Oncogenic Signaling Pathways in The Cancer Genome Atlas

Cell

Volumn 173, Issue 2, 2018, Pages 321-337.e10

  Sanchez Vega, Francisco ^a   Mina, Marco ^b   Armenia, Joshua ^a   Chatila, Walid K ^a,aa   Luna, Augustin ^c,d   La, Konnor C ^a   Dimitriadoy, Sofia ^e   Liu, David L ^c,f   Kantheti, Havish S ^g   Saghafinia, Sadegh ^b   Chakravarty, Debyani ^a   Daian, Foysal ^a   Gao, Qingsong ^h   Bailey, Matthew H ^h   Liang, Wen Wei ^h   Foltz, Steven M ^h   Shmulevich, Ilya ⁱ   Ding, Li ^h,j   Heins, Zachary ^a   Ochoa, Angelica ^a   Gross, Benjamin ^a   Gao, Jianjiong ^a,aa   Zhang, Hongxin ^a   Kundra, Ritika ^a   Kandoth, Cyriac ^a   Bahceci, Istemi ^k   Dervishi, Leonard ^k   Dogrusoz, Ugur ^k   Zhou, Wanding ^l   Shen, Hui ^l   Laird, Peter W ^l   Way, Gregory P ^v   Greene, Casey S ^v   Liang, Han ^o   Xiao, Yonghong ^w   Wang, Chen ^x   Iavarone, Antonio ^y   Berger, Alice H ^m   Bivona, Trever G ⁿ   Lazar, Alexander J ^o,aa   Hammer, Gary D ^p   Giordano, Thomas ^p,q,r,aa   Kwong, Lawrence N ^o   McArthur, Grant ^s,z   Huang, Chenfei ^t   Tward, Aaron D ^u   Frederick, Mitchell J ^t   McCormick, Frank ⁿ   Meyerson, Matthew ^c,f   Caesar Johnson, Samantha J ^aa   Demchok, John A ^aa   Felau, Ina ^aa   Kasapi, Melpomeni ^aa   Ferguson, Martin L ^aa   Hutter, Carolyn M ^aa   Sofia, Heidi J ^aa   Tarnuzzer, Roy ^aa   Wang, Zhining ^aa   Yang, Liming ^aa   Zenklusen, Jean C ^aa   Sander, Chris ^c,d   Schultz, Nikolaus ^a   Cherniack, Andrew D ^c,f   Van Allen, Eliezer M ^c,f   Ciriello, Giovanni ^b,o   more..

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

^e PRINCETON UNIVERSITY   (United States)

^f BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^g UNIVERSITY OF TEXAS AT DALLAS   (United States)

^h WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^j Washington University in St Louis School of Medicine   (United States)

^k BILKENT UNIVERSITY   (Turkey)

^l VAN ANDEL RESEARCH INSTITUTE   (United States)

^m USA   (United States)

ⁿ UNIVERSITY OF CALIFORNIA   (United States)

^o UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^p UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^q UNIVERSITY OF MICHIGAN   (United States)

^r UNIVERSITY OF MICHIGAN COMPREHENSIVE CANCER CENTER   (United States)

^s PETER MACCALLUM CANCER CENTRE   (Australia)

^t BAYLOR COLLEGE OF MEDICINE   (United States)

^u UNIVERSITY OF CALIFORNIA   (United States)

^v UNIVERSITY OF PENNSYLVANIA   (United States)

^w TESARO   (United States)

^x Mayo Clinic College of Medicine   (United States)

^y Department of Medicine   (United States)

^z UNIVERSITY OF MELBOURNE   (Australia)

^aa Julia)

more..

Author keywords

cancer genome atlas; cancer genomics; combination therapy; pan cancer; PanCanAtlas; precision oncology; signaling pathways; TCGA; therapeutics; whole exome sequencing

Indexed keywords

BETA CATENIN; DNA; MESSENGER RNA; MYC PROTEIN; NOTCH RECEPTOR; PHOSPHATIDYLINOSITOL 3 KINASE; PROTEIN KINASE B; PROTEIN P53; PROTEIN TYROSINE KINASE; RAS PROTEIN; TRANSCRIPTION FACTOR NRF2; TRANSFORMING GROWTH FACTOR BETA; WNT PROTEIN;

ARTICLE; CANCER GENETICS; CARCINOGENESIS; CELL CYCLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA METHYLATION; GENE EXPRESSION; GENE FUSION; GENE MUTATION; GENOME ANALYSIS; HIPPO SIGNALING; HUMAN; MALIGNANT NEOPLASM; NOTCH SIGNALING; PI3K/AKT SIGNALING; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SOMATIC MUTATION; TGF BETA SIGNALING; GENETIC DATABASE; GENETICS; METABOLISM; NEOPLASM; PATHOLOGY; TUMOR GENE;

DATABASES, GENETIC; GENES, NEOPLASM; HUMANS; NEOPLASMS; PHOSPHATIDYLINOSITOL 3-KINASES; SIGNAL TRANSDUCTION; TRANSFORMING GROWTH FACTOR BETA; TUMOR SUPPRESSOR PROTEIN P53; WNT PROTEINS;

EID: 85044966521     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2018.03.035     Document Type: Article

References (80)

1. Alaei-Mahabadi, B., Bhadury, J., Karlsson, J.W., Nilsson, J.A., Larsson, E., Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. Proc. Natl. Acad. Sci. USA 113 (2016), 13768–13773.
2. Alexandrov, L.B., Nik-Zainal, S., Wedge, D.C., Aparicio, S.A.J.R., Behjati, S., Biankin, A.V., Bignell, G.R., Bolli, N., Borg, A., Børresen-Dale, A.-L., et al. Australian Pancreatic Cancer Genome Initiative ICGC Breast Cancer Consortium ICGC MMML-Seq Consortium, ICGC PedBrain. Signatures of mutational processes in human cancer. Nature 500 (2013), 415–421.
3. Aster, J.C., Blacklow, S.C., Targeting the Notch pathway: twists and turns on the road to rational therapeutics. J. Clin. Oncol. 30 (2012), 2418–2420.
4. Bahceci, I., Dogrusoz, U., La, K.C., Babur, Ö., Gao, J., Schultz, N., PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data. Bioinformatics 33 (2017), 2238–2240.
5. Bailey, M.H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Betrand, D., Weerasinghe, A., Colaprico, A., Kim, J., Wendl, M.C., Reardon, B., et al. Comprehensive Discovery and Characterization of Driver Genes and Mutations in Human Cancers. Cell 173 (2018), 371–385 this issue.
6. Benelli, M., Pescucci, C., Marseglia, G., Severgnini, M., Torricelli, F., Magi, A., Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript. Bioinformatics 28 (2012), 3232–3239.
7. Boland, C.R., Goel, A., Microsatellite instability in colorectal cancer. Gastroenterology 138 (2010), 2073–2087.e3.
8. Brennan, C.W., Verhaak, R.G.W., McKenna, A., Campos, B., Noushmehr, H., Salama, S.R., Zheng, S., Chakravarty, D., Sanborn, J.Z., Berman, S.H., et al., TCGA Research Network. The somatic genomic landscape of glioblastoma. Cell 155 (2013), 462–477.
9. Buijs, J.T., Stayrook, K.R., Guise, T.A., The role of TGF-β in bone metastasis: novel therapeutic perspectives. Bonekey Rep., 1, 2012, 96.
10. Campbell, J.D., Alexandrov, A., Kim, J., Wala, J., Berger, A.H., Pedamallu, C.S., Shukla, S.A., Guo, G., Brooks, A.N., Murray, B.A., et al., Cancer Genome Atlas Research Network. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat. Genet. 48 (2016), 607–616.
11. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487 (2012), 330–337.
12. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490 (2012), 61–70.
13. Cancer Genome Atlas Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517 (2015), 576–582.
14. Cancer Genome Atlas Network. Genomic Classification of Cutaneous Melanoma. Cell 161 (2015), 1681–1696.
15. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455 (2008), 1061–1068.
16. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474 (2011), 609–615.
17. Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489 (2012), 519–525.
18. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499 (2013), 43–49.
19. Cancer Genome Atlas Research Network, Kandoth, C., Schultz, N., Cherniack, A.D., Akbani, R., Liu, Y., Shen, H., Robertson, A.G., Pashtan, I., Shen, R., Benz, C.C., et al. Integrated genomic characterization of endometrial carcinoma. Nature 497 (2013), 67–73.
20. Cancer Genome Atlas Research Network, Weinstein, J.N., Collisson, E.A., Mills, G.B., Shaw, K.R., Ozenberger, B.A., Ellrott, K., Shmulevich, I., Sander, C., Stuart, J.M., The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45 (2013), 1113–1120.
21. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507 (2014), 315–322.
22. Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature 511 (2014), 543–550.
23. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513 (2014), 202–209.
24. Cancer Genome Atlas Research Network. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159 (2014), 676–690.
25. Cancer Genome Atlas Research Network. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell 169 (2017), 1327–1341.e23.
26. Cancer Genome Atlas Research Network Analysis Working Group: Asan University BC Cancer Agency Brigham and Women's Hospital Broad Institute Brown University Case Western Reserve University Dana-Farber Cancer Institute Duke University Greater Poland Cancer Centre Harvard Medical School, et-al. Integrated genomic characterization of oesophageal carcinoma. Nature 541 (2017), 169–175.
27. Cerami, E., Gao, J., Dogrusoz, U., Gross, B.E., Sumer, S.O., Aksoy, B.A., Jacobsen, A., Byrne, C.J., Heuer, M.L., Larsson, E., et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2 (2012), 401–404.
28. Cerami, E.G., Gross, B.E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G.D., Sander, C., Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 39 (2011), D685–D690.
29. Chakravarty, D., Gao, J., Phillips, S.M., Kundra, R., Zhang, H., Wang, J., Rudolph, J.E., Yaeger, R., Soumerai, T., Nissan, M.H., et al. OncoKB: A Precision Oncology Knowledge Base. JCO Precis. Oncol. 2017, 2017.
30. Chakravarty, D., Pedraza, A.M., Cotari, J., Liu, A.H., Punko, D., Kokroo, A., Huse, J.T., Altan-Bonnet, G., Brennan, C.W., EGFR and PDGFRA co-expression and heterodimerization in glioblastoma tumor sphere lines. Sci. Rep., 7, 2017, 9043.
31. Chang, M.T., Asthana, S., Gao, S.P., Lee, B.H., Chapman, J.S., Kandoth, C., Gao, J., Socci, N.D., Solit, D.B., Olshen, A.B., et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nat. Biotechnol. 34 (2016), 155–163.
32. Chang, M.T., Bhattarai, T.S., Schram, A.M., Bielski, C.M., Donoghue, M.T.A., Jonsson, P., Chakravarty, D., Phillips, S., Kandoth, C., Penson, A., et al. Accelerating Discovery of Functional Mutant Alleles in Cancer. Cancer Discov. 8 (2018), 174–183.
33. Ciriello, G., Miller, M.L., Aksoy, B.A., Senbabaoglu, Y., Schultz, N., Sander, C., Emerging landscape of oncogenic signatures across human cancers. Nat. Genet. 45 (2013), 1127–1133.
34. Davis, C.F., Ricketts, C.J., Wang, M., Yang, L., Cherniack, A.D., Shen, H., Buhay, C., Kang, H., Kim, S.C., Fahey, C.C., et al., The Cancer Genome Atlas Research Network. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell 26 (2014), 319–330.
35. Ellrott, K., Bailey, M.H., Saksena, G., Covington, K.R., Kandoth, C., Stewart, C., Hess, J., Ma, S., McLellan, M., Sofia, H.J., et al. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst, 6, 2018, 10.1016/j.cels.2018.03.002.
36. Etemadmoghadam, D., Weir, B.A., Au-Yeung, G., Alsop, K., Mitchell, G., George, J., Davis, S., D'Andrea, A.D., Simpson, K., Hahn, W.C., Bowtell, D.D., Australian Ovarian Cancer Study Group. Synthetic lethality between CCNE1 amplification and loss of BRCA1. Proc. Natl. Acad. Sci. USA 110 (2013), 19489–19494.
37. FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest, A.R., Kawaji, H., Rehli, M., Baillie, J.K., de Hoon, M.J., Haberle, V., Lassmann, T., Kulakovskiy, I.V., Lizio, M., Itoh, M., et al. A promoter-level mammalian expression atlas. Nature 507 (2014), 462–470.
38. Gao, J., Ciriello, G., Sander, C., Schultz, N., Collection, integration and analysis of cancer genomic profiles: from data to insight. Curr. Opin. Genet. Dev. 24 (2014), 92–98.
39. Gao, J., Chang, M.T., Johnsen, H.C., Gao, S.P., Sylvester, B.E., Sumer, S.O., Zhang, H., Solit, D.B., Taylor, B.S., Schultz, N., Sander, C., 3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets. Genome Med., 9, 2017, 4.
40. Gao, Q., Liang, W.-W., Foltz, S.M., Mutharasu, G., Jayasinghe, R.G., Cao, S., Liao, W.-W., Reynolds, S.M., Wyczalkowski, M.A., Yao, L., et al. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep, 23, 2018, 10.1016/j.celrep.2018.03.050.
41. Garraway, L.A., Lander, E.S., Lessons from the cancer genome. Cell 153 (2013), 17–37.
42. Ge, Z., Leighton, J., Wang, Y., Peng, X., Chen, Z., Chen, H., Sun, Y., Yao, F., Li, J., Zhang, H., et al. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell Rep, 23, 2018, 10.1016/j.celrep.2018.03.047.
43. Hanahan, D., Weinberg, R.A., The hallmarks of cancer. Cell 100 (2000), 57–70.
44. Hanahan, D., Weinberg, R.A., Hallmarks of cancer: the next generation. Cell 144 (2011), 646–674.
45. Hartmaier, R.J., Albacker, L.A., Chmielecki, J., Bailey, M., He, J., Goldberg, M.E., Ramkissoon, S., Suh, J., Elvin, J.A., Chiacchia, S., et al. High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis. Cancer Res. 77 (2017), 2464–2475.
46. Hoadley, K.A., Yau, C., Wolf, D.M., Cherniack, A.D., Tamborero, D., Ng, S., Leiserson, M.D.M., Niu, B., McLellan, M.D., Uzunangelov, V., et al., Cancer Genome Atlas Research Network. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 158 (2014), 929–944.
47. Hoadley, K.A., Yau, C., Hinoue, T., Wolf, M.D., Lazar, J.A., Drill, E., Shen, R., Taylor, M.A., Cherniack, D.A., Akbani, R., et al. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell, 173, 2018, 10.1016/j.cell.2018.03.022.
48. Jayasinghe, R.G., Cao, S., Gao, Q., Wendl, M.C., Vo, N.S., Reynolds, S.M., Zhao, Y., Climente-González, H., Chai, S., Wang, F., et al. Systematic analysis of splice site-creating mutations in cancer. Cell Rep, 23, 2018, 10.1016/j.celrep.2018.03.052.
49. Joshi-Tope, G., Gillespie, M., Vastrik, I., D'Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G.R., Wu, G.R., Matthews, L., et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 33 (2005), D428–D432.
50. Kanehisa, M., Goto, S., KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28 (2000), 27–30.
51. Korkut, A., Zaidi, S., Kanchi, R., Berger, A., Robertson, G., Kwong, L., Datto, M., Roszik, J., Ling, S., Ravikumar, V., et al. A PanCancer molecular analysis of disruptions in the TGF-β pathway. Cancer Cell, 2017.
52. Laroche-Clary, A., Chaire, V., Algeo, M.-P., Derieppe, M.-A., Loarer, F.L., Italiano, A., Combined targeting of MDM2 and CDK4 is synergistic in dedifferentiated liposarcomas. J. Hematol. Oncol., 10, 2017, 123.
53. Lawrence, M.S., Stojanov, P., Polak, P., Kryukov, G.V., Cibulskis, K., Sivachenko, A., Carter, S.L., Stewart, C., Mermel, C.H., Roberts, S.A., et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499 (2013), 214–218.
54. Lawrence, M.S., Stojanov, P., Mermel, C.H., Robinson, J.T., Garraway, L.A., Golub, T.R., Meyerson, M., Gabriel, S.B., Lander, E.S., Getz, G., Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505 (2014), 495–501.
55. Lepri, F., De Luca, A., Stella, L., Rossi, C., Baldassarre, G., Pantaleoni, F., Cordeddu, V., Williams, B.J., Dentici, M.L., Caputo, V., et al. SOS1 mutations in Noonan syndrome: molecular spectrum, structural insights on pathogenic effects, and genotype-phenotype correlations. Hum. Mutat. 32 (2011), 760–772.
56. Mermel, C.H., Schumacher, S.E., Hill, B., Meyerson, M.L., Beroukhim, R., Getz, G., GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol., 12, 2011, R41.
57. Mina, M., Raynaud, F., Tavernari, D., Battistello, E., Sungalee, S., Saghafinia, S., Laessle, T., Sanchez-Vega, F., Schultz, N., Oricchio, E., Ciriello, G., Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies. Cancer Cell 32 (2017), 155–168.e6.
58. Mitsuishi, Y., Taguchi, K., Kawatani, Y., Shibata, T., Nukiwa, T., Aburatani, H., Yamamoto, M., Motohashi, H., Nrf2 redirects glucose and glutamine into anabolic pathways in metabolic reprogramming. Cancer Cell 22 (2012), 66–79.
59. Nissan, M.H., Pratilas, C.A., Jones, A.M., Ramirez, R., Won, H., Liu, C., Tiwari, S., Kong, L., Hanrahan, A.J., Yao, Z., et al. Loss of NF1 in cutaneous melanoma is associated with RAS activation and MEK dependence. Cancer Res. 74 (2014), 2340–2350.
60. Pai, S.G., Carneiro, B.A., Mota, J.M., Costa, R., Leite, C.A., Barroso-Sousa, R., Kaplan, J.B., Chae, Y.K., Giles, F.J., Wnt/beta-catenin pathway: modulating anticancer immune response. J. Hematol. Oncol., 10, 2017, 101.
61. Park, H.W., Guan, K.-L., Regulation of the Hippo pathway and implications for anticancer drug development. Trends Pharmacol. Sci. 34 (2013), 581–589.
62. Peng, X., Chen, Z., Farshidfar, F., Xu, X., Lorenzi, P., Wang, Y., Cheng, F., Tan, L., Mojumdar, K., Du, D., et al. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep, 23, 2018, 10.1016/j.celrep.2018.03.077.
63. Rayner, E., van Gool, I.C., Palles, C., Kearsey, S.E., Bosse, T., Tomlinson, I., Church, D.N., A panoply of errors: polymerase proofreading domain mutations in cancer. Nat. Rev. Cancer 16 (2016), 71–81.
64. Schaub, F.X., Dhankani, V., Berger, A.C., Trivedi, M., Richardson, A.B., Shaw, R., Zhao, W., Zhang, X., Ventura, A., Liu, Y., et al. Alterations of the MYC oncogene and its Proximal Network across The Cancer Genome Atlas. Cell Syst, 6, 2018, 10.1016/j.cels.2018.03.003.
65. Schram, A.M., Berger, M.F., Hyman, D.M., Precision oncology: Charting a path forward to broader deployment of genomic profiling. PLoS Med., 14, 2017, e1002242.
66. Seiler, M., Peng, S., Agrawal, A.A., Palacino, J., Teng, T., Zhu, P., Smith, P.G., Cancer Genome Atlas Research Network, The, Buonamici, S., Yu, L., et al. Survey of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell Rep, 23, 2018, 10.1016/j.celrep.2018.01.088.
67. Sheen, Y.Y., Kim, M.-J., Park, S.-A., Park, S.-Y., Nam, J.-S., Targeting the Transforming Growth Factor-β Signaling in Cancer Therapy. Biomol. Ther. (Seoul) 21 (2013), 323–331.
68. Sholl, L.M., Do, K., Shivdasani, P., Cerami, E., Dubuc, A.M., Kuo, F.C., Garcia, E.P., Jia, Y., Davineni, P., Abo, R.P., et al. Institutional implementation of clinical tumor profiling on an unselected cancer population. JCI Insight, 1, 2016, e87062.
69. Sun, C., Wang, L., Huang, S., Heynen, G.J.J.E., Prahallad, A., Robert, C., Haanen, J., Blank, C., Wesseling, J., Willems, S.M., et al. Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma. Nature 508 (2014), 118–122.
70. Takebe, N., Nguyen, D., Yang, S.X., Targeting notch signaling pathway in cancer: clinical development advances and challenges. Pharmacol. Ther. 141 (2014), 140–149.
71. Knijnenburg, T., Wang, L., Zimmermann, M., Chambwe, N., Gao, G., Cherniack, A., Fan, H., Shen, H., Way, G., Greene, C., et al. Genomic and Molecular Landscape of DNA Damage Repair Deficiency Across The Cancer Genome Atlas. Cell Rep, 23, 2018, 10.1016/j.celrep.2018.03.076.
72. Triche, T.J. Jr., Weisenberger, D.J., Van Den Berg, D., Laird, P.W., Siegmund, K.D., Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res., 41, 2013, e90.
73. Unni, A.M., Lockwood, W.W., Zejnullahu, K., Lee-Lin, S.-Q., Varmus, H., Evidence that synthetic lethality underlies the mutual exclusivity of oncogenic KRAS and EGFR mutations in lung adenocarcinoma. eLife, 4, 2015, e06907.
74. Vogelstein, B., Kinzler, K.W., Cancer genes and the pathways they control. Nat. Med. 10 (2004), 789–799.
75. Vogelstein, B., Papadopoulos, N., Velculescu, V.E., Zhou, S., Diaz, L.A. Jr., Kinzler, K.W., Cancer genome landscapes. Science 339 (2013), 1546–1558.
76. Wang, Z., Yang, B., Zhang, M., Guo, W., Wu, Z., Wang, Y., Jia, L., Li, S.The Cancer Genome Atlas Research Network, Xie, W., Yang, D., LncRNA epigenetic landscape analysis identifies EPIC1 as an oncogenic lncRNA that interacts with MYC and promotes cell cycle progression in cancer. Cancer Cell, 33, 2018, 10.1016/j.ccell.2018.03.006.
77. Way, G.P., Sanchez-Vega, F., La, K., Armenia, J., Chatila, W.K., Luna, A., Sander, C., Cherniack, A.D., Mina, M., Ciriello, G., et al. Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep, 23, 2018, 10.1016/j.celrep.2018.03.046.
78. Whitfield, J.R., Beaulieu, M.-E., Soucek, L., Strategies to Inhibit Myc and Their Clinical Applicability. Front. Cell Dev. Biol., 5, 2017, 10.
79. Zehir, A., Benayed, R., Shah, R.H., Syed, A., Middha, S., Kim, H.R., Srinivasan, P., Gao, J., Chakravarty, D., Devlin, S.M., et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat. Med. 23 (2017), 703–713.
80. Zhang, Y., Kwok-Shing Ng, P., Kucherlapati, M., Chen, F., Liu, Y., Tsang, Y.H., de Velasco, G., Jeong, K.J., Akbani, R., Hadjipanayis, A., et al. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell 31 (2017), 820–832.e3.