Open Access Research article

Genome-wide genetic aberrations of thymoma using cDNA microarray based comparative genomic hybridization

Gui Youn Lee12, Woo Ick Yang23, Hei Cheul Jeung1, Sang Chul Kim1, Min Young Seo1, Chan Hee Park12, Hyun Cheol Chung1245 and Sun Young Rha1245*

Author Affiliations

1 Cancer Metastasis Research Center, National Biochip Research Center, Yonsei University College of Medicine, Seoul, Korea

2 Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea

3 Department of Pathology, Yonsei University College of Medicine, Seoul, Korea

4 Yonsei Cancer Center, Yonsei Cancer Research Institute, Yonsei University College of Medicine, Seoul, Korea

5 Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea

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BMC Genomics 2007, 8:305  doi:10.1186/1471-2164-8-305

Published: 3 September 2007



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.


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.


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.