Systematic analysis of cDNA microarray-based CGH.
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 log(2) 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 log(2) 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.
Park
Chan Hee
CH
Cancer Metastasis Research Center, Yonsei University College of Medicine, Seoul 120-752, Korea.
Jeong
Ha Jin
HJ
Choi
Yeon Ho
YH
Kim
Sang Cheol
SC
Jeong
Hei Chul
HC
Park
Kyu Hyun
KH
Lee
Gui Yeon
GY
Kim
Tae Soo
TS
Yang
Sang Wha
SW
Ahn
Sung Whan
SW
Kim
Yang Seok
YS
Rha
Sun Young
SY
Chung
Hyun Cheol
HC
D002877:Chromosomes, Human / Q000235:genetics; D005260:Female; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis