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Impact of DNA amplification on gene expression patterns in breast cancer

Hyman, Elizabeth; Kauraniemi, Paivikki; Hautaniemi, Sampsa; Wolf, Maija; Mousses, Spyro; Rozenblum, Ester; Ringnér, Markus LU ; Sauter, Guido; Monni, Outi and Elkahloun, Abdel, et al. (2002) In Cancer Research 62(21). p.6240-6245
Abstract
Genetic changes underlie tumor progression and may lead to cancer-specific expression of critical genes. Over 1100 publications have described the use of comparative genomic hybridization (CGH) to analyze the pattern of copy number alterations in cancer, but very few of the genes affected are known. Here, we performed high-resolution CGH analysis on cDNA microarrays in breast cancer and directly compared copy number and mRNA expression levels of 13,824 genes to quantitate the impact of genomic changes on gene expression. We identified and mapped the boundaries of 24 independent amplicons, ranging in size from 0.2 to 12 Mb. Throughout the genome, both high- and low-level copy number changes had a substantial impact on gene expression, with... (More)
Genetic changes underlie tumor progression and may lead to cancer-specific expression of critical genes. Over 1100 publications have described the use of comparative genomic hybridization (CGH) to analyze the pattern of copy number alterations in cancer, but very few of the genes affected are known. Here, we performed high-resolution CGH analysis on cDNA microarrays in breast cancer and directly compared copy number and mRNA expression levels of 13,824 genes to quantitate the impact of genomic changes on gene expression. We identified and mapped the boundaries of 24 independent amplicons, ranging in size from 0.2 to 12 Mb. Throughout the genome, both high- and low-level copy number changes had a substantial impact on gene expression, with 44% of the highly amplified genes showing overexpression and 10.5% of the highly overexpressed genes being amplified. Statistical analysis with random permutation tests identified 270 genes whose expression levels across 14 samples were systematically attributable to gene amplification. These included most previously described amplified genes in breast cancer and many novel targets for genomic alterations, including the HOXB7 gene, the presence of which in a novel amplicon at 17q21.3 was validated in 10.2% of primary breast cancers and associated with poor patient prognosis. In conclusion, CGH on cDNA microarrays revealed hundreds of novel genes whose overexpression is attributable to gene amplification. These genes may provide insights to the clonal evolution and progression of breast cancer and highlight promising therapeutic targets. (Less)
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Contribution to journal
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published
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in
Cancer Research
volume
62
issue
21
pages
6240 - 6245
publisher
American Association for Cancer Research Inc.
external identifiers
  • pmid:12414653
  • scopus:0036829790
ISSN
1538-7445
language
English
LU publication?
no
id
567486bb-81ee-4448-8e81-be5c8f5b8275 (old id 1123878)
alternative location
http://cancerres.aacrjournals.org/content/62/21/6240.long
http://cancerres.aacrjournals.org/cgi/content/abstract/62/21/6240
date added to LUP
2008-05-23 08:41:09
date last changed
2017-12-10 04:27:12
@article{567486bb-81ee-4448-8e81-be5c8f5b8275,
  abstract     = {Genetic changes underlie tumor progression and may lead to cancer-specific expression of critical genes. Over 1100 publications have described the use of comparative genomic hybridization (CGH) to analyze the pattern of copy number alterations in cancer, but very few of the genes affected are known. Here, we performed high-resolution CGH analysis on cDNA microarrays in breast cancer and directly compared copy number and mRNA expression levels of 13,824 genes to quantitate the impact of genomic changes on gene expression. We identified and mapped the boundaries of 24 independent amplicons, ranging in size from 0.2 to 12 Mb. Throughout the genome, both high- and low-level copy number changes had a substantial impact on gene expression, with 44% of the highly amplified genes showing overexpression and 10.5% of the highly overexpressed genes being amplified. Statistical analysis with random permutation tests identified 270 genes whose expression levels across 14 samples were systematically attributable to gene amplification. These included most previously described amplified genes in breast cancer and many novel targets for genomic alterations, including the HOXB7 gene, the presence of which in a novel amplicon at 17q21.3 was validated in 10.2% of primary breast cancers and associated with poor patient prognosis. In conclusion, CGH on cDNA microarrays revealed hundreds of novel genes whose overexpression is attributable to gene amplification. These genes may provide insights to the clonal evolution and progression of breast cancer and highlight promising therapeutic targets.},
  author       = {Hyman, Elizabeth and Kauraniemi, Paivikki and Hautaniemi, Sampsa and Wolf, Maija and Mousses, Spyro and Rozenblum, Ester and Ringnér, Markus and Sauter, Guido and Monni, Outi and Elkahloun, Abdel and Kallioniemi, Olli-P and Kallioniemi, Anne},
  issn         = {1538-7445},
  language     = {eng},
  number       = {21},
  pages        = {6240--6245},
  publisher    = {American Association for Cancer Research Inc.},
  series       = {Cancer Research},
  title        = {Impact of DNA amplification on gene expression patterns in breast cancer},
  volume       = {62},
  year         = {2002},
}