TY - JOUR
T1 - Comprehensive genome-wide comparison of DNA and RNA level scan using microarray technology for identification of candidate cancer-related genes in the HL-60 cell line
AU - Ulger, Celal
AU - Toruner, Gokce A.
AU - Alkan, Mualla
AU - Mohammed, Mansoor
AU - Damani, Shamsha
AU - Kang, Jason
AU - Galante, Anthony
AU - Aviv, Hana
AU - Soteropoulos, Patricia
AU - Tolias, Peter P.
AU - Schwalb, Marvin N.
AU - Dermody, James J.
N1 - Funding Information:
We thank Ms. Angela Fajardo for technical assistance in FISH experiments, and Ms. Patricia DeAngelo for karyotyping. The Center for Applied Genomics is supported in part with grants to P. Tolias from the New Jersey Commission on Science and Technology and National Institutes of Health grant CA83213. C. Ulger and G.A Toruner were supported in part by The Tomorows Children's Fund.
PY - 2003/11
Y1 - 2003/11
N2 - Genome-wide scans for DNA and RNA changes in the HL-60 cell line relative to normal leukocytes were conducted. Microarray-based comparative genome hybridization (CGH) studies were performed with the Spectral Genomics Human Bacterial Artificial Chromosome (BAC) 3MB system. Transcriptional measurements of approximately 12,500 human genes were monitored using Affymetrix U95A GeneChips. In HL-60, genomic DNA amplification of the 8q24 locus, trisomy 18, and deletions at loci 5q11.2∼q31, 6q12, 9p21.3∼p22, 10p12∼p15, 14q22∼q31, 17p12∼p13.3, and monosomy X were detected. After obtaining locus information about the RNA transcripts from the Affymetrix database, 4368 genes were stratified both according to status of RNA expression and the DNA copy number of their designated loci. The expression level of 2326 (53.25%) of 4368 transcripts is concordant with DNA copy number. Examples of specific, highly expressed, cancer-associated genes in amplified loci include SERPINB10, MYC, TYMS, HEC, and EPB41L3, while CD14, GZMK, TCF7, FOS, MLH3, CTNNA1, IRF1, VIM, CRK, MAP3K1, STAM, MAX, SFRG5, ENC1, PURA, MNT, RASA1, GLRX, UBE2B, NR3C1, PTENP1, BS69, COPEB, SKIP, PIM2, and MIC2 represent cancer-associated genes in deleted loci with decreased expression. The complementary usage of genome-wide DNA and RNA scans should enhance the identification of candidate genes in the neoplastic process.
AB - Genome-wide scans for DNA and RNA changes in the HL-60 cell line relative to normal leukocytes were conducted. Microarray-based comparative genome hybridization (CGH) studies were performed with the Spectral Genomics Human Bacterial Artificial Chromosome (BAC) 3MB system. Transcriptional measurements of approximately 12,500 human genes were monitored using Affymetrix U95A GeneChips. In HL-60, genomic DNA amplification of the 8q24 locus, trisomy 18, and deletions at loci 5q11.2∼q31, 6q12, 9p21.3∼p22, 10p12∼p15, 14q22∼q31, 17p12∼p13.3, and monosomy X were detected. After obtaining locus information about the RNA transcripts from the Affymetrix database, 4368 genes were stratified both according to status of RNA expression and the DNA copy number of their designated loci. The expression level of 2326 (53.25%) of 4368 transcripts is concordant with DNA copy number. Examples of specific, highly expressed, cancer-associated genes in amplified loci include SERPINB10, MYC, TYMS, HEC, and EPB41L3, while CD14, GZMK, TCF7, FOS, MLH3, CTNNA1, IRF1, VIM, CRK, MAP3K1, STAM, MAX, SFRG5, ENC1, PURA, MNT, RASA1, GLRX, UBE2B, NR3C1, PTENP1, BS69, COPEB, SKIP, PIM2, and MIC2 represent cancer-associated genes in deleted loci with decreased expression. The complementary usage of genome-wide DNA and RNA scans should enhance the identification of candidate genes in the neoplastic process.
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U2 - 10.1016/S0165-4608(03)00155-9
DO - 10.1016/S0165-4608(03)00155-9
M3 - Article
C2 - 14580768
AN - SCOPUS:0142155150
VL - 147
SP - 28
EP - 35
JO - Cancer Genetics and Cytogenetics
JF - Cancer Genetics and Cytogenetics
SN - 0165-4608
IS - 1
ER -