|
Status |
Public on Dec 14, 2022 |
Title |
Ovarian Clear Cell Carcinoma 53 recurrence |
Sample type |
genomic |
|
|
Source name |
recurrence 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.
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|
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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 |
|