CGH profiles of sporadic basal-like breast tumors
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE22401 | GEO | 2010/10/26
SECONDARY ACCESSION(S): PRJNA128675
REPOSITORIES: GEO
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Project description:Genomic DNA from sporadic breast tumours was isolated and analysed using array CGH. The NKI 1MB BAC/PAC micro array was used to identify chromosomal aberrations of all tumours. Keywords: sporadic breast tumour, CGH
2010-07-05 | GSE9114 | GEO
Project description:Amplification of chromosomal region 11q13, containing the cell cycle regulatory gene CCND1, is frequently found in breast cancer and other malignancies. It is associated with the favourable oestrogen receptor (ER) positive breast tumour phenotype, but also with poor prognosis and treatment failure. 11q13 spans almost 14 Mb and contains more than 200 genes and is affected by various patterns of copy number gains, suggesting complex mechanisms and selective pressure during tumour progression. In the present study we used 32k tiling BAC array CGH to analyse 94 CCND1-amplified breast tumours from sporadic, hereditary and familial breast cancers to fine map chromosome 11q13. A set containing 281 CCND1-non-amplified breast tumours was used for comparisons. We used gene expression data to further validate the functional effect of gene amplification. We identified six core regions covering 11q13.1-q14.1 that were amplified in different combinations. The major core contained CCND1, whereas two cores were found proximal of CCND1 and three distal. The majority of the CCND1-amplified tumours were ER-positive and classified as luminal B. Furthermore, we found that CCND1 amplification is associated with a more aggressive phenotype within histological grade 2 tumours and luminal A subtype tumours. Amplification was equally prevalent in familial and sporadic tumours, but strikingly rare in BRCA1- and BRCA2- mutated tumours. We conclude that 11q13 includes many potential target genes in addition to CCND1. Genomic profiling of 94 CCND1-amplified breast tumors using tiling BAC aCGH. A number of cases were hybridized as replicates or replicate as dye-swaps.
2011-11-23 | E-GEOD-32578 | biostudies-arrayexpress
Project description:Amplification of chromosomal region 11q13, containing the cell cycle regulatory gene CCND1, is frequently found in breast cancer and other malignancies. It is associated with the favourable oestrogen receptor (ER) positive breast tumour phenotype, but also with poor prognosis and treatment failure. 11q13 spans almost 14 Mb and contains more than 200 genes and is affected by various patterns of copy number gains, suggesting complex mechanisms and selective pressure during tumour progression. In the present study we used 32k tiling BAC array CGH to analyse 94 CCND1-amplified breast tumours from sporadic, hereditary and familial breast cancers to fine map chromosome 11q13. A set containing 281 CCND1-non-amplified breast tumours was used for comparisons. We used gene expression data to further validate the functional effect of gene amplification. We identified six core regions covering 11q13.1-q14.1 that were amplified in different combinations. The major core contained CCND1, whereas two cores were found proximal of CCND1 and three distal. The majority of the CCND1-amplified tumours were ER-positive and classified as luminal B. Furthermore, we found that CCND1 amplification is associated with a more aggressive phenotype within histological grade 2 tumours and luminal A subtype tumours. Amplification was equally prevalent in familial and sporadic tumours, but strikingly rare in BRCA1- and BRCA2- mutated tumours. We conclude that 11q13 includes many potential target genes in addition to CCND1.
2011-11-23 | GSE32578 | GEO
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2008-12-25 | GSE7950 | GEO
Project description:Background: Amyotrophic lateral sclerosis (ALS) is a devastating disorder of the central nervous system that leads to progressive loss of upper and lower motor neurons. Most cases are sporadic and of unknown aetiology. In this study, we screened 71 patients with sporadic ALS for the presence of DNA copy number variations, in order to identify novel candidate disease genes. Methods: We have used sub-megabase resolution BAC array comparative genomic hybridisation to detect genomic imbalances in our ALS patient cohort. In order to distinguish phenotypically neutral copy number variations occurring frequently in the normal population from disease-associated aberrations, we screened our results against both the Database of Genomic Variants and a reference data set of approximately 700 normal individuals and probands with other disorders analysed in our laboratory. Aberrations with potential relevance for disease aetiology were verified by oligo array CGH. Findings: In 71 patients with sporadic ALS, we identified a total of six duplications and seven deletions that scored above our threshold. Twelve of these thirteen variations were smaller than 1Mb. Seven were observed exclusively in ALS patients and thus likely play causal roles in the disorder. Analysis of these regions highlighted, for example, the SLC1A7 (EAAT5) glutamate transporter and the kinesin family member KIF9 as good positional and functional candidate genes for ALS. Interpretation: Non-polymorphic sub-microscopic duplications and deletions observable by array CGH are frequent in patients with sporadic ALS. Analysis of such aberrations serves as an excellent starting point in deciphering the aetiology of this complex disease. Keywords: array CGH A cohort of 71 ALS patients was analysed by means of a submegabase resolution BAC array. No replicates were included. Experiments were done without dye swap.
2008-12-24 | E-GEOD-7950 | biostudies-arrayexpress
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2005-04-01 | E-MEXP-298 | biostudies-arrayexpress
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2011-01-01 | E-MEXP-2576 | biostudies-arrayexpress
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