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High resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

ABSTRACT: An oligo array based high-resolution analysis of copy number alterations in 171 primary breast tumors of relatively small size and low NPI, and 49 breast cancer cell-lines. Objectives of the study were to study the molecular taxonomy and the genomic aberration patterns in a breast cancer cohort representative of breast cancer demographics. Keywords: array comparative genomic hybridisation

ORGANISM(S): Homo sapiens

PROVIDER: GSE8757 | GEO | 2007/08/16

SECONDARY ACCESSION(S): PRJNA102031

REPOSITORIES: GEO

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High resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

Project description:An oligo array based high-resolution analysis of copy number alterations in 171 primary breast tumors of relatively small size and low NPI, and 49 breast cancer cell-lines. Objectives of the study were to study the molecular taxonomy and the genomic aberration patterns in a breast cancer cohort representative of breast cancer demographics. Keywords: array comparative genomic hybridisation 171 primary breast tumors from Nottingham City Hospital and 49 breast cancer cell-lines were hybridised with male DNA as reference.

2007-08-16 | E-GEOD-8757 | biostudies-arrayexpress

KFAM CGH

Project description:Breast cancer samples from patients with BRCA2 mutation. Comparative genomic hybridization by array of BRCA2 tumors.

2012-11-23 | E-MEXP-3690 | biostudies-arrayexpress

CGH profiles of sporadic breast tumors

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

Genome-wide screening for complete genetic loss in PCa by CGH onto cDNA arrays

Project description:We demonstrate that comparative genomic hybridisation (CGH) onto cDNA microarrays may be used to carry out genome-wide screens for regions of genetic loss, including homozygous (complete) deletions that may represent the possible location of tumour suppressor genes in human cancer. Screening of the prostate cancer cell lines LNCaP, PC3 and DU145 allowed the mapping of specific regions where genome copy number appeared altered and led to the identification of two novel regions of complete loss at 17q21.31 (500 kb spanning STAT3) and at 10q23.1 (50-350 kb spanning SFTPA2) in the PC3 cell line. Keywords: Tumour vs normal comparison, array CGH

2006-10-28 | GSE6138 | GEO

Normal karyotype CLL show high rate of SF3B1 mutations and genomic arrays aberrations with impact on time to treatment

Project description:Chronic Lymphocytic Leukemia (CLL) is a heterogeneous disease with a variable clinical course strictly dependent on cytogenetic and molecular features. However, in 15-20% of cases both conventional cytogenetic and FISH analyses do not show any kind of abnormality. With the aim to identify dependable molecular prognostic factors in this subgroup, we evaluated 171 CLL patients, without aberrations detected by chromosome banding and FISH analysis. A comprehensive analysis was performed including genomic arrays (CGH+SNP), IGHV status, flow cytometry and a targeted sequencing. By genomic arrays, we detected 73 aberrations in 39 patients (23%). Most frequently, patients had 1 aberration (25/171; 15%), while 14 patients (8%) had at least 2 aberrations. IGHV unmutated status was present in 53/171 (31%) patients. SF3B1 was the most frequently mutated gene (26/171 patients; 15%), followed by NOTCH1 (n=15, 9%), ATM (n=5; 3%); TP53 (n=5; 3%); KLHL6 (n=5; 3%); MYD88 (n=5; 3%) and XPO1 (n=5; 3%). At univariate analysis, an adverse impact on time to treatment (TTT) was evident for SF3B1 mutations, higher white blood cell count, higher CLL cells percentage by flow cytometry, CD38 positivity, IGHV unmutated status and at least 2 genomic array abnormalities. Of them, SF3B1 mutations, CLL cells percentage, IGHV unmutated status and number of genomic array aberrations maintained their impact in multivariate analysis. In conclusion, integrating genomic and molecular data, we identified patients at higher risk for treatment need. Therefore, we suggest to evaluate these factors for a better prognostic stratification of normal karyotype CLL subset.

2017-08-31 | GSE103306 | GEO

CGH profiles of sporadic basal-like breast tumors

2010-10-26 | GSE22401 | GEO

Trichoderma reesei QM6a CGH self hybridization

Project description:We perform a self hybridisation comprative genomic hybridization (CGH) in order to validate the probe tiling design we done on Trichoderma reesei. This hybridization was done using QM6a wild type strain.

2010-03-16 | GSE17752 | GEO

Genomic profiling of 49 gastric cancer cell lines by array-based comparative genomic hybridization

Project description:In this study, we investigated amplifications and deletions of 49 gastric cancer cell lines by 244k oligonucleotide-based array comparative genomic hybridization.

2016-12-01 | GSE74839 | GEO

Radiation-specific DNA copy number aberration in rat mammary carcinoma.

Project description:Breast cancer ranks top in the incidence among the main sites of female cancer in Japan. The epidemiological study on atomic bomb survivors has suggested that the excess relative risk for breast cancer is higher than any other sites. Little is known, however, about the molecular mechanisms of breast cancer induction by radiation. Therefore, we analyzed here the genome-wide copy number aberration of radiation-induced rat mammary carcinomas using microarray-based comparative genomic hybridization (array-CGH). Mammary carcinomas were induced by 2 Gy gamma irradiation of Sprague-Dawley (SD) rats at 3 or 7 weeks of age. We examined 14 mammary carcinomas induced by gamma-irradiation (2 Gy) and found 26 aberrations including trisomies of chromosomes 4 and 10 in 3 and 1 carcinomas, respectively, and deletion of chromosomes 3q35q36 and 5q32 (Cdkn2a and Cdkn2b region) in 2 and 2 carcinomas, respectively. On the other hand, only one aberration (amplification of chromosome 10q31) was observed in four spontaneous mammary carcinomas. These results suggest that the trisomy of chromosome 4 and deletion of chromosomes 3q35q36 and 5q32 were associated with radiation exposure. We performed aCGH on mammary carcinoma in Sprague-Dawley rat to identify radiation-specific DNA copy number aberration compared with spontaneous mammary carcinoma.

2010-08-08 | E-GEOD-16128 | biostudies-arrayexpress

Radiation-specific DNA copy number aberration in rat mammary carcinoma.

2010-08-09 | GSE16128 | GEO

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