;143(1):29–36.
Article
CAS
PubMed
Google Scholar
Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics. 2005;21(20):3940–1.
Article
CAS
PubMed
Google Scholar
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, et al. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol. 2014;32(9):926–32.
Article
PubMed Central
CAS
PubMed
Google Scholar
Doggett NA, Xie G, Meincke LJ, Sutherland RD, Mundt MO, Berbari NS, et al. A 360-kb interchromosomal duplication of the human HYDIN locus. Genomics. 2006;88(6):762–71.
Article
CAS
PubMed
Google Scholar
Samuels Y, Wang Z, Bardelli A, Silliman N, Ptak J, Szabo S, et al. High frequency of mutations of the PIK3CA gene in human cancers. Science. 2004;304(5670):554.
Article
CAS
PubMed
Google Scholar
Venet D, Dumont JE, Detours V. Most random gene expression signatures are significantly associated with breast cancer outcome. PLoS Comput Biol. 2011;7(10):e1002240.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2(5):401–4.
Article
PubMed
Google Scholar
Bashashati A, Haffari G, Ding J, Ha G, Lui K, Rosner J, et al. DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol. 2012;13(12):R124.
Article
PubMed Central
PubMed
Google Scholar
Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010;26(12):i237–45.
Article
PubMed Central
CAS
PubMed
Google Scholar
Andre F, Bachelot T, Commo F, Campone M, Arnedos M, Dieras V, et al. Comparative genomic hybridisation array and DNA sequencing to direct treatment of metastatic breast cancer: a multicentre, prospective trial (SAFIR01/UNICANCER). Lancet Oncol. 2014;15(3):267–74.
Article
CAS
PubMed
Google Scholar
Madden SF, Clarke C, Gaule P, Aherne ST, O'Donovan N, Clynes M, et al. BreastMark: an integrated approach to mining publicly available transcriptomic datasets relating to breast cancer outcome. Breast Cancer Res. 2013;15(4):R52.
Article
PubMed Central
PubMed
Google Scholar
Gyorffy 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;8(12):e82241.
Article
PubMed Central
PubMed
Google Scholar