{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T13:31:50Z","timestamp":1793971910899,"version":"4.8.0"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Thymoma is a heterogeneous group of tumors in biology and clinical behavior. Even though thymoma is divided into five subgroups following the World Health Organization classification, the nature of the disease is mixed within the subgroups.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We investigated the molecular characteristics of genetic changes variation of thymoma using cDNA microarray based-comparative genomic hybridization (CGH) with a 17 K cDNA microarray in an indirect, sex-matched design. Genomic DNA from the paraffin embedded 39 thymoma tissues (A 6, AB 11, B1 7, B2 7, B3 8) labeled with Cy-3 was co-hybridized with the reference placenta gDNA labeled with Cy-5. Using the CAMVS software, we investigated the deletions on chromosomes 1, 2, 3, 4, 5, 6, 8, 12, 13 and 18 throughout the thymoma. Then, we evaluated the genetic variations of thymoma based on the subgroups and the clinical behavior. First, the 36 significant genes differentiating five subgroups were selected by Significance Analysis of Microarray. Based on these genes, type AB was suggested to be heterogeneous at the molecular level as well as histologically. Next, we observed that the thymoma was divided into A, B (1, 2) and B3 subgroups with 33 significant genes. In addition, we selected 70 genes differentiating types A and B3, which differ largely in clinical behaviors. Finally, the 11 heterogeneous AB subtypes were able to correctly assign into A and B (1, 2) types based on their genetic characteristics.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>In our study, we observed the genome-wide chromosomal aberrations of thymoma and identified significant gene sets with genetic variations related to thymoma subgroups, which might provide useful information for thymoma pathobiology.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-8-305","type":"journal-article","created":{"date-parts":[[2007,9,4]],"date-time":"2007-09-04T06:13:23Z","timestamp":1188886403000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Genome-wide genetic aberrations of thymoma using cDNA microarray based comparative genomic hybridization"],"prefix":"10.1186","volume":"8","author":[{"given":"Gui Youn","family":"Lee","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Woo Ick","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hei Cheul","family":"Jeung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sang Chul","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min Young","family":"Seo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chan Hee","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyun Cheol","family":"Chung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sun Young","family":"Rha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,9,3]]},"reference":[{"key":"1018_CR1","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1016\/S0022-5223(20)31934-6","volume":"42","author":"PE Bernatz","year":"1961","unstructured":"Bernatz PE, Harrison EG, Clagett OT: Thymoma: clinicopathologic study. J Thorac Cardiovasc Surg. 1961, 42: 424-44.","journal-title":"J Thorac Cardiovasc Surg"},{"key":"1018_CR2","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1007\/BF00737071","volume":"407","author":"M Marino","year":"1985","unstructured":"Marino M, M\u00fcller-Hermelink HK: Thymoma and thymic carcinoma: relation of thymic epithelial cells to the cortical and medullary differentiation of thymus. Virchows Arch Pathol Anat. 1985, 407: 119-149. 10.1007\/BF00737071.","journal-title":"Virchows Arch Pathol Anat"},{"key":"1018_CR3","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/978-3-662-12823-7_10","volume":"10","author":"T Kirchner","year":"1989","unstructured":"Kirchner T, M\u00fcller-Hermelink H-K: New approaches to the diagnosias of thymic epithelial tumors. Progr Surg Pathol. 1989, 10: 167-189.","journal-title":"Progr Surg Pathol"},{"key":"1018_CR4","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1097\/00000478-199212000-00003","volume":"16","author":"T Kirchner","year":"1992","unstructured":"Kirchner T, Schalke B, Buchwald J, Ritter M, Marx A, M\u00fcller-Hermelink H-K: Well-differentiated thymic carcinoma: an organotypical low-grade carcinoma with relationship to cortical carcinoma. Am J Surg Pathol. 1992, 16: 1153-1169. 10.1097\/00000478-199212000-00003.","journal-title":"Am J Surg Pathol"},{"key":"1018_CR5","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1093\/ajcp\/111.6.826","volume":"111","author":"S Suster","year":"1999","unstructured":"Suster S, Moran CA: Thymoma, atypical thymoma, and thymic carcinoma: a novel conceptual approach to the classification of thymic epithelial neoplasm. Am J Clin Pathol. 1999, 111: 826-833.","journal-title":"Am J Clin Pathol"},{"key":"1018_CR6","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1016\/0046-8177(93)90109-T","volume":"24","author":"L Quintanilla-Martinez","year":"1993","unstructured":"Quintanilla-Martinez L, Wilkins EW, Ferry JA, Harris NL: Thymoma: morphologic subclassification correlates with invasiveness and immunologic features: a study of 122 cases. Hum Pathol. 1993, 24: 958-969. 10.1016\/0046-8177(93)90109-T.","journal-title":"Hum Pathol"},{"key":"1018_CR7","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1002\/1097-0142(19940715)74:2<606::AID-CNCR2820740212>3.0.CO;2-T","volume":"74","author":"L Quintanilla-Martinez","year":"1994","unstructured":"Quintanilla-Martinez L, Wilkins EW, Choi N, Efird J, Hug E, Harris NL: Thymoma. Histologic subclassification is an independent prognostic factor. Cancer. 1994, 74: 606-617. 10.1002\/1097-0142(19940715)74:2<606::AID-CNCR2820740212>3.0.CO;2-T.","journal-title":"Cancer"},{"key":"1018_CR8","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1097\/00000478-199906000-00017","volume":"23","author":"A Marx","year":"1999","unstructured":"Marx A, M\u00fcller-Hermelink HK: Thymoma and thymic carcinoma. Am J Surg Pathol. 1999, 23: 739-742. 10.1097\/00000478-199906000-00017.","journal-title":"Am J Surg Pathol"},{"key":"1018_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-642-60157-6_1","volume-title":"Histological typing of tumours of the thymus. In: World Health Organization International Histological Classification of Tumours","author":"J Rosai","year":"1999","unstructured":"Rosai J, Sobin LH: Histological typing of tumours of the thymus. In: World Health Organization International Histological Classification of Tumours. 1999, Heidelberg: Springer Verlag, 1-65."},{"key":"1018_CR10","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1007\/BF02899381","volume":"59","author":"K Mukai","year":"1990","unstructured":"Mukai K, Sato Y, Hirohashi S, Shimosato Y: Expression of ras p21 protein by thymoma. Virchows Arch B Cell Pathol Incl Mol Pathol. 1990, 59: 11-16.","journal-title":"Virchows Arch B Cell Pathol Incl Mol Pathol"},{"key":"1018_CR11","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1007\/BF01608334","volume":"422","author":"H Tateyama","year":"1993","unstructured":"Tateyama H, Mizuno T, Tada T, Eimoto T, Hashimoto T, Masaoka A: Thymic epithelial tumors: evaluation of malignant grade by quantification of proliferating cell nuclear antigen and nucleolar organizer regions. Virchows Arch A Pathol Anat Histopathol. 1993, 422: 265-269. 10.1007\/BF01608334.","journal-title":"Virchows Arch A Pathol Anat Histopathol"},{"key":"1018_CR12","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/S0046-8177(96)90140-9","volume":"27","author":"WI Yang","year":"1996","unstructured":"Yang WI, Efird JT, Quintanilla-Martinez L, Choi N, Narris NL: Cell kinetic study of thymic epithelial tumor using PCNA (PC10) and Ki-67 (MIB-1) antibodies. Hum Pathol. 1996, 27: 70-76. 10.1016\/S0046-8177(96)90140-9.","journal-title":"Hum Pathol"},{"key":"1018_CR13","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1046\/j.1365-2559.1996.d01-540.x","volume":"29","author":"FF Chen","year":"1996","unstructured":"Chen FF, Yan JJ, Chang KC, Lai WW, Chen RMJ, Jin YT: Immunohistochemical localization of Mcl-1 and bcl-2 proteins in thymic epithelial tumors. Histopathology. 1996, 29: 541-547. 10.1046\/j.1365-2559.1996.d01-540.x.","journal-title":"Histopathology"},{"key":"1018_CR14","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1002\/(SICI)1097-0215(19971127)73:5<639::AID-IJC5>3.0.CO;2-Y","volume":"73","author":"H Hirabayashi","year":"1997","unstructured":"Hirabayashi H, Fujii Y, Sakaguchi M, Tanaka H, Yoon HE, Komoto Y, Inoue M, Miyoshi S, Matsuda H: p16INK4, pRB, P53 and cyclin D1 expression and hypermethylation of CDKN2 gene in thymoma and thymic carcinoma. J Cancer. 1997, 73: 639-644. 10.1002\/(SICI)1097-0215(19971127)73:5<639::AID-IJC5>3.0.CO;2-Y.","journal-title":"J Cancer"},{"key":"1018_CR15","doi-asserted-by":"publisher","first-page":"37","DOI":"10.3349\/ymj.1998.39.1.37","volume":"39","author":"WI Yang","year":"1998","unstructured":"Yang WI, Yang KM, Hong SW, Kim KD: E-Cadherin expression in thymomas. Yonsei Med J. 1998, 39: 37-44.","journal-title":"Yonsei Med J"},{"key":"1018_CR16","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/S0165-5728(97)00242-7","volume":"85","author":"M Perrens","year":"1998","unstructured":"Perrens M, Labouyrie E, Groppi A, Dubus P, Carles D, Velly JF, de Mascarel A, Merlio JP: Expression of NGF receptors in normal and pathological human thymus. J Neuroimmunol. 1998, 85: 11-21. 10.1016\/S0165-5728(97)00242-7.","journal-title":"J Neuroimmunol"},{"key":"1018_CR17","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1016\/S0003-4975(01)03434-8","volume":"73","author":"I Yoshino","year":"2002","unstructured":"Yoshino I, Kase S, Yano T, Sugio K, Sugimachi K: Expression status of E-cadherin and alpha-, beta-, and gamma-catenins in thymoma. Ann Thorac Surg. 2002, 73: 933-937. 10.1016\/S0003-4975(01)03434-8.","journal-title":"Ann Thorac Surg"},{"key":"1018_CR18","doi-asserted-by":"publisher","first-page":"5078","DOI":"10.1158\/1078-0432.CCR-05-0070","volume":"11","author":"A Baldi","year":"2005","unstructured":"Baldi A, Ambrogi V, Mineo D, Mellone P, Campioni M, Citro G, Mineo TC: Analysis of cell cycle regulator proteins in encapsulated thymoma. Clin Cancer Res. 2005, 11: 5078-83. 10.1158\/1078-0432.CCR-05-0070.","journal-title":"Clin Cancer Res"},{"key":"1018_CR19","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/S0002-9440(10)64536-1","volume":"157","author":"A Zettl","year":"2000","unstructured":"Zettl A, Str\u00f6bel P, Wagner K, Katzenberger T, Ott G, Rosenwald A, Peters K, Krein A, Semik M, M\u00fcller-Hermelink HK, Marx A: Recurrent Genetic Aberrations in Thymoma and Thymic Carcinoma. Am J Pathol. 2000, 157: 257-266.","journal-title":"Am J Pathol"},{"key":"1018_CR20","doi-asserted-by":"publisher","first-page":"1853","DOI":"10.1016\/S0002-9440(10)63031-3","volume":"159","author":"R Zhou","year":"2001","unstructured":"Zhou R, Zettl A, Str\u00f6bel P, Wagner K, M\u00fcller-Hermelink HK, Zhang SjSJ, Marx A, Starostik P: Thymic epithelial tumors can develop along two different pathogenetic pathways. Am J Pathol. 2001, 159: 1853-1860.","journal-title":"Am J Pathol"},{"key":"1018_CR21","first-page":"3708","volume":"63","author":"M Inoue","year":"2003","unstructured":"Inoue M, Starostik P, Zettl A, Str\u00f6bel P, Schwarz S, Scaravilli F, Henry K, Willcox N, M\u00fcller-Hermelink H-K, Marx A: Correlating Genetic Aberrations with World Health Organization-defined Histology and Stage across the Spectrum of Thymomas. Cancer Res. 2003, 63: 3708-3715.","journal-title":"Cancer Res"},{"key":"1018_CR22","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1002\/ijc.11101","volume":"105","author":"R Penzel","year":"2003","unstructured":"Penzel R, Hoegel J, Schmitz W, Nlaeker H, Morresi-Hauf A, Aulmann S, Hecker E, Mechtersheimer G, Otto HF, Rieker RJ: Clusters of chromosomal imbalances in thymic epithelial tumours are associated with the WHO classification and the staging system according to Masaoka. Int J Cancer. 2003, 105: 494-498. 10.1002\/ijc.11101.","journal-title":"Int J Cancer"},{"key":"1018_CR23","doi-asserted-by":"publisher","first-page":"5116","DOI":"10.1073\/pnas.091062498","volume":"98","author":"GT Virginia","year":"2001","unstructured":"Virginia GT, Robert T, Gilbert C: Significance analysis of microarrays applied to the ionizing radiation response. PNAS. 2001, 98: 5116-5121. 10.1073\/pnas.091062498.","journal-title":"PNAS"},{"key":"1018_CR24","doi-asserted-by":"publisher","first-page":"6567","DOI":"10.1073\/pnas.082099299","volume":"99","author":"T Robert","year":"2002","unstructured":"Robert T, Trevor H, Balasubramanian N, Gilbert C: Diagnosis of multiple cancer types by shrunken centroids of gene expression. PNAS. 2002, 99: 6567-6572. 10.1073\/pnas.082099299.","journal-title":"PNAS"},{"key":"1018_CR25","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/0165-4608(89)90112-X","volume":"41","author":"U Kristoffersson","year":"1989","unstructured":"Kristoffersson U, Heim S, Mandahl N, Akerman M, Mitelman F: Multiple clonal chromosome aberrations in two thymomas. Cancer Genet Cytogenet. 1989, 41: 93-98. 10.1016\/0165-4608(89)90112-X.","journal-title":"Cancer Genet Cytogenet"},{"key":"1018_CR26","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/S0165-4608(98)00183-6","volume":"110","author":"H Sonobe","year":"1999","unstructured":"Sonobe H, Takeuchi T, Ohtsuki Y, Taguchi T, Shimizu K: A thymoma with clonal complex chromosome abnormalities. Cancer Genet Cytogenet. 1999, 110: 72-74. 10.1016\/S0165-4608(98)00183-6.","journal-title":"Cancer Genet Cytogenet"},{"key":"1018_CR27","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.5858\/2000-124-1714-CPOAT","volume":"124","author":"I Mirza","year":"2000","unstructured":"Mirza I, Kazimi SN, Ligi R, Burns J, Braza F: Cytogenetic profile of a thymoma. A case report and review of the literature. Arch Pathol Lab Med. 2000, 124: 1714-1716.","journal-title":"Arch Pathol Lab Med"},{"key":"1018_CR28","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1002\/ijc.10624","volume":"101","author":"H Sasaki","year":"2002","unstructured":"Sasaki H, Ide N, Fukai I, Kiriyama M, Yamakawa Y, Fujii Y: Gene expression analysis of human thymoma correlates with tumor stage. Int J Cancer. 2002, 101: 342-347. 10.1002\/ijc.10624.","journal-title":"Int J Cancer"},{"key":"1018_CR29","doi-asserted-by":"publisher","first-page":"1507","DOI":"10.1016\/S0002-9440(10)64426-4","volume":"161","author":"M Inoue","year":"2002","unstructured":"Inoue M, Marx A, Zettl A, Str\u00f6bel P, Starostik P, M\u00fcller-Hermelink H-K, Starostik P: Chromosome 6 suffers frequent and multiple aberrations in thymoma. Am J Pathol. 2002, 161: 1507-1513.","journal-title":"Am J Pathol"},{"key":"1018_CR30","first-page":"17","volume":"13","author":"MY Seo","year":"2004","unstructured":"Seo MY, Rha SY, Yang SH, Kim SC, Lee GY, Park CH, Yang WI, Ahn JB, Park BW, Chung HC: The pattern of gene copy number changes in bilateral breast cancer surveyed by cDNA microarray-based comparative genomic hybridization. Int J Mol Med. 2004, 13: 17-24.","journal-title":"Int J Mol Med"},{"key":"1018_CR31","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1158\/1078-0432.612.11.2","volume":"11","author":"SH Yang","year":"2005","unstructured":"Yang SH, Seo MY, Jeong HJ, Jeung HC, Shin J, Kim SC, Noh SH, Chung HC, Rha SY: Gene copy number change events at chromosome 20 and their association with recurrence in gastric cancer patients. Clin Cancer Res. 2005, 11: 612-620.","journal-title":"Clin Cancer Res"},{"key":"1018_CR32","first-page":"261","volume":"17","author":"CH Park","year":"2006","unstructured":"Park CH, Jeong HJ, Choi YH, Kim SC, Jeong HC, Park KH, Lee GY, Kim TS, Yang SW, Ahn SW, Kim YS, Rha SY, Chung HC: Systematic analysis of cDNA microarray-based CGH. Int J Mol Med. 2006, 17: 261-267.","journal-title":"Int J Mol Med"},{"key":"1018_CR33","doi-asserted-by":"publisher","first-page":"12963","DOI":"10.1073\/pnas.162471999","volume":"99","author":"JR Pollack","year":"2002","unstructured":"Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE: Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Nat Acad Sci. 2002, 99: 12963-12968. 10.1073\/pnas.162471999.","journal-title":"Proc Nat Acad Sci"},{"key":"1018_CR34","doi-asserted-by":"publisher","first-page":"1919","DOI":"10.1093\/bioinformatics\/btl269","volume":"22","author":"WNV Wieringen","year":"2006","unstructured":"Wieringen WNV, Belien JAM, Vosse SJ, Achame EM, Ylstra B: ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data. Bioinformatics. 2006, 22: 1919-1920. 10.1093\/bioinformatics\/btl269.","journal-title":"Bioinformatics"},{"key":"1018_CR35","doi-asserted-by":"publisher","first-page":"1149","DOI":"10.1101\/gr.5076506","volume":"16","author":"SJ Diskin","year":"2006","unstructured":"Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ, Weber BL, Maris JM, Grant GR: STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res. 2006, 16: 1149-1158. 10.1101\/gr.5076506.","journal-title":"Genome Res"},{"issue":"29","key":"1018_CR36","doi-asserted-by":"publisher","first-page":"7322","DOI":"10.1200\/JCO.2005.03.2821","volume":"23","author":"S Bilke","year":"2005","unstructured":"Bilke S, Chen QR, Westerman F, Schwab M, Catchpoole D, Khan J: Inferring a tumor progression model for neuroblastoma from genomic data. J Clin Oncol. 2005, 23 (29): 7322-7331. 10.1200\/JCO.2005.03.2821.","journal-title":"J Clin Oncol"},{"key":"1018_CR37","unstructured":"SOURCE. [http:\/\/source.stanford.edu]"},{"key":"1018_CR38","doi-asserted-by":"publisher","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","author":"BE Michael","year":"1998","unstructured":"Michael BE, Paul TS, Patrick OB, David B: Cluster analysis and display of genome-wide expression patterns. PNAS. 1998, 95: 14863-14868. 10.1073\/pnas.95.25.14863.","journal-title":"PNAS"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-8-305.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,14]],"date-time":"2023-05-14T00:44:06Z","timestamp":1684025046000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-8-305"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,9,3]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1018"],"URL":"https:\/\/doi.org\/10.1186\/1471-2164-8-305","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,9,3]]},"assertion":[{"value":"11 August 2006","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 September 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 September 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"305"}}