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PLoS One. 2012;7(9):e46088. doi: 10.1371/journal.pone.0046088. Epub 2012 Sep 28.

Amplified and homozygously deleted genes in glioblastoma: impact on gene expression levels.

Author information

1
Centre for Neuroscience and Cell Biology, University of Coimbra, Portugal.

Abstract

BACKGROUND:

Glioblastoma multiforme (GBM) displays multiple amplicons and homozygous deletions that involve relevant pathogenic genes and other genes whose role remains unknown.

METHODOLOGY:

Single-nucleotide polymorphism (SNP)-arrays were used to determine the frequency of recurrent amplicons and homozygous deletions in GBM (n = 46), and to evaluate the impact of copy number alterations (CNA) on mRNA levels of the genes involved.

PRINCIPAL FINDINGS:

Recurrent amplicons were detected for chromosomes 7 (50%), 12 (22%), 1 (11%), 4 (9%), 11 (4%), and 17 (4%), whereas homozygous deletions involved chromosomes 9p21 (52%) and 10q (22%). Most genes that displayed a high correlation between DNA CNA and mRNA levels were coded in the amplified chromosomes. For some amplicons the impact of DNA CNA on mRNA expression was restricted to a single gene (e.g., EGFR at 7p11.2), while for others it involved multiple genes (e.g., 11 and 5 genes at 12q14.1-q15 and 4q12, respectively). Despite homozygous del(9p21) and del(10q23.31) included multiple genes, association between these DNA CNA and RNA expression was restricted to the MTAP gene.

CONCLUSIONS:

Overall, our results showed a high frequency of amplicons and homozygous deletions in GBM with variable impact on the expression of the genes involved, and they contributed to the identification of other potentially relevant genes.

PMID:
23029397
PMCID:
PMC3460955
DOI:
10.1371/journal.pone.0046088
[Indexed for MEDLINE]
Free PMC Article

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