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


RESULTS
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.


CONCLUSIONS
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.
Lee
Gui Youn
GY
Cancer Metastasis Research Center, National Biochip Research Center, Yonsei University College of Medicine, Seoul, Korea. leegy@yuhs.ac
Yang
Woo Ick
WI
Jeung
Hei Cheul
HC
Kim
Sang Chul
SC
Seo
Min Young
MY
Park
Chan Hee
CH
Chung
Hyun Cheol
HC
Rha
Sun Young
SY
D000328:Adult; D000368:Aged; D002872:Chromosome Deletion; D018076:DNA, Complementary; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D013945:Thymoma / Q000235:genetics*
D018076:DNA, Complementary