|
| Status |
Public on Dec 14, 2022 |
| Title |
Ovarian Clear Cell Carcinoma 53 |
| Sample type |
genomic |
| |
|
| Source name |
primary Ovarian Clear Cell Carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
manual re-centering: no
|
| Treatment protocol |
None
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from OCCC FFPE tissue sections using a QIAmp DNA FFPE Tissue kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
80 ng of genomic DNA was subjected to SNP array OncoScan® FFPE (Thermo) according to manufacturer's instructions
|
| |
|
| Hybridization protocol |
According to manufacturer's instructions
|
| Scan protocol |
The arrays were processed and loaded into the GeneChip® Scanner 3000 7G (Thermo Fisher Scientific/Affymetrix).
|
| Description |
FFPE-derived genomic DNA was hybridyzed to OncoScan
|
| Data processing |
The CEL files were generated by Affymetrix Gene Chip Command Console® software (v. 4.0). CEL files containing the raw data were processed via the Affymetrix OncoScan Console (Thermo). CN gains/amplifications were considered when the log R ratio (LRR) was > 0.1, and CN loss/deletions were considered when the LRR was < -0.1. The ASCAT algorithm was used to infer tumor ploidy, allele-specific copy numbers and segmentation. The ASCAT package for R used the following parameters: ascat.predictGermlineGenotypes(platform = "AffyOncoScan") and ascat.runAscat(gamma = 0.9).
Weighted Log2 ratios, Allellic Differences and B-allele frequencies are provided in the matrix tables. Three OSCHP files required manual re-centering.
|
| |
|
| Submission date |
Dec 13, 2022 |
| Last update date |
Dec 14, 2022 |
| Contact name |
Martin - Roffe |
| E-mail(s) |
MRoffe@cheo.on.ca
|
| Organization name |
CHEO Research Institute
|
| Street address |
401 Smyth Rd
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H 5B2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21558 |
| Series (1) |
| GSE220891 |
Genomic landscapes of ovarian clear cell carcinoma from Latin countries reveal aberrations linked to survival and progression |
|
