PMID- 15352123
OWN - NLM
STAT- MEDLINE
DCOM- 20041119
LR  - 20061115
IS  - 0899-1987 (Print)
IS  - 0899-1987 (Linking)
VI  - 41
IP  - 1
DP  - 2004 Sep
TI  - Gene expression microarray analysis and genome databases facilitate the 
      characterization of a chromosome 22 derived homogeneously staining region.
PG  - 17-38
AB  - Karyotype and fluorescence in situ hybridization (FISH) analyses previously 
      identified a homogeneously staining region (HSR) derived from chromosome 22 in 
      OV90, an epithelial ovarian cancer (EOC) cell line. Affymetrix expression 
      microarrays in combination with the UniGene and Human Genome Browser databases 
      were used to identify the candidate genes comprising the amplicon of the HSR, 
      based on comparison of expression profiles of OV90, EOC cell lines lacking HSRs 
      and primary cultures of normal ovarian surface epithelial (NOSE) cells. A group 
      of probe sets displaying a minimum 3-fold overexpression with a high reliability 
      score (P-call) in OV90 were identified which represented genes that mapped within 
      a 1-2 Mb interval on chromosome 22. A large number of probe sets, some of which 
      represent the same genes, displayed no evidence of overexpression and/or low 
      reliability scores (A-call). An investigation of the probe set sequences with the 
      Affymetrix and Sanger Institute Chromosome 22 Group databases revealed that some 
      of the probe sets displaying discordant results for the same gene were 
      complementary to intronic sequences and/or the antisense strand. Microarray 
      results were validated by RT-PCR. Genomic analysis suggests that the HSR was 
      derived from the amplification of a 1.1 Mb interval defined by the chromosomal 
      map positions of ZNF74 and Hs.372662, at 22q11.21. The deduced amplicon is 
      derived from a complex region of chromosome 22 that harbors low-copy repeats 
      (LCRs). The amplicon contains 18 genes as likely targets for gene amplification. 
      This study illustrates that large-scale expression microarray analysis in 
      combination with genome databases is sufficient for deducing target genes 
      associated with amplicons and stresses the importance of investigating probe set 
      design before engaging in validation studies.
CI  - Copyright 2004 Wiley-Liss, Inc.
FAU - Arcand, Suzanna L
AU  - Arcand SL
AD  - Department of Human Genetics, McGill University, Montreal, Canada.
FAU - Mes-Masson, Anne-Marie
AU  - Mes-Masson AM
FAU - Provencher, Diane
AU  - Provencher D
FAU - Hudson, Thomas J
AU  - Hudson TJ
FAU - Tonin, Patricia N
AU  - Tonin PN
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Mol Carcinog
JT  - Molecular carcinogenesis
JID - 8811105
RN  - 0 (Coloring Agents)
SB  - IM
MH  - Cell Line, Tumor
MH  - Chromosome Mapping
MH  - Chromosomes, Human, Pair 22/*genetics/ultrastructure
MH  - Coloring Agents
MH  - Female
MH  - Gene Expression Regulation, Neoplastic/genetics
MH  - Humans
MH  - In Situ Hybridization, Fluorescence
MH  - Karyotyping
MH  - Oligonucleotide Array Sequence Analysis/*methods
MH  - Ovarian Neoplasms/*genetics
EDAT- 2004/09/08 05:00
MHDA- 2004/12/16 09:00
CRDT- 2004/09/08 05:00
PHST- 2004/09/08 05:00 [pubmed]
PHST- 2004/12/16 09:00 [medline]
PHST- 2004/09/08 05:00 [entrez]
AID - 10.1002/mc.20038 [doi]
PST - ppublish
SO  - Mol Carcinog. 2004 Sep;41(1):17-38. doi: 10.1002/mc.20038.