Fletcher CDM, Unni KK, Mertens F, editors: WHO classification of tumours; pathology and genetics: tumours of soft tissue and bone. 2002, Lyon, France: IARC Press
Helman LJ, Meltzer P: Mechanisms of sarcoma development. Nat Rev Cancer. 2003, 3 (9): 685-694. 10.1038/nrc1168.
Article
CAS
PubMed
Google Scholar
Borden EC, Baker LH, Bell RS, Bramwell V, Demetri GD, Eisenberg BL, Fletcher CD, Fletcher JA, Ladanyi M, Meltzer P: Soft tissue sarcomas of adults: state of the translational science. Clin Cancer Res. 2003, 9 (6): 1941-1956.
PubMed
Google Scholar
Allander SV, Illei PB, Chen Y, Antonescu CR, Bittner M, Ladanyi M, Meltzer PS: Expression profiling of synovial sarcoma by cDNA microarrays: association of ERBB2, IGFBP2, and ELF3 with epithelial differentiation. Am J Pathol. 2002, 161 (5): 1587-1595.
Article
CAS
PubMed Central
PubMed
Google Scholar
Allander SV, Nupponen NN, Ringner M, Hostetter G, Maher GW, Goldberger N, Chen Y, Carpten J, Elkahloun AG, Meltzer PS: Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile. Cancer Res. 2001, 61 (24): 8624-8628.
CAS
PubMed
Google Scholar
Baer C, Nees M, Breit S, Selle B, Kulozik AE, Schaefer KL, Braun Y, Wai D, Poremba C: Profiling and functional annotation of mRNA gene expression in pediatric rhabdomyosarcoma and Ewing's sarcoma. Int J Cancer. 2004, 110 (5): 687-694. 10.1002/ijc.20171.
Article
CAS
PubMed
Google Scholar
Baird K, Davis S, Antonescu CR, Harper UL, Walker RL, Chen Y, Glatfelter AA, Duray PH, Meltzer PS: Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res. 2005, 65 (20): 9226-9235. 10.1158/0008-5472.CAN-05-1699.
Article
CAS
PubMed
Google Scholar
Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D: Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. Am J Pathol. 2003, 163 (6): 2383-2395.
Article
CAS
PubMed Central
PubMed
Google Scholar
Nagayama S, Katagiri T, Tsunoda T, Hosaka T, Nakashima Y, Araki N, Kusuzaki K, Nakayama T, Tsuboyama T, Nakamura T: Genome-wide analysis of gene expression in synovial sarcomas using a cDNA microarray. Cancer Res. 2002, 62 (20): 5859-5866.
CAS
PubMed
Google Scholar
Segal NH, Pavlidis P, Antonescu CR, Maki RG, Noble WS, DeSantis D, Woodruff JM, Lewis JJ, Brennan MF, Houghton AN: Classification and subtype prediction of adult soft tissue sarcoma by functional genomics. Am J Pathol. 2003, 163 (2): 691-700.
Article
CAS
PubMed Central
PubMed
Google Scholar
Segal NH, Pavlidis P, Noble WS, Antonescu CR, Viale A, Wesley UV, Busam K, Gallardo H, DeSantis D, Brennan MF: Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling. J Clin Oncol. 2003, 21 (9): 1775-1781. 10.1200/JCO.2003.10.108.
Article
CAS
PubMed
Google Scholar
Skubitz KM, Skubitz AP: Characterization of sarcomas by means of gene expression. J Lab Clin Med. 2004, 144 (2): 78-91. 10.1016/j.lab.2004.04.005.
Article
CAS
PubMed
Google Scholar
Wachtel M, Dettling M, Koscielniak E, Stegmaier S, Treuner J, Simon-Klingenstein K, Buhlmann P, Niggli FK, Schafer BW: Gene expression signatures identify rhabdomyosarcoma subtypes and detect a novel t(2;2)(q35;p23) translocation fusing PAX3 to NCOA1. Cancer Res . 2004, 64 (16): 5539-5545. 10.1158/0008-5472.CAN-04-0844.
Article
CAS
PubMed
Google Scholar
West RB, van de Rijn M: The role of microarray technologies in the study of soft tissue tumours. Histopathology. 2006, 48 (1): 22-31. 10.1111/j.1365-2559.2005.02286.x.
Article
CAS
PubMed
Google Scholar
Fukukawa C, Nakamura Y, Katagiri T: Molecular target therapy for synovial sarcoma. Future oncology (London, England). 2005, 1 (6): 805-812. 10.2217/14796694.1.6.805.
Article
CAS
Google Scholar
Ishibe T, Nakayama T, Okamoto T, Aoyama T, Nishijo K, Shibata KR, Shima Y, Nagayama S, Katagiri T, Nakamura Y: Disruption of fibroblast growth factor signal pathway inhibits the growth of synovial sarcomas: potential application of signal inhibitors to molecular target therapy. Clin Cancer Res. 2005, 11 (7): 2702-2712. 10.1158/1078-0432.CCR-04-2057.
Article
CAS
PubMed
Google Scholar
Lubieniecka JM, Nielsen TO: cDNA microarray-based translational research in soft tissue sarcoma. Journal of surgical oncology . 2005, 92 (4): 267-271. 10.1002/jso.20409.
Article
PubMed
Google Scholar
Nagayama S, Fukukawa C, Katagiri T, Okamoto T, Aoyama T, Oyaizu N, Imamura M, Toguchida J, Nakamura Y: Therapeutic potential of antibodies against FZD 10, a cell-surface protein, for synovial sarcomas. Oncogene. 2005, 24 (41): 6201-6212. 10.1038/sj.onc.1208780.
Article
CAS
PubMed
Google Scholar
Nielsen TO, West RB, Linn SC, Alter O, Knowling MA, O'Connell JX, Zhu S, Fero M, Sherlock G, Pollack JR: Molecular characterisation of soft tissue tumours: a gene expression study. Lancet. 2002, 359 (9314): 1301-1307. 10.1016/S0140-6736(02)08270-3.
Article
CAS
PubMed
Google Scholar
Lee YF, John M, Edwards S, Clark J, Flohr P, Maillard K, Edema M, Baker L, Mangham DC, Grimer R: Molecular classification of synovial sarcomas, leiomyosarcomas and malignant fibrous histiocytomas by gene expression profiling. Br J Cancer. 2003, 88 (4): 510-515. 10.1038/sj.bjc.6600766.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ren B, Yu YP, Jing L, Liu L, Michalopoulos GK, Luo JH, Rao UN: Gene expression analysis of human soft tissue leiomyosarcomas. Hum Pathol. 2003, 34 (6): 549-558. 10.1016/S0046-8177(03)00014-5.
Article
CAS
PubMed
Google Scholar
Lee YF, John M, Falconer A, Edwards S, Clark J, Flohr P, Roe T, Wang R, Shipley J, Grimer RJ: A gene expression signature associated with metastatic outcome in human leiomyosarcomas. Cancer Res. 2004, 64 (20): 7201-7204. 10.1158/0008-5472.CAN-04-1673.
Article
CAS
PubMed
Google Scholar
Berner JM, Forus A, Elkahloun A, Meltzer PS, Fodstad O, Myklebost O: Separate amplified regions encompassing CDK4 and MDM2 in human sarcomas. Genes Chromosomes Cancer. 1996, 17 (4): 254-259. 10.1002/(SICI)1098-2264(199612)17:4<254::AID-GCC7>3.0.CO;2-2.
Article
CAS
PubMed
Google Scholar
Pisters PW, Leung DH, Woodruff J, Shi W, Brennan MF: Analysis of prognostic factors in 1,041 patients with localized soft tissue sarcomas of the extremities. J Clin Oncol. 1996, 14 (5): 1679-1689.
CAS
PubMed
Google Scholar
Koea JB, Leung D, Lewis JJ, Brennan MF: Histopathologic type: an independent prognostic factor in primary soft tissue sarcoma of the extremity?. Ann Surg Oncol. 2003, 10 (4): 432-440. 10.1245/ASO.2003.05.014.
Article
PubMed
Google Scholar
Giaccia AJ, Simon MC, Johnson R: The biology of hypoxia: the role of oxygen sensing in development, normal function, and disease. Genes Dev. 2004, 18 (18): 2183-2194. 10.1101/gad.1243304.
Article
CAS
PubMed Central
PubMed
Google Scholar
Shimoji T, Kanda H, Kitagawa T, Kadota K, Asai R, Takahashi K, Kawaguchi N, Matsumoto S, Hayashizaki Y, Okazaki Y: Clinico-molecular study of dedifferentiation in well-differentiated liposarcoma. Biochem Biophys Res Commun. 2004, 314 (4): 1133-1140. 10.1016/j.bbrc.2003.12.203.
Article
CAS
PubMed
Google Scholar
Suehara Y, Kondo T, Fujii K, Hasegawa T, Kawai A, Seki K, Beppu Y, Nishimura T, Kurosawa H, Hirohashi S: Proteomic signatures corresponding to histological classification and grading of soft-tissue sarcomas. Proteomics. 2006
Google Scholar
Crew AJ, Clark J, Fisher C, Gill S, Grimer R, Chand A, Shipley J, Gusterson BA, Cooper CS: Fusion of SYT to two genes, SSX1 and SSX2, encoding proteins with homology to the Kruppel-associated box in human synovial sarcoma. Embo J. 1995, 14 (10): 2333-2340.
CAS
PubMed Central
PubMed
Google Scholar
Skytting B, Nilsson G, Brodin B, Xie Y, Lundeberg J, Uhlen M, Larsson O: A novel fusion gene, SYT-SSX4, in synovial sarcoma. J Natl Cancer Inst. 1999, 91 (11): 974-975. 10.1093/jnci/91.11.974.
Article
CAS
PubMed
Google Scholar
Kato H, Tjernberg A, Zhang W, Krutchinsky AN, An W, Takeuchi T, Ohtsuki Y, Sugano S, de Bruijn DR, Chait BT: SYT associates with human SNF/SWI complexes and the C-terminal region of its fusion partner SSX1 targets histones. J Biol Chem. 2002, 277 (7): 5498-5505. 10.1074/jbc.M108702200.
Article
CAS
PubMed
Google Scholar
Perani M, Ingram CJ, Cooper CS, Garrett MD, Goodwin GH: Conserved SNH domain of the proto-oncoprotein SYT interacts with components of the human chromatin remodelling complexes, while the QPGY repeat domain forms homo-oligomers. Oncogene. 2003, 22 (50): 8156-8167. 10.1038/sj.onc.1207031.
Article
CAS
PubMed
Google Scholar
Thaete C, Brett D, Monaghan P, Whitehouse S, Rennie G, Rayner E, Cooper CS, Goodwin G: Functional domains of the SYT and SYT-SSX synovial sarcoma translocation proteins and co-localization with the SNF protein BRM in the nucleus. Hum Mol Genet. 1999, 8 (4): 585-591. 10.1093/hmg/8.4.585.
Article
CAS
PubMed
Google Scholar
Smith TA, Machen SK, Fisher C, Goldblum JR: Usefulness of cytokeratin subsets for distinguishing monophasic synovial sarcoma from malignant peripheral nerve sheath tumor. Am J Clin Pathol. 1999, 112 (5): 641-648.
CAS
PubMed
Google Scholar
Hirota S, Isozaki K, Moriyama Y, Hashimoto K, Nishida T, Ishiguro S, Kawano K, Hanada M, Kurata A, Takeda M: Gain-of-function mutations of c-kit in human gastrointestinal stromal tumors. Science. 1998, 279 (5350): 577-580. 10.1126/science.279.5350.577.
Article
CAS
PubMed
Google Scholar
Sircar K, Hewlett BR, Huizinga JD, Chorneyko K, Berezin I, Riddell RH: Interstitial cells of Cajal as precursors of gastrointestinal stromal tumors. Am J Surg Pathol. 1999, 23 (4): 377-389. 10.1097/00000478-199904000-00002.
Article
CAS
PubMed
Google Scholar
Crozat A, Aman P, Mandahl N, Ron D: Fusion of CHOP to a novel RNA-binding protein in human myxoid liposarcoma. Nature. 1993, 363 (6430): 640-644. 10.1038/363640a0.
Article
CAS
PubMed
Google Scholar
Demetri GD, Fletcher CD, Mueller E, Sarraf P, Naujoks R, Campbell N, Spiegelman BM, Singer S: Induction of solid tumor differentiation by the peroxisome proliferator-activated receptor-gamma ligand troglitazone in patients with liposarcoma. Proc Natl Acad Sci USA. 1999, 96 (7): 3951-3956. 10.1073/pnas.96.7.3951.
Article
CAS
PubMed Central
PubMed
Google Scholar
Tontonoz P, Singer S, Forman BM, Sarraf P, Fletcher JA, Fletcher CD, Brun RP, Mueller E, Altiok S, Oppenheim H: Terminal differentiation of human liposarcoma cells induced by ligands for peroxisome proliferator-activated receptor gamma and the retinoid X receptor. Proc Natl Acad Sci USA. 1997, 94 (1): 237-241. 10.1073/pnas.94.1.237.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pedeutour F, Forus A, Coindre JM, Berner JM, Nicolo G, Michiels JF, Terrier P, Ranchere-Vince D, Collin F, Myklebost O: Structure of the supernumerary ring and giant rod chromosomes in adipose tissue tumors. Genes Chromosomes Cancer. 1999, 24 (1): 30-41. 10.1002/(SICI)1098-2264(199901)24:1<30::AID-GCC5>3.0.CO;2-P.
Article
CAS
PubMed
Google Scholar
Shimada S, Ishizawa T, Ishizawa K, Matsumura T, Hasegawa T, Hirose T: The value of MDM2 and CDK4 amplification levels using real-time polymerase chain reaction for the differential diagnosis of liposarcomas and their histologic mimickers. Hum Pathol. 2006, 37 (9): 1123-1129. 10.1016/j.humpath.2006.04.010.
Article
CAS
PubMed
Google Scholar
Skubitz KM, Cheng EY, Clohisy DR, Thompson RC, Skubitz AP: Differential gene expression in liposarcoma, lipoma, and adipose tissue. Cancer Invest. 2005, 23 (2): 105-118.
CAS
PubMed
Google Scholar
Gustafson P, Akerman M, Alvegard TA, Coindre JM, Fletcher CD, Rydholm A, Willen H: Prognostic information in soft tissue sarcoma using tumour size, vascular invasion and microscopic tumour necrosis-the SIN-system. Eur J Cancer. 2003, 39 (11): 1568-1576. 10.1016/S0959-8049(03)00369-1.
Article
CAS
PubMed
Google Scholar
Ohali A, Avigad S, Zaizov R, Ophir R, Horn-Saban S, Cohen IJ, Meller I, Kollender Y, Issakov J, Yaniv I: Prediction of high risk Ewing's sarcoma by gene expression profiling. Oncogene. 2004, 23 (55): 8997-9006. 10.1038/sj.onc.1208060.
Article
CAS
PubMed
Google Scholar
Brizel DM, Scully SP, Harrelson JM, Layfield LJ, Bean JM, Prosnitz LR, Dewhirst MW: Tumor oxygenation predicts for the likelihood of distant metastases in human soft tissue sarcoma. Cancer Res. 1996, 56 (5): 941-943.
CAS
PubMed
Google Scholar
Brizel DM, Sibley GS, Prosnitz LR, Scher RL, Dewhirst MW: Tumor hypoxia adversely affects the prognosis of carcinoma of the head and neck. Int J Radiat Oncol Biol Phys. 1997, 38 (2): 285-289. 10.1016/S0360-3016(97)00101-6.
Article
CAS
PubMed
Google Scholar
Evans SM, Fraker D, Hahn SM, Gleason K, Jenkins WT, Jenkins K, Hwang WT, Zhang P, Mick R, Koch CJ: EF5 binding and clinical outcome in human soft tissue sarcomas. Int J Radiat Oncol Biol Phys. 2006, 64 (3): 922-927. 10.1016/j.ijrobp.2005.05.068.
Article
CAS
PubMed
Google Scholar
Nordsmark M, Alsner J, Keller J, Nielsen OS, Jensen OM, Horsman MR, Overgaard J: Hypoxia in human soft tissue sarcomas: adverse impact on survival and no association with p53 mutations. Br J Cancer . 2001, 84 (8): 1070-1075. 10.1054/bjoc.2001.1728.
Article
CAS
PubMed Central
PubMed
Google Scholar
Shintani K, Matsumine A, Kusuzaki K, Matsubara T, Satonaka H, Wakabayashi T, Hoki Y, Uchida A: Expression of hypoxia-inducible factor (HIF)-1alpha as a biomarker of outcome in soft-tissue sarcomas. Virchows Arch. 2006, 449 (6): 673-681. 10.1007/s00428-006-0304-4.
Article
CAS
PubMed
Google Scholar
Dang CV, Semenza GL: Oncogenic alterations of metabolism. Trends Biochem Sci. 1999, 24 (2): 68-72. 10.1016/S0968-0004(98)01344-9.
Article
CAS
PubMed
Google Scholar
Maseide K, Kandel RA, Bell RS, Catton CN, O'Sullivan B, Wunder JS, Pintilie M, Hedley D, Hill RP: Carbonic anhydrase IX as a marker for poor prognosis in soft tissue sarcoma. Clin Cancer Res. 2004, 10 (13): 4464-4471. 10.1158/1078-0432.CCR-03-0541.
Article
CAS
PubMed
Google Scholar
Bastiaannet E, Groen H, Jager PL, Cobben DC, van der Graaf WT, Vaalburg W, Hoekstra HJ: The value of FDG-PET in the detection, grading and response to therapy of soft tissue and bone sarcomas; a systematic review and meta-analysis. Cancer Treat Rev. 2004, 30 (1): 83-101. 10.1016/j.ctrv.2003.07.004.
Article
CAS
PubMed
Google Scholar
Folpe AL, Lyles RH, Sprouse JT, Conrad EU, Eary JF: (F-18) fluorodeoxyglucose positron emission tomography as a predictor of pathologic grade and other prognostic variables in bone and soft tissue sarcoma. Clin Cancer Res. 2000, 6 (4): 1279-1287.
CAS
PubMed
Google Scholar
Nordsmark M, Hoyer M, Keller J, Nielsen OS, Jensen OM, Overgaard J: The relationship between tumor oxygenation and cell proliferation in human soft tissue sarcomas. Int J Radiat Oncol Biol Phys. 1996, 35 (4): 701-708. 10.1016/0360-3016(96)00132-0.
Article
CAS
PubMed
Google Scholar
Tateishi U, Yamaguchi U, Seki K, Terauchi T, Arai Y, Hasegawa T: Glut-1 expression and enhanced glucose metabolism are associated with tumour grade in bone and soft tissue sarcomas: a prospective evaluation by [(18)F]fluorodeoxyglucose positron emission tomography. Eur J Nucl Med Mol Imaging. 2006, 33 (6): 683-691. 10.1007/s00259-005-0044-8.
Article
CAS
PubMed
Google Scholar
Detwiller KY, Fernando NT, Segal NH, Ryeom SW, D'Amore PA, Yoon SS: Analysis of hypoxia-related gene expression in sarcomas and effect of hypoxia on RNA interference of vascular endothelial cell growth factor A. Cancer Res. 2005, 65 (13): 5881-5889. 10.1158/0008-5472.CAN-04-4078.
Article
CAS
PubMed
Google Scholar
The UniGene database. [http://www.ncbi.nlm.nih.gov/UniGene]
Fernebro J, Francis P, Eden P, Borg A, Panagopoulos I, Mertens F, Vallon-Christersson J, Akerman M, Rydholm A, Bauer HC: Gene expression profiles relate to SS18/SSX fusion type in synovial sarcoma. Int J Cancer. 2006, 118 (5): 1165-72. 10.1002/ijc.21475.
Article
CAS
PubMed
Google Scholar
The BioArray Software Environment (BASE) website. [http://base.onk.lu.se/int/]
Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C: BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol. 2002, 3 (8): SOFTWARE0003-10.1186/gb-2002-3-8-software0003.
Article
PubMed Central
PubMed
Google Scholar
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002, 30 (4): e15-10.1093/nar/30.4.e15.
Article
PubMed Central
PubMed
Google Scholar
TMeV version 4.0 is freely available at the TM4 microarray software suite website. [http://www.tm4.org/mev.html]
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M: TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003, 34 (2): 374-378.
CAS
PubMed
Google Scholar
Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999, 286 (5439): 531-537. 10.1126/science.286.5439.531.
Article
CAS
PubMed
Google Scholar
The EASE software is freely available at the DAVID Bioinformatics Resources 2007 website of the National Institute of Allergy and Infectious Diseases (NIAID), NIH. [http://david.abcc.ncifcrf.gov/]
Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA: Identifying biological themes within lists of genes with EASE. Genome Biol. 2003, 4 (10): R70-10.1186/gb-2003-4-10-r70.
Article
PubMed Central
PubMed
Google Scholar
Schoenfeld DA, Richter JR: Nomograms for calculating the number of patients needed for a clinical trial with survival as an endpoint. Biometrics. 1982, 38 (1): 163-170. 10.2307/2530299.
Article
CAS
PubMed
Google Scholar
DeLong ER, DeLong DM, Clarke-Pearson DL: Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics. 1988, 44 (3): 837-845. 10.2307/2531595.
Article
CAS
PubMed
Google Scholar