Overlay analysis of the oligonucleotide array gene expression profiles and copy number abnormalities as determined by array comparative genomic hybridization in medulloblastomas

Ken C. Lo, Michael R. Rossi, Tania Burkhardt, Scott L. Pomeroy, John Kenneth Cowell

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Combined analysis of gene expression array data and array-based comparative genomic hybridization data have been used in a series of 26 pediatric brain tumors to define up- and downregulated genes that coincide with losses, gains, and amplifications involving specific chromosome regions. Frequent losses were defined in chromosome arms 3q, 6q, 8p, 10q, 16q, 17p, and gains were identified in chromosome 7, and chromosome arms 9p and 17q. Amplification of a 2p region was seen in only one tumor, which corresponded to increased expression of the MYCN and DDX1 genes. To facilitate the analysis of the two data sets, we have developed a custom overlay tool that defines genes that are underexpressed in regions of deletions and overexpressed in regions of gain, across the genome and specifically within regions showing recurrent involvement in medulloblastomas.

Original languageEnglish (US)
Pages (from-to)53-66
Number of pages14
JournalGenes Chromosomes and Cancer
Volume46
Issue number1
DOIs
StatePublished - Jan 1 2007

Fingerprint

Medulloblastoma
Comparative Genomic Hybridization
Oligonucleotide Array Sequence Analysis
Transcriptome
Chromosomes
Genes
Chromosomes, Human, Pair 7
Brain Neoplasms
Down-Regulation
Genome
Pediatrics
Gene Expression
Neoplasms

ASJC Scopus subject areas

  • Genetics
  • Cancer Research

Cite this

Overlay analysis of the oligonucleotide array gene expression profiles and copy number abnormalities as determined by array comparative genomic hybridization in medulloblastomas. / Lo, Ken C.; Rossi, Michael R.; Burkhardt, Tania; Pomeroy, Scott L.; Cowell, John Kenneth.

In: Genes Chromosomes and Cancer, Vol. 46, No. 1, 01.01.2007, p. 53-66.

Research output: Contribution to journalArticle

@article{9f8e8b5797d84ab6834e8fe91ec50ed9,
title = "Overlay analysis of the oligonucleotide array gene expression profiles and copy number abnormalities as determined by array comparative genomic hybridization in medulloblastomas",
abstract = "Combined analysis of gene expression array data and array-based comparative genomic hybridization data have been used in a series of 26 pediatric brain tumors to define up- and downregulated genes that coincide with losses, gains, and amplifications involving specific chromosome regions. Frequent losses were defined in chromosome arms 3q, 6q, 8p, 10q, 16q, 17p, and gains were identified in chromosome 7, and chromosome arms 9p and 17q. Amplification of a 2p region was seen in only one tumor, which corresponded to increased expression of the MYCN and DDX1 genes. To facilitate the analysis of the two data sets, we have developed a custom overlay tool that defines genes that are underexpressed in regions of deletions and overexpressed in regions of gain, across the genome and specifically within regions showing recurrent involvement in medulloblastomas.",
author = "Lo, {Ken C.} and Rossi, {Michael R.} and Tania Burkhardt and Pomeroy, {Scott L.} and Cowell, {John Kenneth}",
year = "2007",
month = "1",
day = "1",
doi = "10.1002/gcc.20388",
language = "English (US)",
volume = "46",
pages = "53--66",
journal = "Genes Chromosomes and Cancer",
issn = "1045-2257",
publisher = "Wiley-Liss Inc.",
number = "1",

}

TY - JOUR

T1 - Overlay analysis of the oligonucleotide array gene expression profiles and copy number abnormalities as determined by array comparative genomic hybridization in medulloblastomas

AU - Lo, Ken C.

AU - Rossi, Michael R.

AU - Burkhardt, Tania

AU - Pomeroy, Scott L.

AU - Cowell, John Kenneth

PY - 2007/1/1

Y1 - 2007/1/1

N2 - Combined analysis of gene expression array data and array-based comparative genomic hybridization data have been used in a series of 26 pediatric brain tumors to define up- and downregulated genes that coincide with losses, gains, and amplifications involving specific chromosome regions. Frequent losses were defined in chromosome arms 3q, 6q, 8p, 10q, 16q, 17p, and gains were identified in chromosome 7, and chromosome arms 9p and 17q. Amplification of a 2p region was seen in only one tumor, which corresponded to increased expression of the MYCN and DDX1 genes. To facilitate the analysis of the two data sets, we have developed a custom overlay tool that defines genes that are underexpressed in regions of deletions and overexpressed in regions of gain, across the genome and specifically within regions showing recurrent involvement in medulloblastomas.

AB - Combined analysis of gene expression array data and array-based comparative genomic hybridization data have been used in a series of 26 pediatric brain tumors to define up- and downregulated genes that coincide with losses, gains, and amplifications involving specific chromosome regions. Frequent losses were defined in chromosome arms 3q, 6q, 8p, 10q, 16q, 17p, and gains were identified in chromosome 7, and chromosome arms 9p and 17q. Amplification of a 2p region was seen in only one tumor, which corresponded to increased expression of the MYCN and DDX1 genes. To facilitate the analysis of the two data sets, we have developed a custom overlay tool that defines genes that are underexpressed in regions of deletions and overexpressed in regions of gain, across the genome and specifically within regions showing recurrent involvement in medulloblastomas.

UR - http://www.scopus.com/inward/record.url?scp=33751075209&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33751075209&partnerID=8YFLogxK

U2 - 10.1002/gcc.20388

DO - 10.1002/gcc.20388

M3 - Article

C2 - 17044047

AN - SCOPUS:33751075209

VL - 46

SP - 53

EP - 66

JO - Genes Chromosomes and Cancer

JF - Genes Chromosomes and Cancer

SN - 1045-2257

IS - 1

ER -