Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Co-amplification at 8p and 11q in breast tumors and cell lines with 8p11q array Genomic Comparative Hybridization

ABSTRACT: Co-amplification at chromosomes 8p11-8p12 and 11q12-11q14 occurs often in breast tumors, suggesting possible cooperation between genes in these regions in oncogenesis. We used high resolution array comparative genomic hybridization (array CGH) to map the minimal amplified regions. The 8p and 11q amplicons are complex and consist of at least four amplicon cores at each site. Candidate genes mapping to these regions were identified by combining copy number and RNA and protein expression analyses. Funcational analysis for transformation was further carried out with candidate genes to determine candidate oncogenes. Near tiling path coverage of 8p11q array CGH experiments with breast cell lines and ductal invasive and lymph node-negative breast tumors.

ORGANISM(S): Homo sapiens

SUBMITTER: Serena kwek

PROVIDER: E-GEOD-12761 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Co-amplified genes at 8p12 and 11q13 in breast tumors cooperate with two major pathways in oncogenesis.

Kwek S S SS Roy R R Zhou H H Climent J J Martinez-Climent J A JA Fridlyand J J Albertson D G DG

Oncogene 20090330 17

Co-amplification at chromosomes 8p11-8p12 and 11q12-11q14 occurs often in breast tumors, suggesting possible cooperation between genes in these regions in oncogenesis. We used high-resolution array comparative genomic hybridization (array CGH) to map the minimal amplified regions. The 8p and 11q amplicons are complex and consist of at least four amplicon cores at each site. Candidate oncogenes mapping to these regions were identified by combining copy number and RNA and protein expression analys ...[more]

PMID: 19330026

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Project description:Primary serous ovarian carcinoma (OVCA) and serous Fallopian tube carcinoma (FTC), both belonging to the BRCA-linked tumour spectrum, share many properties and are treated similarly. However, a detailed molecular comparison has been lacking. We hypothesized that comparative genomic studies of serous OVCAs and FTCs should point to gene regions critically involved in their tumorigenesis. Array comparative genomic hybridization (array CGH) analysis indicated that serous OVCAs and serous FTCs displayed common but also more distinctive patterns of recurrent changes. Targeted gene identification using a dedicated multiplex ligation-dependent probe amplification (MLPA) probe set directly identified EIF2C2 on 8q as a potentially important driver gene. Other previously unappreciated gained/amplified genes included PSMB4 on 1q, MTSS1 on 8q, TEAD4 and TSPAN9 on 12p, and BCAS4 on 20q. SPINT2 and ACTN4 on 19q were predominantly found in FTCs. Gains/amplifications of CCNE1 and MYC, often in conjunction with changes in genes of the AKT pathway, EVI1 and PTK2, seemed to be involved at earlier stages, whereas changes of ERBB2 were associated with advanced stages. The only BRCA1-mutated FTC shared common denominators with the sporadic tumours. In conclusion, the data suggest that serous OVCAs and FTCs, although related, exhibit differences in genomic profiles. In addition to known pathways, new genes/pathways are likely to be involved, with changes in an miRNA-associated gene, EIF2C2, as one important new feature. Dedicated MLPA sets constitute potentially important tools for differential diagnosis and may provide footholds for tailored therapy. This study also includes 13 of the 14 Fallopian tube carcinoma samples T10112, T10119, T10116, T10118, T10121, T10129, T10109, T10125, T10117, T10126, T10102c, T10107, T10131a (i.e., GSM172360..GSM172530) in Series GSE7180. Genome-wide array CGH experiments of serous ovarian and Fallopian tube carcinomas to determine DNA-change profiles for both tumour types.

Dataset Information

Co-amplification at 8p and 11q in breast tumors and cell lines with 8p11q array Genomic Comparative Hybridization

Publications

Co-amplified genes at 8p12 and 11q13 in breast tumors cooperate with two major pathways in oncogenesis.

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