Breast tumor copy number aberration phenotypes and genomic instability

Jane Fridlyand, Antoine M. Snijders, Bauke Ylstra, Hua Li, Adam Olshen, Richard Segraves, Shanaz Dairkee, Taku Tokuyasu, Britt Marie Ljung, Ajay N. Jain, Jane McLennan, John Ziegler, Kwang-Yung Chin, Sandy Devries, Heidi Feiler, Joe Gray, Frederic Waldman, Daniel Pinkel, Donna G. Albertson

Research output: Contribution to journalArticle

224 Citations (Scopus)

Abstract

Background: Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability phenotypes when mutated (e.g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes. Methods: We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability. Results: We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability. Conclusion: Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome.

Original languageEnglish (US)
Article number96
JournalBMC Cancer
Volume6
DOIs
StatePublished - Apr 18 2006
Externally publishedYes

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Genomic Instability
Breast Neoplasms
Phenotype
Telomere
Neoplasms
Chromosomal Instability
Genes
Gene Expression
Mitosis
Maintenance
Genome
Mutation
Comparative Genomic Hybridization
DNA
DNA Replication
DNA Repair
Cell Cycle

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Fridlyand, J., Snijders, A. M., Ylstra, B., Li, H., Olshen, A., Segraves, R., ... Albertson, D. G. (2006). Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer, 6, [96]. https://doi.org/10.1186/1471-2407-6-96

Breast tumor copy number aberration phenotypes and genomic instability. / Fridlyand, Jane; Snijders, Antoine M.; Ylstra, Bauke; Li, Hua; Olshen, Adam; Segraves, Richard; Dairkee, Shanaz; Tokuyasu, Taku; Ljung, Britt Marie; Jain, Ajay N.; McLennan, Jane; Ziegler, John; Chin, Kwang-Yung; Devries, Sandy; Feiler, Heidi; Gray, Joe; Waldman, Frederic; Pinkel, Daniel; Albertson, Donna G.

In: BMC Cancer, Vol. 6, 96, 18.04.2006.

Research output: Contribution to journalArticle

Fridlyand, J, Snijders, AM, Ylstra, B, Li, H, Olshen, A, Segraves, R, Dairkee, S, Tokuyasu, T, Ljung, BM, Jain, AN, McLennan, J, Ziegler, J, Chin, K-Y, Devries, S, Feiler, H, Gray, J, Waldman, F, Pinkel, D & Albertson, DG 2006, 'Breast tumor copy number aberration phenotypes and genomic instability', BMC Cancer, vol. 6, 96. https://doi.org/10.1186/1471-2407-6-96
Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R et al. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer. 2006 Apr 18;6. 96. https://doi.org/10.1186/1471-2407-6-96
Fridlyand, Jane ; Snijders, Antoine M. ; Ylstra, Bauke ; Li, Hua ; Olshen, Adam ; Segraves, Richard ; Dairkee, Shanaz ; Tokuyasu, Taku ; Ljung, Britt Marie ; Jain, Ajay N. ; McLennan, Jane ; Ziegler, John ; Chin, Kwang-Yung ; Devries, Sandy ; Feiler, Heidi ; Gray, Joe ; Waldman, Frederic ; Pinkel, Daniel ; Albertson, Donna G. / Breast tumor copy number aberration phenotypes and genomic instability. In: BMC Cancer. 2006 ; Vol. 6.
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abstract = "Background: Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability phenotypes when mutated (e.g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes. Methods: We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability. Results: We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability. Conclusion: Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome.",
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AU - Snijders, Antoine M.

AU - Ylstra, Bauke

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AU - Olshen, Adam

AU - Segraves, Richard

AU - Dairkee, Shanaz

AU - Tokuyasu, Taku

AU - Ljung, Britt Marie

AU - Jain, Ajay N.

AU - McLennan, Jane

AU - Ziegler, John

AU - Chin, Kwang-Yung

AU - Devries, Sandy

AU - Feiler, Heidi

AU - Gray, Joe

AU - Waldman, Frederic

AU - Pinkel, Daniel

AU - Albertson, Donna G.

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N2 - Background: Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability phenotypes when mutated (e.g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes. Methods: We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability. Results: We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability. Conclusion: Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome.

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