Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene expression level changes

Ken C. Lo, Michael R. Rossi, Jeffrey LaDuca, David G. Hicks, Yaron Turpaz, Lesleyann Hawthorn, John Kenneth Cowell

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Copy number abnormalities (CNAs) in tumor cells are presumed to affect expression levels of genes located in region of abnormality. To investigate this relationship we have surveyed the losses, gains and amplifications in 30 glioblastomas using array comparative genome hybridization and compared these data with gene expression changes in the same tumors using the Affymetrix UI33Plus2.0 oligonucleotide arrays. The two datasets were overlaid using our in-house overlay tool which highlights concordance between CNAs and expression level changes for the same tumors. In this survey we have highlighted genes frequently overexpressed in amplified regions on chromosomes 1, 4, 11, and 12 and have identified novel amplicons on these chromosomes. Deletions of specific regions on chromosomes 9, 10, 11, 14, and 15 have also been correlated with reduced gene expression in the regions of minimal overlap. In addition we describe a novel approach for comparing gene expression levels between tumors based on the presence or absence of chromosome CNAs. This genome wide screen provides an efficient and comprehensive survey of genes which potentially serve as the drivers for the CNAs in GBM. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

Original languageEnglish (US)
Pages (from-to)875-894
Number of pages20
JournalGenes Chromosomes and Cancer
Volume46
Issue number10
DOIs
StatePublished - Oct 1 2007
Externally publishedYes

Fingerprint

Glioblastoma
Gene Expression
Genes
Neoplasms
Chromosomes
Chromosomes, Human, Pair 10
Chromosomes, Human, Pair 9
Chromosomes, Human, Pair 4
Comparative Genomic Hybridization
Chromosomes, Human, Pair 1
Oligonucleotide Array Sequence Analysis
Genome
Surveys and Questionnaires

ASJC Scopus subject areas

  • Genetics
  • Cancer Research

Cite this

Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene expression level changes. / Lo, Ken C.; Rossi, Michael R.; LaDuca, Jeffrey; Hicks, David G.; Turpaz, Yaron; Hawthorn, Lesleyann; Cowell, John Kenneth.

In: Genes Chromosomes and Cancer, Vol. 46, No. 10, 01.10.2007, p. 875-894.

Research output: Contribution to journalArticle

@article{7e3c850697514a018231133e4130d7ed,
title = "Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene expression level changes",
abstract = "Copy number abnormalities (CNAs) in tumor cells are presumed to affect expression levels of genes located in region of abnormality. To investigate this relationship we have surveyed the losses, gains and amplifications in 30 glioblastomas using array comparative genome hybridization and compared these data with gene expression changes in the same tumors using the Affymetrix UI33Plus2.0 oligonucleotide arrays. The two datasets were overlaid using our in-house overlay tool which highlights concordance between CNAs and expression level changes for the same tumors. In this survey we have highlighted genes frequently overexpressed in amplified regions on chromosomes 1, 4, 11, and 12 and have identified novel amplicons on these chromosomes. Deletions of specific regions on chromosomes 9, 10, 11, 14, and 15 have also been correlated with reduced gene expression in the regions of minimal overlap. In addition we describe a novel approach for comparing gene expression levels between tumors based on the presence or absence of chromosome CNAs. This genome wide screen provides an efficient and comprehensive survey of genes which potentially serve as the drivers for the CNAs in GBM. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.",
author = "Lo, {Ken C.} and Rossi, {Michael R.} and Jeffrey LaDuca and Hicks, {David G.} and Yaron Turpaz and Lesleyann Hawthorn and Cowell, {John Kenneth}",
year = "2007",
month = "10",
day = "1",
doi = "10.1002/gcc.20474",
language = "English (US)",
volume = "46",
pages = "875--894",
journal = "Genes Chromosomes and Cancer",
issn = "1045-2257",
publisher = "Wiley-Liss Inc.",
number = "10",

}

TY - JOUR

T1 - Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene expression level changes

AU - Lo, Ken C.

AU - Rossi, Michael R.

AU - LaDuca, Jeffrey

AU - Hicks, David G.

AU - Turpaz, Yaron

AU - Hawthorn, Lesleyann

AU - Cowell, John Kenneth

PY - 2007/10/1

Y1 - 2007/10/1

N2 - Copy number abnormalities (CNAs) in tumor cells are presumed to affect expression levels of genes located in region of abnormality. To investigate this relationship we have surveyed the losses, gains and amplifications in 30 glioblastomas using array comparative genome hybridization and compared these data with gene expression changes in the same tumors using the Affymetrix UI33Plus2.0 oligonucleotide arrays. The two datasets were overlaid using our in-house overlay tool which highlights concordance between CNAs and expression level changes for the same tumors. In this survey we have highlighted genes frequently overexpressed in amplified regions on chromosomes 1, 4, 11, and 12 and have identified novel amplicons on these chromosomes. Deletions of specific regions on chromosomes 9, 10, 11, 14, and 15 have also been correlated with reduced gene expression in the regions of minimal overlap. In addition we describe a novel approach for comparing gene expression levels between tumors based on the presence or absence of chromosome CNAs. This genome wide screen provides an efficient and comprehensive survey of genes which potentially serve as the drivers for the CNAs in GBM. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

AB - Copy number abnormalities (CNAs) in tumor cells are presumed to affect expression levels of genes located in region of abnormality. To investigate this relationship we have surveyed the losses, gains and amplifications in 30 glioblastomas using array comparative genome hybridization and compared these data with gene expression changes in the same tumors using the Affymetrix UI33Plus2.0 oligonucleotide arrays. The two datasets were overlaid using our in-house overlay tool which highlights concordance between CNAs and expression level changes for the same tumors. In this survey we have highlighted genes frequently overexpressed in amplified regions on chromosomes 1, 4, 11, and 12 and have identified novel amplicons on these chromosomes. Deletions of specific regions on chromosomes 9, 10, 11, 14, and 15 have also been correlated with reduced gene expression in the regions of minimal overlap. In addition we describe a novel approach for comparing gene expression levels between tumors based on the presence or absence of chromosome CNAs. This genome wide screen provides an efficient and comprehensive survey of genes which potentially serve as the drivers for the CNAs in GBM. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

UR - http://www.scopus.com/inward/record.url?scp=34548726049&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34548726049&partnerID=8YFLogxK

U2 - 10.1002/gcc.20474

DO - 10.1002/gcc.20474

M3 - Article

C2 - 17620294

AN - SCOPUS:34548726049

VL - 46

SP - 875

EP - 894

JO - Genes Chromosomes and Cancer

JF - Genes Chromosomes and Cancer

SN - 1045-2257

IS - 10

ER -