|
| Status |
Public on Sep 15, 2015 |
| Title |
TB09.1124_benign |
| Sample type |
genomic |
| |
|
| Source name |
tissue core
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: benign
tumour gleason: see matched tumour sample
tumour %: N/A
(derived data) iclusterplus group: clust4
extra-capsular extension (ece): see matched tumour sample
positive surgical margins (psm): see matched tumour sample
biochemical relapse (bcr): Y
time to bcr (months): 13
tmprss2: ERG gene fusion status: see matched tumour sample
age at diag: 56
psa at diag: 5.3
clinical stage: T2a NxMX
pathology stage: pT3a N0Mx
total follow up (months): 46.027397260274
|
| Treatment protocol |
When available (i.e not CRPC samples), matched tumour and benign tissues were identified and prepared from RP surgical tissue as described in Warren et al. (2013). The Prostate. 73: 194-202. Matched whole blood samples were obtained from selected samples at treatment clinics.
|
| Growth protocol |
N/A - surgical tissue or whole blood samples
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen AllPrep, according to manufacturer's instructions.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina label protocol; samples run by AROS (Denmark)
|
| |
|
| Hybridization protocol |
Standard Illumina hyb protocol; samples run by AROS (Denmark)
|
| Scan protocol |
Standard Illumina scan protocol; samples run by AROS (Denmark)
|
| Description |
benign robotic radical prostatectomy tissue from patient TB09.1124
A2146_processed_data.txt, column TB09.1124_7_B
|
| Data processing |
Data were pre-processed and quality checked using ‘Call Rate QC’ (AROS), gender calls from PennCNV (Wang et al., 2007); sample pairings were confirmed using BADGER (Lynch et al., 2012).
|
| |
|
| Submission date |
Sep 14, 2015 |
| Last update date |
Dec 01, 2015 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20641 |
| Series (2) |
| GSE70770 |
Prostate cancer stratification using molecular profiles |
| GSE73011 |
Prostate cancer stratification using molecular profiles [CamCap genotype second set] |
|
