Erratum: Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer (Cell (2017) 171(3) (540–556.e25) (S0092867417310565) (10.1016/j.cell.2017.09.007));Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

Cell

Volumn 171, Issue 3, 2017, Pages 540-556.e25

  Robertson, A Gordon ^a,q   Kim, Jaegil ^b,q   Al Ahmadie, Hikmat ^c,q   Bellmunt, Joaquim ^d,q   Guo, Guangwu ^d,q   Cherniack, Andrew D ^b,q   Hinoue, Toshinori ^e,q   Laird, Peter W ^e,q   Hoadley, Katherine A ^f,q   Akbani, Rehan ^g,q   Castro, Mauro A A ^h,q   Gibb, Ewan A ^a,q   Kanchi, Rupa S ^g,q   Gordenin, Dmitry A ^i,q   Shukla, Sachet A ^d,q   Sanchez Vega, Francisco ^c,q   Hansel, Donna E ^j,q   Czerniak, Bogdan A ^g,q   Reuter, Victor E ^c,q   Su, Xiaoping ^g,q   de Sa Carvalho, Benilton ^k,q   Chagas, Vinicius S ^h,q   Mungall, Karen L ^a,q   Sadeghi, Sara ^a,q   Pedamallu, Chandra Sekhar ^b   Lu, Yiling ^g,q   Klimczak, Leszek J ^i,q   Zhang, Jiexin ^g,q   Choo, Caleb ^a,q   Ojesina, Akinyemi I ^l,q   Bullman, Susan ^b,q   Leraas, Kristen M ^m,q   Lichtenberg, Tara M ^m,q   Wu, Catherine J ^n,q   Schultz, Nikolaus ^q   Getz, Gad ^b,q   Meyerson, Matthew ^d,q   Mills, Gordon B ^g,q   McConkey, David J ^o,q   Albert, Monique ^q   Alexopoulou, Iakovina ^q   Ally, Adrian ^q   Antic, Tatjana ^q   Aron, Manju ^q   Balasundaram, Miruna ^q   Bartlett, John ^q   Baylin, Stephen B ^q   Beaver, Allison ^q   Birol, Inanc ^q   Boice, Lori ^q   Bootwalla, Moiz S ^q   Bowen, Jay ^q   Bowlby, Reanne ^q   Brooks, Denise ^q   Broom, Bradley M ^q   Bshara, Wiam ^q   Burks, Eric ^q   Cárcano, Flavio M ^q   Carlsen, Rebecca ^q   Carvalho, Andre L ^q   Castle, Eric P ^q   Castro, Patricia ^q   Catto, James W ^q   Chesla, David W ^q   Chuah, Eric ^q   Chudamani, Sudha ^q   Cortessis, Victoria K ^q   Cottingham, Sandra L ^q   Crain, Daniel ^q   Curley, Erin ^q   Daneshmand, Siamak ^q   Demchok, John A ^q   Dhalla, Noreen ^q   Djaladat, Hooman ^q   Eckman, John ^q   Egea, Sophie C ^q   Engel, Jay ^q   Felau, Ina ^q   Ferguson, Martin L ^q   Gardner, Johanna ^q   Gastier Foster, Julie M ^q   Gerken, Mark ^q   Gomez Fernandez, Carmen R ^q   Harr, Jodi ^q   Hartmann, Arndt ^q   Herbert, Lynn M ^q   Ho, Thai H ^q   Holt, Robert A ^q   Hutter, Carolyn M ^q   Jones, Steven J M ^q   Jorda, Merce ^q   Kahnoski, Richard J ^q   Kasaian, Katayoon ^q   Kwiatkowski, David J ^n,q   Lai, Phillip H ^q   Lane, Brian R ^q   Lerner, Seth P ^p,q   Liu, Jia ^q   Lolla, Laxmi ^q   Lotan, Yair ^q   Lucchesi, Fabiano R ^q   Ma, Yussanne ^q   Machado, Roberto D ^q   Maglinte, Dennis T ^q   Mallery, David ^q   Marra, Marco A ^q   Martin, Sue E ^q   Mayo, Michael ^q   Meraney, Anoop ^q   Moinzadeh, Alireza ^q   Moore, Richard A ^q   Mora Pinero, Edna M ^q   Morris, Scott ^q   Morrison, Carl ^q   Mungall, Andrew J ^q   Myers, Jerome B ^q   Naresh, Rashi ^q   O'Donnell, Peter H ^q   Parekh, Dipen J ^q   Parfitt, Jeremy ^q   Paulauskis, Joseph D ^q   Sekhar Pedamallu, Chandra ^q   Penny, Robert J ^q   Pihl, Todd ^q   Porten, Sima ^q   Quintero Aguilo, Mario E ^q   Ramirez, Nilsa C ^q   Rathmell, W Kimryn ^q   Rieger Christ, Kimberly ^q   Saller, Charles ^q   Salner, Andrew ^q   Sandusky, George ^q   Scapulatempo Neto, Cristovam ^q   Schein, Jacqueline E ^q   Schuckman, Anne K ^q   Shelton, Candace ^q   Shelton, Troy ^q   Simko, Jeff ^q   Singh, Parminder ^q   Sipahimalani, Payal ^q   Smith, Norm D ^q   Sofia, Heidi J ^q   Sorcini, Andrea ^q   Stanton, Melissa L ^q   Steinberg, Gary D ^q   Stoehr, Robert ^q   Sullivan, Travis ^q   Sun, Qiang ^q   Tam, Angela ^q   Tarnuzzer, Roy ^q   Tarvin, Katherine ^q   Taubert, Helge ^q   Thiessen, Nina ^q   Thorne, Leigh ^q   Tse, Kane ^q   Tucker, Kelinda ^q   Van Den Berg, David J ^q   van Kessel, Kim E ^q   Wach, Sven ^q   Wan, Yunhu ^q   Wang, Zhining ^q   Weinstein, John N ^g,q   Weisenberger, Daniel J ^q   Wise, Lisa ^q   Wong, Tina ^q   Wu, Ye ^q   Yang, Liming ^q   Zach, Leigh Anne ^q   Zenklusen, Jean C ^q   more..

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

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

^c MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^d DANA FARBER CANCER INSTITUTE   (United States)

^e VAN ANDEL RESEARCH INSTITUTE   (United States)

^f UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

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

^h FEDERAL UNIVERSITY OF PARANÁ   (Brazil)

ⁱ NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^j UNIVERSITY OF CALIFORNIA   (United States)

^k UNIVERSITY OF CAMPINAS   (Brazil)

^l UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^m THE RESEARCH INSTITUTE AT NATIONWIDE CHILDREN S HOSPITAL   (United States)

ⁿ HARVARD MEDICAL SCHOOL   (United States)

^o JOHNS HOPKINS UNIVERSITY   (United States)

^p BAYLOR COLLEGE OF MEDICINE   (United States)

^q Julia)

more..

Author keywords

APOBEC mutation; basal mRNA subtype; DNA methylation; lncRNA transcriptome; luminal mRNA subtype; microRNA; muscle invasive bladder cancer; neoantigen; neuronal subtype; regulon

Indexed keywords

APOLIPOPROTEIN B MRNA EDITING ENZYME CATALYTIC POLYPEPTIDE LIKE; LONG UNTRANSLATED RNA; MESSENGER RNA; MICRORNA;

ADULT; AGED; ARTICLE; CANCER GENETICS; CANCER SURVIVAL; CARCINOMA IN SITU; COHORT ANALYSIS; CONTROLLED STUDY; EPITHELIAL MESENCHYMAL TRANSITION; FEMALE; GENE CLUSTER; GENE EXPRESSION; GENE MUTATION; HUMAN; HUMAN TISSUE; MALE; MUSCLE INVASIVE BLADDER CANCER; MUTAGENESIS; MUTATIONAL LOAD; PRIORITY JOURNAL; BLADDER; CLUSTER ANALYSIS; DNA METHYLATION; GENETICS; MIDDLE AGED; PATHOLOGY; SMOOTH MUSCLE; SURVIVAL ANALYSIS; URINARY BLADDER NEOPLASMS;

AGED; CLUSTER ANALYSIS; DNA METHYLATION; HUMANS; MICRORNAS; MIDDLE AGED; MUSCLE, SMOOTH; RNA, LONG NONCODING; SURVIVAL ANALYSIS; URINARY BLADDER; URINARY BLADDER NEOPLASMS;

EID: 85030652738     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2018.07.036     Document Type: Erratum

References (115)

1. Aine, M., Eriksson, P., Liedberg, F., Sjödahl, G., Höglund, M., Biological determinants of bladder cancer gene expression subtypes. Sci. Rep., 5, 2015, 10957.
2. Akbani, R., Ng, P.K., Werner, H.M., Shahmoradgoli, M., Zhang, F., Ju, Z., Liu, W., Yang, J.Y., Yoshihara, K., Li, J., et al. A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nat. Commun., 5, 2014, 3887.
3. Al-Ahmadie, H.A., Iyer, G., Lee, B.H., Scott, S.N., Mehra, R., Bagrodia, A., Jordan, E.J., Gao, S.P., Ramirez, R., Cha, E.K., et al. Frequent somatic CDH1 loss-of-function mutations in plasmacytoid variant bladder cancer. Nat. Genet. 48 (2016), 356–358.
4. Alexandrov, L.B., Nik-Zainal, S., Wedge, D.C., Aparicio, S.A., 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.
5. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J., Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25 (1997), 3389–3402.
6. Balbás-Martínez, C., Sagrera, A., Carrillo-de-Santa-Pau, E., Earl, J., Márquez, M., Vazquez, M., Lapi, E., Castro-Giner, F., Beltran, S., Bayés, M., et al. Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy. Nat. Genet. 45 (2013), 1464–1469.
7. Bibikova, M., Le, J., Barnes, B., Saedinia-Melnyk, S., Zhou, L., Shen, R., Gunderson, K.L., Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 1 (2009), 177–200.
8. Bibikova, M., Barnes, B., Tsan, C., Ho, V., Klotzle, B., Le, J.M., Delano, D., Zhang, L., Schroth, G.P., Gunderson, K.L., et al. High density DNA methylation array with single CpG site resolution. Genomics 98 (2011), 288–295.
9. Biton, A., Bernard-Pierrot, I., Lou, Y., Krucker, C., Chapeaublanc, E., Rubio-Pérez, C., López-Bigas, N., Kamoun, A., Neuzillet, Y., Gestraud, P., et al. Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes. Cell Rep. 9 (2014), 1235–1245.
10. Breyer, J., Wirtz, R.M., Laible, M., Schlombs, K., Erben, P., Kriegmair, M.C., Stoehr, R., Eidt, S., Denzinger, S., Burger, M., et al. ESR1, ERBB2, and Ki67 mRNA expression predicts stage and grade of non-muscle-invasive bladder carcinoma (NMIBC). Virchows Arch. 469 (2016), 547–552.
11. Campan, M., Weisenberger, D.J., Trinh, B., Laird, P.W., MethyLight. Methods Mol. Biol. 507 (2009), 325–337.
12. Campbell, T.M., Castro, M.A.A., de Santiago, I., Fletcher, M.N.C., Halim, S., Prathalingam, R., Ponder, B.A.J., Meyer, K.B., FGFR2 risk SNPs confer breast cancer risk by augmenting oestrogen responsiveness. Carcinogenesis 37 (2016), 741–750.
13. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490 (2012), 61–70.
14. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507 (2014), 315–322.
15. Cancer Genome Atlas Research Network. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159 (2014), 676–690.
16. Cancer Genome Atlas Research Network. Integrated genomic and molecular characterization of cervical cancer. Nature, 2017.
17. Cappellen, D., De Oliveira, C., Ricol, D., de Medina, S., Bourdin, J., Sastre-Garau, X., Chopin, D., Thiery, J.P., Radvanyi, F., Frequent activating mutations of FGFR3 in human bladder and cervix carcinomas. Nat. Genet. 23 (1999), 18–20.
18. Carter, S.L., Cibulskis, K., Helman, E., McKenna, A., Shen, H., Zack, T., Laird, P.W., Onofrio, R.C., Winckler, W., Weir, B.A., et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30 (2012), 413–421.
19. Castro, M.A., de Santiago, I., Campbell, T.M., Vaughn, C., Hickey, T.E., Ross, E., Tilley, W.D., Markowetz, F., Ponder, B.A., Meyer, K.B., Regulators of genetic risk of breast cancer identified by integrative network analysis. Nat. Genet. 48 (2016), 12–21.
20. Castro, M.A., Wang, X., Fletcher, M.N., Meyer, K.B., and Markowetz, F. (2016b). RTN: Reconstruction of transcriptional networks and analysis of master regulators (R/Bioconductor package).
21. Chakravarty, D., Gao, J., Phillips, S., 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. 1 (2017), 1–16.
22. Chan, K.S., Volkmer, J.P., Weissman, I., Cancer stem cells in bladder cancer: A revisited and evolving concept. Curr. Opin. Urol. 20 (2010), 393–397.
23. Chen, Y., Yao, H., Thompson, E.J., Tannir, N.M., Weinstein, J.N., Su, X., VirusSeq: Software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. Bioinformatics 29 (2013), 266–267.
24. Choi, W., Czerniak, B., Ochoa, A., Su, X., Siefker-Radtke, A., Dinney, C., McConkey, D.J., Intrinsic basal and luminal subtypes of muscle-invasive bladder cancer. Nat. Rev. Urol. 11 (2014), 400–410.
25. Choi, W., Porten, S., Kim, S., Willis, D., Plimack, E.R., Hoffman-Censits, J., Roth, B., Cheng, T., Tran, M., Lee, I.L., et al. Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy. Cancer Cell 25 (2014), 152–165.
26. Chu, J., Sadeghi, S., Raymond, A., Jackman, S.D., Nip, K.M., Mar, R., Mohamadi, H., Butterfield, Y.S., Robertson, A.G., Birol, I., BioBloom tools: Fast, accurate and memory-efficient host species sequence screening using bloom filters. Bioinformatics 30 (2014), 3402–3404.
27. Chu, A., Robertson, G., Brooks, D., Mungall, A.J., Birol, I., Coope, R., Ma, Y., Jones, S., Marra, M.A., Large-scale profiling of microRNAs for The Cancer Genome Atlas. Nucleic Acids Res., 44, 2016, e3.
28. Cibulskis, K., Lawrence, M.S., Carter, S.L., Sivachenko, A., Jaffe, D., Sougnez, C., Gabriel, S., Meyerson, M., Lander, E.S., Getz, G., Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31 (2013), 213–219.
29. Cuzick, J., Swanson, G.P., Fisher, G., Brothman, A.R., Berney, D.M., Reid, J.E., Mesher, D., Speights, V.O., Stankiewicz, E., Foster, C.S., et al., Transatlantic Prostate Group. Prognostic value of an RNA expression signature derived from cell cycle proliferation genes in patients with prostate cancer: A retrospective study. Lancet Oncol. 12 (2011), 245–255.
30. Dadhania, V., Zhang, M., Zhang, L., Bondaruk, J., Majewski, T., Siefker-Radtke, A., Guo, C.C., Dinney, C., Cogdell, D.E., Zhang, S., et al. Meta-analysis of the luminal and basal subtypes of bladder cancer and the identification of signature immunohistochemical markers for clinical use. EBioMedicine 12 (2016), 105–117.
31. Damrauer, J.S., Hoadley, K.A., Chism, D.D., Fan, C., Tiganelli, C.J., Wobker, S.E., Yeh, J.J., Milowsky, M.I., Iyer, G., Parker, J.S., Kim, W.Y., Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology. Proc. Natl. Acad. Sci. USA 111 (2014), 3110–3115.
32. DeGraff, D.J., Cates, J.M., Mauney, J.R., Clark, P.E., Matusik, R.J., Adam, R.M., When urothelial differentiation pathways go wrong: Implications for bladder cancer development and progression. Urol. Oncol. 31 (2013), 802–811.
33. Dennison, J.B., Shahmoradgoli, M., Liu, W., Ju, Z., Meric-Bernstam, F., Perou, C.M., Sahin, A.A., Welm, A., Oesterreich, S., Sikora, M.J., et al. High intratumoral stromal content defines reactive breast cancer as a low-risk breast cancer subtype. Clin. Cancer Res. 22 (2016), 5068–5078.
34. Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T.R., STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29 (2013), 15–21.
35. Dyrskjøt, L., Kruhøffer, M., Thykjaer, T., Marcussen, N., Jensen, J.L., Møller, K., Ørntoft, T.F., Gene expression in the urinary bladder: A common carcinoma in situ gene expression signature exists disregarding histopathological classification. Cancer Res. 64 (2004), 4040–4048.
36. Eriksson, P., Aine, M., Veerla, S., Liedberg, F., Sjödahl, G., Höglund, M., Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems. BMC Med. Genomics, 8, 2015, 25.
37. Fletcher, M.N., Castro, M.A., Wang, X., de Santiago, I., O'Reilly, M., Chin, S.F., Rueda, O.M., Caldas, C., Ponder, B.A., Markowetz, F., Meyer, K.B., Master regulators of FGFR2 signalling and breast cancer risk. Nat. Commun., 4, 2013, 2464.
38. Forbes, S.A., Bindal, N., Bamford, S., Cole, C., Kok, C.Y., Beare, D., Jia, M., Shepherd, R., Leung, K., Menzies, A., et al. COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 39 (2011), D945–D950.
39. Friedman, J., Hastie, T., Tibshirani, R., Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33 (2010), 1–22.
40. Gentleman, R., Carey, V., Huber, W., and Hahne, F. (2016). genefilter: Methods for filtering genes from high-throughput experiments (Bioconductor).
41. Getz, G., Höfling, H., Mesirov, J.P., Golub, T.R., Meyerson, M., Tibshirani, R., Lander, E.S., Comment on “The consensus coding sequences of human breast and colorectal cancers”. Science, 317, 2007, 1500.
42. Godoy, G., Gakis, G., Smith, C.L., Fahmy, O., Effects of androgen and estrogen receptor signaling pathways on bladder cancer initiation and progression. Bladder Cancer 2 (2016), 127–137.
43. Gonzalez-Angulo, A.M., Hennessy, B.T., Meric-Bernstam, F., Sahin, A., Liu, W., Ju, Z., Carey, M.S., Myhre, S., Speers, C., Deng, L., et al. Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer. Clin. Proteomics, 8, 2011, 11.
44. Gui, Y., Guo, G., Huang, Y., Hu, X., Tang, A., Gao, S., Wu, R., Chen, C., Li, X., Zhou, L., et al. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat. Genet. 43 (2011), 875–878.
45. Hennessy, B.T., Lu, Y., Poradosu, E., Yu, Q., Yu, S., Hall, H., Carey, M.S., Ravoori, M., Gonzalez-Angulo, A.M., Birch, R., et al. Pharmacodynamic markers of perifosine efficacy. Clin. Cancer Res. 13 (2007), 7421–7431.
46. Hennessy, B.T., Lu, Y., Gonzalez-Angulo, A.M., Carey, M.S., Myhre, S., Ju, Z., Davies, M.A., Liu, W., Coombes, K., Meric-Bernstam, F., et al. A technical assessment of the utility of reverse phase protein arrays for the study of the functional proteome in non-microdissected human breast cancers. Clin. Proteomics 6 (2010), 129–151.
47. Hoadley, K.A., Yau, C., Wolf, D.M., Cherniack, A.D., Tamborero, D., Ng, S., Leiserson, M.D., 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.
48. Hu, J., He, X., Baggerly, K.A., Coombes, K.R., Hennessy, B.T.J., Mills, G.B., Non-parametric quantification of protein lysate arrays. Bioinformatics 23 (2007), 1986–1994.
49. Hutmacher, M.M., Kowalski, K.G., Covariate selection in pharmacometric analyses: A review of methods. Br. J. Clin. Pharmacol. 79 (2015), 132–147.
50. Jones, R.T., Felsenstein, K.M., Theodorescu, D., Pharmacogenomics: Biomarker-directed therapy for bladder cancer. Urol. Clin. North Am. 43 (2016), 77–86.
51. Ju, Z., Liu, W., Roebuck, P.L., Siwak, D.R., Zhang, N., Lu, Y., Davies, M.A., Akbani, R., Weinstein, J.N., Mills, G.B., Coombes, K.R., Development of a robust classifier for quality control of reverse-phase protein arrays. Bioinformatics 31 (2015), 912–918.
52. Kardos, J., Chai, S., Mose, L.E., Selitsky, S.R., Krishnan, B., Saito, R., Iglesia, M.D., Milowsky, M.I., Parker, J.S., Kim, W.Y., Vincent, B.G., Claudin-low bladder tumors are immune infiltrated and actively immune suppressed. JCI Insight, 1, 2016, e85902.
53. Karkera, J.D., Martinez Cardona, G., Bell, K., Gaffney, D., Portale, J.C., Santiago-Walker, A., Moy, C., King, P., Sharp, M., Bahleda, R., et al. Oncogenic characterization and pharmacologic sensitivity of activating fibroblast growth factor receptor (FGFR) genetic alterations to the selective FGFR inhibitor erdafitinib. Mol. Cancer Ther. 16 (2017), 1717–1726.
54. Kasar, S., Kim, J., Improgo, R., Tiao, G., Polak, P., Haradhvala, N., Lawrence, M.S., Kiezun, A., Fernandes, S.M., Bahl, S., et al. Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution. Nat. Commun., 6, 2015, 8866.
55. Kent, W.J., BLAT—the BLAST-like alignment tool. Genome Res. 12 (2002), 656–664.
56. Kim, J., Mouw, K.W., Polak, P., Braunstein, L.Z., Kamburov, A., Kwiatkowski, D.J., Rosenberg, J.E., Van Allen, E.M., D'Andrea, A., Getz, G., Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat. Genet. 48 (2016), 600–606.
57. Knowles, M.A., Hurst, C.D., Molecular biology of bladder cancer: New insights into pathogenesis and clinical diversity. Nat. Rev. Cancer 15 (2015), 25–41.
58. Korn, J.M., Kuruvilla, F.G., McCarroll, S.A., Wysoker, A., Nemesh, J., Cawley, S., Hubbell, E., Veitch, J., Collins, P.J., Darvishi, K., et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat. Genet. 40 (2008), 1253–1260.
59. Kostic, A.D., Ojesina, A.I., Pedamallu, C.S., Jung, J., Verhaak, R.G., Getz, G., Meyerson, M., PathSeq: Software to identify or discover microbes by deep sequencing of human tissue. Nat. Biotechnol. 29 (2011), 393–396.
60. Kuhn, R.M., Haussler, D., Kent, W.J., The UCSC genome browser and associated tools. Brief. Bioinform. 14 (2013), 144–161.
61. 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.
62. 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.
63. Lee, W.P., Stromberg, M.P., Ward, A., Stewart, C., Garrison, E.P., Marth, G.T., MOSAIK: A hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS ONE, 9, 2014, e90581.
64. Ler, L.D., Ghosh, S., Chai, X., Thike, A.A., Heng, H.L., Siew, E.Y., Dey, S., Koh, L.K., Lim, J.Q., Lim, W.K., et al. Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2. Sci. Transl. Med., 2017, 10.1126/scitranslmed.aai8312 Published online February 22, 2017.
65. Li, B., Dewey, C.N., RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics, 12, 2011, 323.
66. Li, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 (2009), 1754–1760.
67. Li, J., Tibshirani, R., Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data. Stat. Methods Med. Res. 22 (2013), 519–536.
68. Liang, J., Shao, S.H., Xu, Z.X., Hennessy, B., Ding, Z., Larrea, M., Kondo, S., Dumont, D.J., Gutterman, J.U., Walker, C.L., et al. The energy sensing LKB1-AMPK pathway regulates p27(kip1) phosphorylation mediating the decision to enter autophagy or apoptosis. Nat. Cell Biol. 9 (2007), 218–224.
69. Lim, S., Koh, M.J., Jeong, H.J., Cho, N.H., Choi, Y.D., Cho, Y., Lee, H.Y., Rha, S.Y., Fibroblast growth factor receptor 1 overexpression is associated with poor survival in patients with resected muscle invasive urothelial carcinoma. Yonsei Med. J. 57 (2016), 831–839.
70. Losada, A., Cohesin in cancer: Chromosome segregation and beyond. Nat. Rev. Cancer 14 (2014), 389–393.
71. Mak, M.P., Tong, P., Diao, L., Cardnell, R.J., Gibbons, D.L., William, W.N., Skoulidis, F., Parra, E.R., Rodriguez-Canales, J., Wistuba, I.I., et al. A patient-derived, pan-cancer EMT signature identifies global molecular alterations and immune target enrichment following epithelial-to-mesenchymal transition. Clin. Cancer Res. 22 (2016), 609–620.
72. Margolin, A.A., Wang, K., Lim, W.K., Kustagi, M., Nemenman, I., Califano, A., Reverse engineering cellular networks. Nat. Protoc. 1 (2006), 662–671.
73. McCarroll, S.A., Kuruvilla, F.G., Korn, J.M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M.H., de Bakker, P.I., Maller, J.B., Kirby, A., et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40 (2008), 1166–1174.
74. 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.
75. Moch, H., Cubilla, A.L., Humphrey, P.A., Reuter, V.E., Ulbright, T.M., The 2016 WHO classification of tumours of the urinary system and male genital organs-part A: Renal, penile, and testicular tumours. Eur. Urol. 70 (2016), 93–105.
76. Mullokandov, G., Baccarini, A., Ruzo, A., Jayaprakash, A.D., Tung, N., Israelow, B., Evans, M.J., Sachidanandam, R., Brown, B.D., High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries. Nat. Methods 9 (2012), 840–846.
77. Neeley, E.S., Kornblau, S.M., Coombes, K.R., Baggerly, K.A., Variable slope normalization of reverse phase protein arrays. Bioinformatics 25 (2009), 1384–1389.
78. Nguyen, Q., Carninci, P., Expression specificity of disease-associated lncRNAs: Toward personalized medicine. Curr. Top. Microbiol. Immunol. 394 (2016), 237–258.
79. Nielsen, M., Andreatta, M., NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med., 8, 2016, 33.
80. Nogova, L., Sequist, L.V., Perez Garcia, J.M., Andre, F., Delord, J.P., Hidalgo, M., Schellens, J.H., Cassier, P.A., Camidge, D.R., Schuler, M., et al. Evaluation of BGJ398, a fibroblast growth factor receptor 1-3 kinase inhibitor, in patients with advanced solid tumors harboring genetic alterations in fibroblast growth factor receptors: Results of a global phase i, dose-escalation and dose-expansion study. J. Clin. Oncol. 35 (2017), 157–165.
81. Olshen, A.B., Venkatraman, E.S., Lucito, R., Wigler, M., Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5 (2004), 557–572.
82. R Core Development Team. R: A Language and Environment for Statistical Computing. 2016, R Foundation for Statistical Computing.
83. Ratan, A., Olson, T.L., Loughran, T.P. Jr., Miller, W., Identification of indels in next-generation sequencing data. BMC Bioinformatics, 16, 2015, 42.
84. Rebouissou, S., Hérault, A., Letouzé, E., Neuzillet, Y., Laplanche, A., Ofualuka, K., Maillé, P., Leroy, K., Riou, A., Lepage, M.L., et al. CDKN2A homozygous deletion is associated with muscle invasion in FGFR3-mutated urothelial bladder carcinoma. J. Pathol. 227 (2012), 315–324.
85. Reich, M., Liefeld, T., Gould, J., Lerner, J., Tamayo, P., Mesirov, J.P., GenePattern 2.0. Nat. Genet. 38 (2006), 500–501.
86. Roberts, S.A., Lawrence, M.S., Klimczak, L.J., Grimm, S.A., Fargo, D., Stojanov, P., Kiezun, A., Kryukov, G.V., Carter, S.L., Saksena, G., et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat. Genet. 45 (2013), 970–976.
87. Robertson, G., Schein, J., Chiu, R., Corbett, R., Field, M., Jackman, S.D., Mungall, K., Lee, S., Okada, H.M., Qian, J.Q., et al. De novo assembly and analysis of RNA-seq data. Nat. Methods 7 (2010), 909–912.
88. Rosenberg, J.E., Hoffman-Censits, J., Powles, T., van der Heijden, M.S., Balar, A.V., Necchi, A., Dawson, N., O'Donnell, P.H., Balmanoukian, A., Loriot, Y., et al. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: A single-arm, multicentre, phase 2 trial. Lancet 387 (2016), 1909–1920.
89. Saunders, C.T., Wong, W.S., Swamy, S., Becq, J., Murray, L.J., Cheetham, R.K., Strelka: Accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 28 (2012), 1811–1817.
90. Seiler, R., Ashab, H.A., Erho, N., van Rhijn, B.W., Winters, B., Douglas, J., Van Kessel, K.E., Fransen van de Putte, E.E., Sommerlad, M., Wang, N.Q., et al. Impact of molecular subtypes in muscle-invasive bladder cancer on predicting response and survival after neoadjuvant chemotherapy. Eur. Urol., 2017 S0302-2838(17)30251-8.
91. Sharma, P., Callahan, M.K., Bono, P., Kim, J., Spiliopoulou, P., Calvo, E., Pillai, R.N., Ott, P.A., de Braud, F., Morse, M., et al. Nivolumab monotherapy in recurrent metastatic urothelial carcinoma (CheckMate 032): A multicentre, open-label, two-stage, multi-arm, phase 1/2 trial. Lancet Oncol. 17 (2016), 1590–1598.
92. Shukla, S.A., Rooney, M.S., Rajasagi, M., Tiao, G., Dixon, P.M., Lawrence, M.S., Stevens, J., Lane, W.J., Dellagatta, J.L., Steelman, S., et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat. Biotechnol. 33 (2015), 1152–1158.
93. Siegel, R.L., Miller, K.D., Jemal, A., Cancer Statistics, 2017. CA Cancer J. Clin. 67 (2017), 7–30.
94. Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J., Birol, I., ABySS: a parallel assembler for short read sequence data. Genome Res. 19 (2009), 1117–1123.
95. Sjödahl, G., Lauss, M., Lövgren, K., Chebil, G., Gudjonsson, S., Veerla, S., Patschan, O., Aine, M., Fernö, M., Ringnér, M., et al. A molecular taxonomy for urothelial carcinoma. Clin. Cancer Res. 18 (2012), 3377–3386.
96. Sjödahl, G., Eriksson, P., Liedberg, F., Höglund, M., Molecular classification of urothelial carcinoma: Global mRNA classification versus tumour-cell phenotype classification. J. Pathol. 242 (2017), 113–125.
97. Tan, V.Y., Févotte, C., Automatic relevance determination in nonnegative matrix factorization with the β-divergence. IEEE Trans. Pattern Anal. Mach. Intell. 35 (2013), 1592–1605.
98. Thomson, D.W., Dinger, M.E., Endogenous microRNA sponges: Evidence and controversy. Nat. Rev. Genet. 17 (2016), 272–283.
99. Tibes, R., Qiu, Y., Lu, Y., Hennessy, B., Andreeff, M., Mills, G.B., Kornblau, S.M., Reverse phase protein array: Validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol. Cancer Ther. 5 (2006), 2512–2521.
100. Trapnell, C., Pachter, L., Salzberg, S.L., TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25 (2009), 1105–1111.
101. Trapnell, C., Hendrickson, D.G., Sauvageau, M., Goff, L., Rinn, J.L., Pachter, L., Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31 (2013), 46–53.
102. 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.
103. Van Allen, E.M., Mouw, K.W., Kim, P., Iyer, G., Wagle, N., Al-Ahmadie, H., Zhu, C., Ostrovnaya, I., Kryukov, G.V., O'Connor, K.W., et al. Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma. Cancer Discov. 4 (2014), 1140–1153.
104. van Rhijn, B.W., Lurkin, I., Radvanyi, F., Kirkels, W.J., van der Kwast, T.H., Zwarthoff, E.C., The fibroblast growth factor receptor 3 (FGFR3) mutation is a strong indicator of superficial bladder cancer with low recurrence rate. Cancer Res. 61 (2001), 1265–1268.
105. Walter, S., Tiemeier, H., Variable selection: Current practice in epidemiological studies. Eur. J. Epidemiol. 24 (2009), 733–736.
106. Wang, K., Singh, D., Zeng, Z., Coleman, S.J., Huang, Y., Savich, G.L., He, X., Mieczkowski, P., Grimm, S.A., Perou, C.M., et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res., 38, 2010, e178.
107. Warrick, J.I., Walter, V., Yamashita, H., Chung, E., Shuman, L., Amponsa, V.O., Zheng, Z., Chan, W., Whitcomb, T.L., Yue, F., et al. FOXA1, GATA3 and PPAR cooperate to drive luminal subtype in bladder cancer: A molecular analysis of established human cell lines. Sci. Rep., 6, 2016, 38531.
108. Wilkerson, M.D., Hayes, D.N., ConsensusClusterPlus: A class discovery tool with confidence assessments and item tracking. Bioinformatics 26 (2010), 1572–1573.
109. Williamson, M.P., Elder, P.A., Shaw, M.E., Devlin, J., Knowles, M.A., p16 (CDKN2) is a major deletion target at 9p21 in bladder cancer. Hum. Mol. Genet. 4 (1995), 1569–1577.
110. Wolff, E.M., Chihara, Y., Pan, F., Weisenberger, D.J., Siegmund, K.D., Sugano, K., Kawashima, K., Laird, P.W., Jones, P.A., Liang, G., Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue. Cancer Res. 70 (2010), 8169–8178.
111. Wu, X., Liu, D., Tao, D., Xiang, W., Xiao, X., Wang, M., Wang, L., Luo, G., Li, Y., Zeng, F., Jiang, G., BRD4 regulates EZH2 transcription through upregulation of C-MYC and represents a novel therapeutic target in bladder cancer. Mol. Cancer Ther. 15 (2016), 1029–1042.
112. Xiao, N., Xu, Q.S., Li, M.Z., hdnom: Building nomograms for penalized Cox models with high-dimensional survival data. bioRxiv, 2016, 10.1101/065524.
113. Xu, R., Harrington, D.P., A semiparametric estimate of treatment effects with censored data. Biometrics 57 (2001), 875–885.
114. Zack, T.I., Schumacher, S.E., Carter, S.L., Cherniack, A.D., Saksena, G., Tabak, B., Lawrence, M.S., Zhsng, C.Z., Wala, J., Mermel, C.H., et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45 (2013), 1134–1140.
115. Zhang, L., Wei, Q., Mao, L., Liu, W., Mills, G.B., Coombes, K., Serial dilution curve: A new method for analysis of reverse phase protein array data. Bioinformatics 25 (2009), 650–654.