|Systematic analysis of cDNA microarray-based CGH|
Authors: Chan Hee Park, Ha Jin Jeong, Yeon Ho Choi, Sang Cheol Kim, Hei Chul Jeong, Kyu Hyun Park, Gui Yeon Lee, Tae Soo Kim, Sang Wha Yang, Sung Whan Ahn, Yang Seok Kim, Sun Young Rha, Hyun Cheol Chung
Cancer Metastasis Research Center, Yonsei University College of Medicine, Seoul 120-752, Korea
cDNA microarray-based CGH (Microarray-CGH) is a useful technique for detecting genomic aberrations with a high resolution. However, the criteria for determining a genomic alteration have not been determined. We evaluated the genome-wide measurement of copy number of each gene in normal gastric and placenta tissues with both sex-matched, direct and sex-mismatched, indirect designs using 17K cDNA microarray. The results revealed the range of genomic copy number of normal tissues to be ±0.3 of the log2 ratio (gain >0.3, loss <−0.3) in the autosomal genes with direct and indirect designs. The copy number at a gene level from the X chromosomal genes using the direct and indirect sex-mismatched designs was ±0.68 of the log2 ratio (amplification >0.68, deletion <−0.68). In summary, the suggested method can be used as a guideline for analysis of genomic aberration using a Microarray-CGH in both direct and indirect designs.