|
| Status |
Public on Dec 31, 2010 |
| Title |
breast cancer X142 |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer FNA biopsy, pre-treatment
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer FNA biopsy
pcr.v.rd: RD
array.qc: Pass
p53 status: WT
er positive vs negative by esr1 mrna gene expression (probe 205225_at): ERpos
er positive vs negative by immunohistochemistry: ERpos
age: 51
prechemo t: 2
prechemo tumor size: 1.5
prechemo n: 1
bmn.grade: 3
|
| Treatment protocol |
Patients received neoadjuvant chemotherapy regimen with 5-Fluorouracil, Doxorubicin (Epirubicin) and Cyclophosphamide
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted from the FNA specimens using Qiagen RNeasy kit following the manufacturer’s instructions (http://www.qiagen.com).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 1 ug total RNA using the BioArray High Yield RNA transcript labeling kit (Enzo Laboratories).
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 ug of cRNA were hybridized to affymetrix U133A arrays overnight at 42C. Microarrays were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000DX. This system is manufactured by Affymetrix Inc in Santa Clara, CA.
|
| Description |
Gene expression data from breast cancer FNA biopsy, pre-treatment
Characteristics legend:
pCR: pathologic complete response was defined as no residual invasive cancer in the breast and lymph nodes after preoperative chemotherapy.
RD: residual disease was defined as any degree of invasive cancer that survived preoperative chemotherapy.
Prechemo T and Prechemo N: were modified by TNM staging system in the American Joint Committee on Cancer
Prechemo Tumor size: Clinical tumor size
BMN.grade: were modified by Black's Nuclear Grade
|
| Data processing |
The data were normalized using dChip version 1.3 followed by logrithm-base-2 sc600 transformation. The dChip version 1.3 was used to calculate Model Based Expression Index (MBEI) values of the arrays using the digital standard microarray MDA-BCNorm.CEL and the probe sensitivity index file UTMDACC-BreastCancerNormalizer.psi as described in Hess, et. al, Pharmacogenomic Predictor of Sensitivity to Preoperative Chemotherapy With Paclitaxel and 5-Fluorouracil, Doxorubicin, and Cyclophosphamide in Breast Cancer, Journal of Clinical Oncology, 24 (26), 2006.
|
| |
|
| Submission date |
Jun 02, 2010 |
| Last update date |
Jun 06, 2022 |
| Contact name |
TAKAYUKI IWAMOTO |
| E-mail(s) |
[email protected]
|
| Organization name |
UT MD Anderson
|
| Department |
Breast medical Oncology
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030-4009 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE22093 |
Expression data from breast cancer FNA biopsies from patients |
|
| Relations |
| Reanalyzed by |
GSE205568 |
