메뉴 건너뛰기




Volumn 32, Issue 7, 2014, Pages 644-652

Assessing the clinical utility of cancer genomic and proteomic data across tumor types

(20)  Yuan, Yuan a,b   Van Allen, Eliezer M c,d   Omberg, Larsson e   Wagle, Nikhil c,d   Amin Mansour, Ali d   Sokolov, Artem f   Byers, Lauren A b   Xu, Yanxun g   Hess, Kenneth R b   Diao, Lixia b   Han, Leng b   Huang, Xuelin b   Lawrence, Michael S d   Weinstein, John N b   Stuart, Josh M f   Mills, Gordon B b   Garraway, Levi A c,d,h   Margolin, Adam A e,j   Getz, Gad d,h,i   Liang, Han a,b  


Author keywords

[No Author keywords available]

Indexed keywords

DISEASES; GENES; RNA; TUMORS;

EID: 84903940391     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2940     Document Type: Article
Times cited : (242)

References (50)
  • 1
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • Cancer Genome Atlas Research Network
    • Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
    • (2008) Nature , vol.455 , pp. 1061-1068
  • 2
    • 79959838081 scopus 로고    scopus 로고
    • Integrated genomic analyses of ovarian carcinoma
    • Cancer Genome Atlas Research Network
    • Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
    • (2011) Nature , vol.474 , pp. 609-615
  • 3
    • 84863922124 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of human colon and rectal cancer
    • Cancer Genome Atlas Research Network
    • Cancer Genome Atlas Research Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012).
    • (2012) Nature , vol.487 , pp. 330-337
  • 4
    • 84866894408 scopus 로고    scopus 로고
    • Comprehensive genomic characterization of squamous cell lung cancers
    • Cancer Genome Atlas Research Network
    • Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519-525 (2012).
    • (2012) Nature , vol.489 , pp. 519-525
  • 5
    • 84877254190 scopus 로고    scopus 로고
    • Integrated genomic characterization of endometrial carcinoma
    • Cancer Genome Atlas Research Network
    • Cancer Genome Atlas Research Network. Integrated genomic characterization of endometrial carcinoma. Nature 497, 67-73 (2013).
    • (2013) Nature , vol.497 , pp. 67-73
  • 6
    • 84879890360 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of clear cell renal cell carcinoma
    • Cancer Genome Atlas Research Network
    • Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499, 43-49 (2013).
    • (2013) Nature , vol.499 , pp. 43-49
  • 7
    • 78649825336 scopus 로고    scopus 로고
    • Current and emerging biomarkers in breast cancer: Prognosis and prediction
    • Weigel, M.T. & Dowsett, M. Current and emerging biomarkers in breast cancer: prognosis and prediction. Endocr. Relat. Cancer 17, R245-R262 (2010).
    • (2010) Endocr. Relat. Cancer , vol.17
    • Weigel, M.T.1    Dowsett, M.2
  • 8
    • 84880452562 scopus 로고    scopus 로고
    • Genomics-driven oncology: Framework for an emerging paradigm
    • Garraway, L. Genomics-driven oncology: framework for an emerging paradigm. J. Clin. Oncol. 31, 1806-1814 (2013).
    • (2013) J. Clin. Oncol. , vol.31 , pp. 1806-1814
    • Garraway, L.1
  • 9
    • 70849116358 scopus 로고    scopus 로고
    • Profiling critical cancer gene mutations in clinical tumor samples
    • MacConaill, L. et al. Profiling critical cancer gene mutations in clinical tumor samples. PLoS ONE 4, e7887 (2009).
    • (2009) PLoS ONE , vol.4
    • MacConaill, L.1
  • 10
    • 21044455139 scopus 로고    scopus 로고
    • Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers
    • Berchuck, A. et al. Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers. Clin. Cancer Res. 11, 3686-3696 (2005).
    • (2005) Clin. Cancer Res. , vol.11 , pp. 3686-3696
    • Berchuck, A.1
  • 11
    • 33747847740 scopus 로고    scopus 로고
    • Adjuvant vinorelbine plus cisplatin versus observation in patients with completely resected stage IB-IIIA non-small-cell lung cancer (Adjuvant Navelbine International Trialist Association [ANITA]): A randomised controlled trial
    • Douillard, J.Y. et al. Adjuvant vinorelbine plus cisplatin versus observation in patients with completely resected stage IB-IIIA non-small-cell lung cancer (Adjuvant Navelbine International Trialist Association [ANITA]): a randomised controlled trial. Lancet Oncol. 7, 719-727 (2006).
    • (2006) Lancet Oncol , vol.7 , pp. 719-727
    • Douillard, J.Y.1
  • 12
    • 84873080330 scopus 로고    scopus 로고
    • External validation and comparison with other models of the International Metastatic Renal-Cell Carcinoma Database Consortium prognostic model: A population-based study
    • Heng, D.Y. et al. External validation and comparison with other models of the International Metastatic Renal-Cell Carcinoma Database Consortium prognostic model: a population-based study. Lancet Oncol. 14, 141-148 (2013).
    • (2013) Lancet Oncol , vol.14 , pp. 141-148
    • Heng, D.Y.1
  • 13
    • 84863562673 scopus 로고    scopus 로고
    • Glioblastoma survival in the United States before and during the temozolomide era
    • Johnson, D.R. & O'Neill, B.P. Glioblastoma survival in the United States before and during the temozolomide era. J. Neurooncol. 107, 359-364 (2012).
    • (2012) J. Neurooncol. , vol.107 , pp. 359-364
    • Johnson, D.R.1    O'Neill, B.P.2
  • 14
    • 0030069896 scopus 로고    scopus 로고
    • Multivariable prognostic models: Issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors
    • Harrell, F., Lee, K. & Mark, D. Multivariable prognostic models: issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors. Stat. Med. 15, 361-387 (1996).
    • (1996) Stat. Med. , vol.15 , pp. 361-387
    • Harrell, F.1    Lee, K.2    Mark, D.3
  • 15
    • 0001287271 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the lasso
    • Tibshirani, R. Regression shrinkage and selection via the lasso. J. R. Stat. Soc., B 58, 267-288 (1996).
    • (1996) J. R. Stat. Soc. B , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 17
    • 1642529511 scopus 로고    scopus 로고
    • Metagenes and molecular pattern discovery using matrix factorization
    • Brunet, J.-P., Tamayo, P., Golub, T. & Mesirov, J. Metagenes and molecular pattern discovery using matrix factorization. Proc. Natl. Acad. Sci. USA 101, 4164-4169 (2004).
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 4164-4169
    • Brunet, J.-P.1    Tamayo, P.2    Golub, T.3    Mesirov, J.4
  • 18
    • 79957516191 scopus 로고    scopus 로고
    • A microRNA survival signature (MiSS) for advanced ovarian cancer
    • Shih, K. et al. A microRNA survival signature (MiSS) for advanced ovarian cancer. Gynecol. Oncol. 121, 444-450 (2011).
    • (2011) Gynecol. Oncol. , vol.121 , pp. 444-450
    • Shih, K.1
  • 19
    • 84871720411 scopus 로고    scopus 로고
    • Selumetinib plus docetaxel for KRAS-mutant advanced non-small-cell lung cancer: A randomised, multicentre, placebo-controlled, phase 2 study
    • Jänne, P.A. et al. Selumetinib plus docetaxel for KRAS-mutant advanced non-small-cell lung cancer: a randomised, multicentre, placebo-controlled, phase 2 study. Lancet Oncol. 14, 38-47 (2013).
    • (2013) Lancet Oncol , vol.14 , pp. 38-47
    • Jänne, P.A.1
  • 20
    • 84877097856 scopus 로고    scopus 로고
    • Characteristics of lung cancers harboring NRAS mutations
    • Ohashi, K. et al. Characteristics of lung cancers harboring NRAS mutations. Clin. Cancer Res. 19, 2584-2591 (2013).
    • (2013) Clin. Cancer Res. , vol.19 , pp. 2584-2591
    • Ohashi, K.1
  • 21
    • 0028933898 scopus 로고
    • Acute-phase protein response and survival duration of patients with pancreatic cancer
    • Falconer, J.S. et al. Acute-phase protein response and survival duration of patients with pancreatic cancer. Cancer 75, 2077-2082 (1995).
    • (1995) Cancer , vol.75 , pp. 2077-2082
    • Falconer, J.S.1
  • 22
    • 0034798212 scopus 로고    scopus 로고
    • Increased expression of matrix metalloproteinases 2 and 9 and tissue inhibitors of metalloproteinases 1 and 2 correlate with poor prognostic variables in renal cell carcinoma
    • Kallakury, B.V. et al. Increased expression of matrix metalloproteinases 2 and 9 and tissue inhibitors of metalloproteinases 1 and 2 correlate with poor prognostic variables in renal cell carcinoma. Clin. Cancer Res. 7, 3113-3119 (2001).
    • (2001) Clin. Cancer Res. , vol.7 , pp. 3113-3119
    • Kallakury, B.V.1
  • 23
    • 84864486088 scopus 로고    scopus 로고
    • Altered death receptor signaling promotes epithelial-to-mesenchymal transition and acquired chemoresistance
    • Antoon, J.W. et al. Altered death receptor signaling promotes epithelial-to-mesenchymal transition and acquired chemoresistance. Sci. Rep. 2, 539 (2012).
    • (2012) Sci. Rep. , vol.2 , pp. 539
    • Antoon, J.W.1
  • 24
    • 84862656001 scopus 로고    scopus 로고
    • The clinical utility of miR-21 as a diagnostic and prognostic marker for renal cell carcinoma
    • Faragalla, H. et al. The clinical utility of miR-21 as a diagnostic and prognostic marker for renal cell carcinoma. J. Mol. Diagn. 14, 385-392 (2012).
    • (2012) J. Mol. Diagn. , vol.14 , pp. 385-392
    • Faragalla, H.1
  • 25
    • 84863393889 scopus 로고    scopus 로고
    • Up-regulation of microRNA-21 correlates with lower kidney cancer survival
    • Zaman, M.S. et al. Up-regulation of microRNA-21 correlates with lower kidney cancer survival. PLoS ONE 7, e31060 (2012).
    • (2012) PLoS ONE , vol.7
    • Zaman, M.S.1
  • 26
    • 84883651195 scopus 로고    scopus 로고
    • MiR-192, miR-194 and miR-215: A convergent microRNA network suppressing tumor progression in renal cell carcinoma
    • Khella, H. et al. miR-192, miR-194 and miR-215: a convergent microRNA network suppressing tumor progression in renal cell carcinoma. Carcinogenesis 34, 2231-2239 (2013).
    • (2013) Carcinogenesis , vol.34 , pp. 2231-2239
    • Khella, H.1
  • 27
    • 79955146655 scopus 로고    scopus 로고
    • MicroRNA let-7f inhibits tumor invasion and metastasis by targeting MYH9 in human gastric cancer
    • Liang, S. et al. MicroRNA let-7f inhibits tumor invasion and metastasis by targeting MYH9 in human gastric cancer. PLoS ONE 6, e18409 (2011).
    • (2011) PLoS ONE , vol.6
    • Liang, S.1
  • 28
    • 84855779125 scopus 로고    scopus 로고
    • Hsa-let-7a functions as a tumor suppressor in renal cell carcinoma cell lines by targeting c-myc
    • Liu, Y., Yin, B., Zhang, C., Zhou, L. & Fan, J. Hsa-let-7a functions as a tumor suppressor in renal cell carcinoma cell lines by targeting c-myc. Biochem. Biophys. Res. Commun. 417, 371-375 (2012).
    • (2012) Biochem. Biophys. Res. Commun. , vol.417 , pp. 371-375
    • Liu, Y.1    Yin, B.2    Zhang, C.3    Zhou, L.4    Fan, J.5
  • 29
    • 84873745782 scopus 로고    scopus 로고
    • MicroRNA-143 functions as a tumor suppressor in human esophageal squamous cell carcinoma
    • Ni, Y. et al. MicroRNA-143 functions as a tumor suppressor in human esophageal squamous cell carcinoma. Gene 517, 197-204 (2012).
    • (2012) Gene , vol.517 , pp. 197-204
    • Ni, Y.1
  • 30
    • 79957648083 scopus 로고    scopus 로고
    • MicroRNA-143 functions as a tumor suppressor in human bladder cancer T24 cells
    • Noguchi, S. et al. MicroRNA-143 functions as a tumor suppressor in human bladder cancer T24 cells. Cancer Lett. 307, 211-220 (2011).
    • (2011) Cancer Lett , vol.307 , pp. 211-220
    • Noguchi, S.1
  • 31
    • 84862284030 scopus 로고    scopus 로고
    • The enhancer of zeste homolog 2 (EZH2), a potential therapeutic target, is regulated by miR-101 in renal cancer cells
    • Sakurai, T. et al. The enhancer of zeste homolog 2 (EZH2), a potential therapeutic target, is regulated by miR-101 in renal cancer cells. Biochem. Biophys. Res. Commun. 422, 607-614 (2012).
    • (2012) Biochem. Biophys. Res. Commun. , vol.422 , pp. 607-614
    • Sakurai, T.1
  • 32
    • 79955166265 scopus 로고    scopus 로고
    • GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
    • Mermel, C. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
    • (2011) Genome Biol , vol.12
    • Mermel, C.1
  • 33
    • 78650735473 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
    • Shi, L. et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat. Biotechnol. 28, 827-838 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 827-838
    • Shi, L.1
  • 34
    • 84880467544 scopus 로고    scopus 로고
    • Clinical analysis and interpretation of cancer genome data
    • Van Allen, E.M., Wagle, N. & Levy, M.A. Clinical analysis and interpretation of cancer genome data. J. Clin. Oncol. 31, 1825-1833 (2013).
    • (2013) J. Clin. Oncol. , vol.31 , pp. 1825-1833
    • Van Allen, E.M.1    Wagle, N.2    Levy, M.A.3
  • 35
    • 84902148239 scopus 로고    scopus 로고
    • Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine
    • doi:10.1038/nm.3559 18 May
    • Van Allen, E.M. et al. Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine. Nat. Med. doi:10.1038/nm.3559 (18 May 2014).
    • (2014) Nat. Med.
    • Van Allen, E.M.1
  • 36
    • 84865833740 scopus 로고    scopus 로고
    • High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing
    • Wagle, N. et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2, 82-93 (2012).
    • (2012) Cancer Discov , vol.2 , pp. 82-93
    • Wagle, N.1
  • 37
    • 84874777853 scopus 로고    scopus 로고
    • Phase II study of the MEK1/MEK2 inhibitor trametinib in patients with metastatic BRAF-mutant cutaneous melanoma previously treated with or without a BRAF inhibitor
    • Kim, K.B. et al. Phase II study of the MEK1/MEK2 inhibitor trametinib in patients with metastatic BRAF-mutant cutaneous melanoma previously treated with or without a BRAF inhibitor. J. Clin. Oncol. 31, 482-489 (2013).
    • (2013) J. Clin. Oncol. , vol.31 , pp. 482-489
    • Kim, K.B.1
  • 38
    • 84867333656 scopus 로고    scopus 로고
    • Genome sequencing identifies a basis for everolimus sensitivity
    • Iyer, G. et al. Genome sequencing identifies a basis for everolimus sensitivity. Science 338, 221 (2012).
    • (2012) Science , vol.338 , pp. 221
    • Iyer, G.1
  • 39
    • 78049510428 scopus 로고    scopus 로고
    • Everolimus for subependymal giant-cell astrocytomas in tuberous sclerosis
    • Krueger, D.A. et al. Everolimus for subependymal giant-cell astrocytomas in tuberous sclerosis. N. Engl. J. Med. 363, 1801-1811 (2010).
    • (2010) N. Engl. J. Med. , vol.363 , pp. 1801-1811
    • Krueger, D.A.1
  • 40
    • 84899680978 scopus 로고    scopus 로고
    • Activating mTOR mutations in a patient with an extraordinary response on a phase i trial of everolimus and pazopanib
    • Wagle, N. et al. Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib. Cancer Discov. 4, 546-553 (2014).
    • (2014) Cancer Discov , vol.4 , pp. 546-553
    • Wagle, N.1
  • 41
    • 84891894051 scopus 로고    scopus 로고
    • The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma
    • Van Allen, E.M. et al. The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. Cancer Discov. 4, 94-109 (2014).
    • (2014) Cancer Discov , vol.4 , pp. 94-109
    • Van Allen, E.M.1
  • 42
    • 84891899026 scopus 로고    scopus 로고
    • MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition
    • Wagle, N. et al. MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. Cancer Discov. 4, 61-68 (2014).
    • (2014) Cancer Discov , vol.4 , pp. 61-68
    • Wagle, N.1
  • 43
    • 84867856045 scopus 로고    scopus 로고
    • Use of personalized molecular biomarkers in the clinical care of adults with glioblastomas
    • Holdhoff, M. et al. Use of personalized molecular biomarkers in the clinical care of adults with glioblastomas. J. Neurooncol. 110, 279-285 (2012).
    • (2012) J. Neurooncol. , vol.110 , pp. 279-285
    • Holdhoff, M.1
  • 44
    • 55349134617 scopus 로고    scopus 로고
    • National Academy of Clinical Biochemistry laboratory medicine practice guidelines for use of tumor markers in testicular, prostate, colorectal, breast, and ovarian cancers
    • Sturgeon, C. et al. National Academy of Clinical Biochemistry laboratory medicine practice guidelines for use of tumor markers in testicular, prostate, colorectal, breast, and ovarian cancers. Clin. Chem. 54, e11-e79 (2008).
    • (2008) Clin. Chem. , vol.54
    • Sturgeon, C.1
  • 45
    • 23244432214 scopus 로고    scopus 로고
    • Identification of clinically useful cancer prognostic factors: What are we missing?
    • McShane, L.M., Altman, D.G. & Sauerbrei, W. Identification of clinically useful cancer prognostic factors: what are we missing? J. Natl. Cancer Inst. 97, 1023-1025 (2005).
    • (2005) J. Natl. Cancer Inst. , vol.97 , pp. 1023-1025
    • McShane, L.M.1    Altman, D.G.2    Sauerbrei, W.3
  • 46
    • 84870674269 scopus 로고    scopus 로고
    • Publication of tumor marker research results: The necessity for complete and transparent reporting
    • McShane, L.M. & Hayes, D.F. Publication of tumor marker research results: the necessity for complete and transparent reporting. J. Clin. Oncol. 30, 4223-4232 (2012).
    • (2012) J. Clin. Oncol. , vol.30 , pp. 4223-4232
    • McShane, L.M.1    Hayes, D.F.2
  • 47
    • 33745641883 scopus 로고    scopus 로고
    • Uses and abuses of tumor markers in the diagnosis, monitoring, and treatment of primary and metastatic breast cancer
    • Henry, N.L. & Hayes, D.F. Uses and abuses of tumor markers in the diagnosis, monitoring, and treatment of primary and metastatic breast cancer. Oncologist 11, 541-552 (2006).
    • (2006) Oncologist , vol.11 , pp. 541-552
    • Henry, N.L.1    Hayes, D.F.2
  • 48
    • 84877734926 scopus 로고    scopus 로고
    • Improving breast cancer survival analysis through competition-based multidimensional modeling
    • Bilal, E. et al. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput. Biol. 9, e1003047 (2013).
    • (2013) PLoS Comput. Biol. , vol.9
    • Bilal, E.1
  • 49
    • 84877765675 scopus 로고    scopus 로고
    • Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer
    • Margolin, A. et al. Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. Sci. Transl. Med. 5, 181re1 (2013).
    • (2013) Sci. Transl. Med. , vol.5
    • Margolin, A.1
  • 50
    • 84860439224 scopus 로고    scopus 로고
    • Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data
    • Yuan, Y., Xu, Y., Xu, J., Ball, R. & Liang, H. Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data. Bioinformatics 28, 1246-1252 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 1246-1252
    • Yuan, Y.1    Xu, Y.2    Xu, J.3    Ball, R.4    Liang, H.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.