Efficient identification of miRNAs for classification of tumor origin

Journal of Molecular Diagnostics

Volumn 16, Issue 1, 2014, Pages 106-115

  Søkilde, Rolf ^a   Vincent, Martin ^a   Møller, Anne K ^b   Hansen, Alastair ^c   Høiby, Poul E ^a   Blondal, Thorarinn ^a   Nielsen, Boye S ^a   Daugaard, Gedske ^b   Møller, Søren ^a   Litman, Thomas ^a  

^a Exiqon AS   (Denmark)

^b Rigshospitalet   (Denmark)

^c GENTOFTE UNIVERSITY HOSPITAL   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

LOCKED NUCLEIC ACID; MICRORNA; MICRORNA 124; MICRORNA 129; MICRORNA 132; MICRORNA 133B; MICRORNA 134; MICRORNA 136; MICRORNA 143; MICRORNA 145; MICRORNA 147B; MICRORNA 16; MICRORNA 202; MICRORNA 214; MICRORNA 218; MICRORNA 23A; MICRORNA 323; MICRORNA 340; MICRORNA 372; MICRORNA 376C; MICRORNA 452; MICRORNA 488; MICRORNA 504; MICRORNA 603; MICRORNA 616; MICRORNA 647; MICRORNA 892B; MICRORNA 95; MICRORNA 96; MICRORNA 99B; UNCLASSIFIED DRUG;

ADRENAL CORTEX CARCINOMA; ARTICLE; BILE DUCT CARCINOMA; CANCER OF UNKNOWN PRIMARY SITE; CLEAR CELL CARCINOMA; COLORECTAL CARCINOMA; EMBRYONAL CARCINOMA; GASTROINTESTINAL STROMAL TUMOR; HUMAN; MELANOMA; METASTASIS; MICROARRAY ANALYSIS; MOLECULAR DIAGNOSIS; NON SEMINOMATOUS GERMINOMA; NUCLEOTIDE SEQUENCE; OVARY ADENOCARCINOMA; PANCREAS ADENOCARCINOMA; PROSTATE ADENOCARCINOMA; REAL TIME POLYMERASE CHAIN REACTION; RNA ISOLATION; SEMINOMA; TRANSITIONAL CELL CARCINOMA;

ALGORITHMS; BASE SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MICRORNAS; MOLECULAR DIAGNOSTIC TECHNIQUES; NEOPLASMS, UNKNOWN PRIMARY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORGAN SPECIFICITY; PARAFFIN EMBEDDING; SEQUENCE ANALYSIS, RNA; TUMOR MARKERS, BIOLOGICAL;

EID: 84890323096     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2013.10.001     Document Type: Article

References (49)

1. F.A. Greco Cancer of unknown primary site Am Soc Clin Oncol Educ Book 2013 2013 175 181
2. D. Daugaard, A. Møller, and B. Petersen Tumors of unknown origin F. Cavalli, S. Kaye, H. Hansen, J. Armitage, M. Piccart-Gebhart, Textbook of Medical Oncology 2009 Informa London 313 322
3. T.R. Golub, D.K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J.P. Mesirov, H. Coller, M.L. Loh, J.R. Downing, M.A. Caligiuri, C.D. Bloomfield, and E.S. Lander Molecular classification of cancer: class discovery and class prediction by gene expression monitoring Science 286 1999 531 537
4. S. Ramaswamy, P. Tamayo, R. Rifkin, S. Mukherjee, C.H. Yeang, M. Angelo, C. Ladd, M. Reich, E. Latulippe, J.P. Mesirov, T. Poggio, W. Gerald, M. Loda, E.S. Lander, and T.R. Golub Multiclass cancer diagnosis using tumor gene expression signatures Proc Natl Acad Sci U S A 98 2001 15149 15154
5. P. Buckhaults, Z. Zhang, Y.C. Chen, T.L. Wang, B. St Croix, S. Saha, A. Bardelli, P.J. Morin, K. Polyak, R.H. Hruban, V.E. Velculescu, and IeM. Shih Identifying tumor origin using a gene expression-based classification map Cancer Res 63 2003 4144 4149
6. X.J. Ma, R. Patel, X. Wang, R. Salunga, J. Murage, R. Desai, J.T. Tuggle, W. Wang, S. Chu, K. Stecker, R. Raja, H. Robin, M. Moore, D. Baunoch, D. Sgroi, and M. Erlander Molecular classification of human cancers using a 92-gene real-time quantitative polymerase chain reaction assay Arch Pathol Lab Med 130 2006 465 473
7. I. Kurahashi, Y. Fujita, T. Arao, T. Kurata, Y. Koh, K. Sakai, K. Matsumoto, M. Tanioka, K. Takeda, Y. Takiguchi, N. Yamamoto, A. Tsuya, N. Matsubara, H. Mukai, H. Minami, N. Chayahara, Y. Yamanaka, K. Miwa, S. Takahashi, S. Takahashi, K. Nakagawa, and K. Nishio A microarray-based gene expression analysis to identify diagnostic biomarkers for unknown primary cancer PLoS One 8 2013 e63249
8. F.A. Greco, W.J. Lennington, D.R. Spigel, and J.D. Hainsworth Molecular profiling diagnosis in unknown primary cancer: accuracy and ability to complement standard pathology J Natl Cancer Inst 105 2013 782 790
9. A. Esquela-Kerscher, and F.J. Slack Oncomirs - microRNAs with a role in cancer Nat Rev Cancer 6 2006 259 269
10. M.V. Iorio, and C.M. Croce microRNA involvement in human cancer Carcinogenesis 33 2012 1126 1133
11. J. Lu, G. Getz, E.A. Miska, E. varez-Saavedra, J. Lamb, D. Peck, A. Sweet-Cordero, B.L. Ebert, R.H. Mak, A.A. Ferrando, J.R. Downing, T. Jacks, H.R. Horvitz, and T.R. Golub MicroRNA expression profiles classify human cancers Nature 435 2005 834 838
12. S. Volinia, G.A. Calin, C.G. Liu, S. Ambs, A. Cimmino, F. Petrocca, R. Visone, M. Iorio, C. Roldo, M. Ferracin, R.L. Prueitt, N. Yanaihara, G. Lanza, A. Scarpa, A. Vecchione, M. Negrini, C.C. Harris, and C.M. Croce A microRNA expression signature of human solid tumors defines cancer gene targets Proc Natl Acad Sci U S A 103 2006 2257 2261
13. E. Meiri, W.C. Mueller, S. Rosenwald, M. Zepeniuk, E. Klinke, T.B. Edmonston, M. Werner, U. Lass, I. Barshack, M. Feinmesser, M. Huszar, F. Fogt, K. Ashkenazi, M. Sanden, E. Goren, N. Dromi, O. Zion, I. Burnstein, A. Chajut, Y. Spector, and R. Aharonov A second-generation microRNA-based assay for diagnosing tumor tissue origin Oncologist 17 2012 801 812
14. G. Pentheroudakis, N. Pavlidis, G. Fountzilas, D. Krikelis, A. Goussia, A. Stoyianni, M. Sanden, B. St Croix, N. Yerushalmi, H. Benjamin, E. Meiri, A. Chajut, S. Rosenwald, R. Aharonov, and Y. Spector Novel microRNA-based assay demonstrates 92% agreement with diagnosis based on clinicopathologic and management data in a cohort of patients with carcinoma of unknown primary Mol Cancer 12 2013 57
15. N. Rosenfeld, R. Aharonov, E. Meiri, S. Rosenwald, Y. Spector, M. Zepeniuk, H. Benjamin, N. Shabes, S. Tabak, A. Levy, D. Lebanony, Y. Goren, E. Silberschein, N. Targan, A. Ben-Ari, S. Gilad, N. Sion-Vardy, A. Tobar, M. Feinmesser, O. Kharenko, O. Nativ, D. Nass, M. Perelman, A. Yosepovich, B. Shalmon, S. Polak-Charcon, E. Fridman, A. Avniel, I. Bentwich, Z. Bentwich, D. Cohen, A. Chajut, and I. Barshack MicroRNAs accurately identify cancer tissue origin Nature Biotechnol 26 2008 462 469
16. S. Rosenwald, S. Gilad, S. Benjamin, D. Lebanony, N. Dromi, A. Faerman, H. Benjamin, R. Tamir, M. Ezagouri, E. Goren, I. Barshack, D. Nass, A. Tobar, M. Feinmesser, N. Rosenfeld, I. Leizerman, K. Ashkenazi, Y. Spector, A. Chajut, and R. Aharonov Validation of a microRNA-based qRT-PCR test for accurate identification of tumor tissue origin Mod Pathol 23 2010 814 823
17. G. Di Leva, and C.M. Croce miRNA profiling of cancer Curr Opin Genet Dev 23 2013 3 11
18. A. Liu, M.T. Tetzlaff, P. Vanbelle, D. Elder, M. Feldman, J.W. Tobias, A.R. Sepulveda, and X. Xu MicroRNA expression profiling outperforms mRNA expression profiling in formalin-fixed paraffin-embedded tissues Int J Clin Exp Pathol 2 2009 519 527
19. U. Siebolts, H. Varnholt, U. Drebber, H.P. Dienes, C. Wickenhauser, and M. Odenthal Tissues from routine pathology archives are suitable for microRNA analyses by quantitative PCR J Clin Pathol 62 2009 84 88
20. M. Castoldi, V. Benes, M.W. Hentze, and M.U. Muckenthaler miChip: a microarray platform for expression profiling of microRNAs based on locked nucleic acid (LNA) oligonucleotide capture probes Methods 43 2007 146 152
21. R. Søkilde, B. Kaczkowski, K. Barken, P. Mouritzen, S. Møller, and T. Litman MicroRNA expression analysis by LNA enhanced microarrays Y. Gusev, MicroRNA Profiling in Cancer: A Bioinformatics Perspective 2009 Pan Stanford Publishing Singapore 23 46
22. A. Kozomara, and S. Griffiths-Jones miRBase: integrating microRNA annotation and deep-sequencing data Nucleic Acids Res 39 2011 D152 D157
23. M.E. Ritchie, J. Silver, A. Oshlack, M. Holmes, D. Diyagama, A. Holloway, and G.K. Smyth A comparison of background correction methods for two-colour microarrays Bioinformatics 23 2007 2700 2707
24. S. Ma, and J. Huang Penalized feature selection and classification in bioinformatics Brief Bioinform 9 2008 392 403
25. R. Tibshirani Regression shrinkage and selection via the lasso J Royal Stat Soc 58 1996 267 288
26. B. Efron, T. Hastie, I. Johnstone, and R. Tibshirani Least angle regression Ann Statist 32 2004 409 499
27. J. Friedman, T. Hastie, and R. Tibshirani Regularization Paths for Generalized Linear Models via Coordinate Descent J Stat Softw 33 2010 1 22
28. G. Pentheroudakis, V. Golfinopoulos, and N. Pavlidis Switching benchmarks in cancer of unknown primary: from autopsy to microarray Eur J Cancer 43 2007 2026 2036
29. J. Li, P. Smyth, R. Flavin, S. Cahill, K. Denning, S. Aherne, S.M. Guenther, J.J. O'Leary, and O. Sheils Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells BMC Biotechnol 7 2007 36
30. R.K. van Laar, X.J. Ma, J.D. de, D. Wehkamp, A.N. Floore, M.O. Warmoes, I. Simon, W. Wang, M. Erlander, L.J. van't Veer, and A.M. Glas Implementation of a novel microarray-based diagnostic test for cancer of unknown primary Int J Cancer 125 2009 1390 1397
31. D. Talantov, J. Baden, T. Jatkoe, K. Hahn, J. Yu, Y. Rajpurohit, Y. Jiang, C. Choi, J.S. Ross, D. Atkins, Y. Wang, and A. Mazumder A quantitative reverse transcriptase-polymerase chain reaction assay to identify metastatic carcinoma tissue of origin J Mol Diagn 8 2006 320 329
32. R.W. Tothill, A. Kowalczyk, D. Rischin, A. Bousioutas, I. Haviv, R.K. van Laar, P.M. Waring, J. Zalcberg, R. Ward, A.V. Biankin, R.L. Sutherland, S.M. Henshall, K. Fong, J.R. Pollack, D.D. Bowtell, and A.J. Holloway An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin Cancer Res 65 2005 4031 4040
33. K.A. Shedden, J.M. Taylor, T.J. Giordano, R. Kuick, D.E. Misek, G. Rennert, D.R. Schwartz, S.B. Gruber, C. Logsdon, D. Simeone, S.L. Kardia, J.K. Greenson, K.R. Cho, D.G. Beer, E.R. Fearon, and S. Hanash Accurate molecular classification of human cancers based on gene expression using a simple classifier with a pathological tree-based framework Am J Pathol 163 2003 1985 1995
34. J.L. Dennis, and K.A. Oien Hunting the primary: novel strategies for defining the origin of tumours J Pathol 205 2005 236 247
35. B.A. Centeno, G. Bloom, D.T. Chen, Z. Chen, M. Gruidl, A. Nasir, and T.Y. Yeatman Hybrid model integrating immunohistochemistry and expression profiling for the classification of carcinomas of unknown primary site J Mol Diagn 12 2010 476 486
36. K.A. Oien Pathologic evaluation of unknown primary cancer Semin Oncol 36 2009 8 37
37. G.C. Bloom, S. Eschrich, J.X. Zhou, D. Coppola, and T.J. Yeatman Elucidation of a protein signature discriminating six common types of adenocarcinoma Int J Cancer 120 2007 769 775
38. A.I. Su, J.B. Welsh, L.M. Sapinoso, S.G. Kern, P. Dimitrov, H. Lapp, P.G. Schultz, S.M. Powell, C.A. Moskaluk, H.F. Frierson Jr., and G.M. Hampton Molecular classification of human carcinomas by use of gene expression signatures Cancer Res 61 2001 7388 7393
39. H.M. Horlings, R.K. van Laar, J.M. Kerst, H.H. Helgason, J. Wesseling, J.J. van der Hoeven, M.O. Warmoes, A. Floore, A. Witteveen, J. Lahti-Domenici, A.M. Glas, L.J. van't Veer, and J.D. de Gene expression profiling to identify the histogenetic origin of metastatic adenocarcinomas of unknown primary J Clin Oncol 26 2008 4435 4441
40. G.R. Varadhachary, D. Talantov, M.N. Raber, C. Meng, K.R. Hess, T. Jatkoe, R. Lenzi, D.R. Spigel, Y. Wang, F.A. Greco, J.L. Abbruzzese, and J.D. Hainsworth Molecular profiling of carcinoma of unknown primary and correlation with clinical evaluation J Clin Oncol 26 2008 4442 4448
41. P. Geurts, A. Irrthum, and L. Wehenkel Supervised learning with decision tree-based methods in computational and systems biology Mol Biosyst 5 2009 1593 1605
42. J. Voigt, M. Mathieu, and F. Bibeau The advent of immunohistochemistry in carcinoma of unknown primary site: a major progress K. Fizazi, Carcinoma of an Unknown Primary Site 2006 Taylor & Francis New York 25 33
43. G.G. Anderson, and L.M. Weiss Determining tissue of origin for metastatic cancers: meta-analysis and literature review of immunohistochemistry performance Appl Immunohistochem Mol Morphol 18 2010 3 8
44. L.M. Weiss, P. Chu, B.E. Schroeder, V. Singh, Y. Zhang, M.G. Erlander, and C.A. Schnabel Blinded comparator study of immunohistochemical analysis versus a 92-gene cancer classifier in the diagnosis of the primary site in metastatic tumors J Mol Diagn 15 2013 263 269
45. K.A. Oien, and J.L. Dennis Diagnostic work-up of carcinoma of unknown primary: from immunohistochemistry to molecular profiling Ann Oncol 23 suppl 10 2012 x271 x277
46. G. Pentheroudakis, E. Briasoulis, and N. Pavlidis Cancer of unknown primary site: missing primary or missing biology? Oncologist 12 2007 418 425
47. G. Varadhachary New strategies for carcinoma of unknown primary: the role of tissue of origin molecular profiling Clin Cancer Res 19 2013 4027 4033
48. S.Y. Park, B.H. Kim, J.H. Kim, S. Lee, and G.H. Kang Panels of immunohistochemical markers help determine primary sites of metastatic adenocarcinoma Arch Pathol Lab Med 131 2007 1561 1567
49. L. Chen, H.X. Yan, W. Yang, L. Hu, L.X. Yu, Q. Liu, L. Li, D.D. Huang, J. Ding, F. Shen, W.P. Zhou, M.C. Wu, and H.Y. Wang The role of microRNA expression pattern in human intrahepatic cholangiocarcinoma J Hepatol 50 2009 358 369