Detection of DNA copy number abnormality by microarray expression analysis.

TitleDetection of DNA copy number abnormality by microarray expression analysis.
Publication TypeJournal Article
Year of Publication2004
AuthorsZhou X, Cole SW, Hu S, Wong DTW
JournalHum Genet
Date Published2004 Apr
KeywordsCell Line, Chromosome Mapping, Chromosomes, Human, Pair 18, Chromosomes, Human, Pair 21, Chromosomes, Human, Pair 9, Gene Dosage, Humans, Oligonucleotide Array Sequence Analysis, Trisomy

Gene copy-number abnormalities (CNAs) are characteristic of solid tumors and are found in association with developmental abnormalities and/or mental retardation. The ultimate impact of CNAs is exerted by the altered expression of encoded genes. We have utilized high-density oligonucleotide arrays from Affymetrix to identify DNA CNAs via their impact on mRNA expression levels. In these studies, we have used three different trisomic cell lines (trisomy 9, trisomy 18, trisomy 21) as models of CNAs and have compared mRNA expression in those trisomic cells with that observed in diploid cell lines of matched tissue origin. Our data clearly show that genes from CNA chromosome regions are substantially over-represented ( P<0.000001 by chi-square analysis) in the differentially expressed subset from comparisons of all three trisomic cell lines with normal matching cells. In addition, we have been able to detect the origin of the duplication by a statistical scan for over-expressed genes. These data show that microarray detection of differential mRNA expression can be used to identify significant DNA CNAs.

Alternate JournalHum. Genet.
PubMed ID14872338
Grant ListDE07296-07 / DE / NIDCR NIH HHS / United States
R01 AI52737 / AI / NIAID NIH HHS / United States
R21 AI49135 / AI / NIAID NIH HHS / United States
R21 CA94216 / CA / NCI NIH HHS / United States