|
| Status |
Public on Oct 24, 2019 |
| Title |
GHE2003 [CNV] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DLBCL tumor biopsy, patient GHE-2003
|
| Organism |
Homo sapiens |
| Characteristics |
ID: GHE2003A
tissue: DLBCL tumor biopsy
age: 63
Sex: MALE
treatment: R-ACVBP+Conso
ipi: 2
age_adjusted_ipi: 1
pfs_time: 65.70841889
cens_pfs: 1
os_time: 65.70841889
cens_os: 1
coo: GC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from frozen tissues using the QiaAmp DNA MINI kit (Qiagen). Its quality was assessed by spectrometry and agarose gel electrophoresis.
|
| Label |
Cy5
|
| Label protocol |
2µg of Whole-Genome Amplified (WGA) DNA were labeled following Agilent protocol (G4410-90010_CGH_Enzymatic_Protocol_v6.2.1). Yield was assessed with a nanodrop system. Tumor DNA was labeled with cyanine-5 (Cy5), and reference DNA (pooled normal male DNA; Promega, Madison, WI) was labeled with cyanine-3 (Cy3).
|
| |
|
| Channel 2 |
| Source name |
PROMEGA reference DNA pool (male)
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from frozen tissues using the QiaAmp DNA MINI kit (Qiagen). Its quality was assessed by spectrometry and agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
2µg of Whole-Genome Amplified (WGA) DNA were labeled following Agilent protocol (G4410-90010_CGH_Enzymatic_Protocol_v6.2.1). Yield was assessed with a nanodrop system. Tumor DNA was labeled with cyanine-5 (Cy5), and reference DNA (pooled normal male DNA; Promega, Madison, WI) was labeled with cyanine-3 (Cy3).
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed according to the manufacturer's recommendations.
|
| Scan protocol |
Arrays were scanned using an Agilent Technologies Scanner G2505C, with FeatureExtraction version 10.5.1.1 (59 arrays), 10.7.1.1 (50 arrays) or 10.7.3.1 (110 arrays, please refer to the provided raw files for details).
|
| Description |
Characteristics definitions:
ID: sample ID
AGE: age at diagnosis
SEX: male (M) or female (F)
TREATMENT: treatment line used
IPI: calculated IPI
Age_Adjusted_IPI: calculated age-adjusted IPI
PFS_TIME: duration of progression free survival (PFS) in months
CENS_PFS: coded as 0 if PFS event, 1 if not
OS_TIME: duration of overall survival (OS) in months
CENS_OS: coded as 0 if OS event, 1 if not
COO: cell of origin according to Affymetrix GeneChip arrays as described in methods
|
| Data processing |
Agilent FeatureExtraction files were parsed and processed using the standard cghRA 1.6.0 protocol (GRCh37 probe remapping, fresh log2-ratio computation from « processedSignal » columns, flagged probe masking, summarization of replicated probes by their medians and WACA correction of wave artifacts). No normalization nor background-correction was applied to log-ratios provided in the data matrix.
|
| |
|
| Submission date |
Sep 05, 2019 |
| Last update date |
Dec 06, 2019 |
| Contact name |
Sylvain Mareschal |
| Organization name |
Hospices Civils de Lyon
|
| Department |
NGS-HCL platform
|
| Lab |
Bioinformatics group
|
| Street address |
Centre de Biopathologie Est, 59 boulevard Pinel
|
| City |
Bron |
| ZIP/Postal code |
69500 |
| Country |
France |
| |
|
| Platform ID |
GPL27429 |
| Series (2) |
| GSE136962 |
Copy Number Variations identified in 225 Diffuse Large B-Cell Lymphoma tumors |
| GSE136971 |
Expression data and Copy Number Variations from Diffuse Large B Cell Lymphoma (DLBCL) patients |
|
