|
| Status |
Public on Aug 02, 2016 |
| Title |
LP S1 |
| Sample type |
genomic |
| |
|
| Source name |
Invasive breast cancer FFPE tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Invasive breast cancer FFPE tissue
grade: 2
er status: Positive
recurrence status: IDC
her2 copy number status: Negative
size (mm): 11
|
| Treatment protocol |
retrospective cases received standard care
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
up to 40x 10 micron FFPE sections were needle microdissected for epithelial cells. Total genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) using a modified protocol: Wu L, Patten N, Yamashiro CT, Chui B (2002) Extraction and amplification of DNA from formalin-fixed, paraffin-embedded tissues. Appl Immunohistochem Mol Morphol 10 (3):269-274
|
| Label |
biotin
|
| Label protocol |
standard affymetrix protocol
|
| |
|
| Hybridization protocol |
standard affymetrix protocol
|
| Scan protocol |
standard affymetrix protocol
|
| Description |
53550
|
| Data processing |
Copy number values were obtained against a baseline of normal DNA samples. Raw data is only available for the single file run on OncoScan v3. The rest are available in 2 matrix files, and have slightly different numbers of probes. Each sample has 5 columns: Copy A, Copy B, Copy number, Allele ratio and Allelic difference. P1 and P2 was run on OncoScan v2.
|
| |
|
| Submission date |
Aug 01, 2016 |
| Last update date |
Aug 02, 2016 |
| Contact name |
TANJINA KADER |
| E-mail(s) |
tanjina.kader@petermac.org
|
| Phone |
426129684
|
| Organization name |
The Sir Peter MacCallum Cancer Centre
|
| Department |
Cancer Genomics
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18602 |
| Series (1) |
| GSE85035 |
Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumour tissue |
|
