E-GEOD-12040 - DNA profiling of serous ovarian and Fallopian tube carcinomas with array CGH and MLPA

Status
Submitted on 7 July 2008, released on 8 July 2008, last updated on 3 May 2014
Organism
Homo sapiens
Samples (56)
Array (1)
Protocols (119)
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.
Experiment type
comparative genomic hybridization by array 
Contacts
Marlies Nowee <me.nowee@vumc.nl>, A M Snijders, D A Rockx, D G Albertson, J C Dorsman, J P Schouten, k Hämäläinen, M E Nowee, P J van Diest, R H Verheijen, R M de Wit, V M Kosma
Citation
DNA profiling of primary serous ovarian and fallopian tube carcinomas with array comparative genomic hybridization and multiplex ligation-dependent probe amplification. Nowee ME, Snijders AM, Rockx DA, de Wit RM, Kosma VM, Hämäläinen K, Schouten JP, Verheijen RH, van Diest PJ, Albertson DG, Dorsman JC.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-12040.idf.txt
Sample and data relationshipE-GEOD-12040.sdrf.txt
Raw data (1)E-GEOD-12040.raw.1.zip
Processed data (1)E-GEOD-12040.processed.1.zip
Experiment designE-GEOD-12040.biosamples.png, E-GEOD-12040.biosamples.svg
Array designA-GEOD-4896.adf.txt
Links