|
| Status |
Public on Feb 17, 2009 |
| Title |
502_tumour_ovary |
| Sample type |
genomic |
| |
|
| Source name |
Tumor, ovary
|
| Organism |
Homo sapiens |
| Characteristics |
Primary tumour
Gender: F
Stage: IIIC
Histology: Ser/PapSer
Grade: 3
|
| Treatment protocol |
DNA was extracted from whole tumor tissue for samples with ≥ 80% neoplastic cells. For samples with < 80% overall tumor cells, needle dissection of serial tumor sections was performed to enrich for the epithelial fraction prior to DNA extraction. Needle-dissected samples were stained with cresyl-violet to facilitate morphological distinction between tumor and stromal elements.
|
| Growth protocol |
Fresh-frozen (LN2) tissue collected at surgery.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a DNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
The mapping array assays were performed according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
DNA was XbaI restriction digested, adapter ligated, PCR amplified, fragmented, labelled and hybridized to a 50K SNP XbaI array according to the manufacturer's instructions.
|
| Scan protocol |
Arrays were washed using an Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to Affymetrix GeneChip Mapping 100K Set Array (50K_Xba240_SNP).
|
| Data processing |
CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Copy number normalization, batch correction and smoothing steps were performed using GISTIC as described in Beroukhim et al., 2007 (PMID 18077431) and Etemadmoghadam et al., in press.
Copy number ratio was generated by normalizing each tumor sample to the mean of normal reference samples with similar baseline signal intensity profiles to minimize systematic noise resulting from undetermined experimental factors. We used the 5 closest references, measured by Euclidean distance between each normal and tumor signal profile. Additional normal (diploid) data (which supplement the 16 reference samples available from the current submission) were obtained from the Broad Institute, Boston (Beroukhim et al., 2007; GSE9635) and from the Affymetrix 100K HapMap Trio Dataset (available from https://www.affymetrix.com/support/technical/sample_data/hapmap_trio_data.affx).
|
| |
|
| Submission date |
Dec 03, 2008 |
| Last update date |
Feb 17, 2009 |
| Contact name |
Dariush Etemadmoghadam |
| E-mail(s) |
dariush.etemadmoghadam@petermac.org
|
| Phone |
61396561149
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
St Andrew's Place
|
| City |
East Melbourne |
| ZIP/Postal code |
3002 |
| Country |
Australia |
| |
|
| Platform ID |
GPL2005 |
| Series (1) |
| GSE13813 |
50K SNP Copy Number Analysis of Ovarian Carcinomas |
|
