|
| Status |
Public on Jan 22, 2016 |
| Title |
Diffuse Large B Cell Lymphoma tumor sample 45 |
| Sample type |
genomic |
| |
|
| Source name |
Diffuse large B cell lymphoma tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Diffuse large B cell lymphoma de novo
type of sample: Tumor sample
tissue: FFPE
type: GC
gender: female
status: exitus
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction on formalin-fixed paraffin-embedded (FFPE) tissue was done with the RecoverAll™ Total Nucleic Acid Isolation Kit (AmbionInc-Applied Biosystems, Foster City, CA, USA) or QuickExtract™ FFPE DNA Extraction Kit (Epicenter Biotechnologies, Madison, WI, USA). DNA from non-tumoral matched samples was isolated using DNAzolor theMagNA Pure LC system (Roche Diagnostics GmbH, Mannheim, Germany).
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix) for OncoScan v2
|
| |
|
| Hybridization protocol |
Affymetrix OncoScan™ FFPE Express
|
| Scan protocol |
Affymetrix® GeneChip® Scanner 3000G to detect target bound to 360k format GeneChip® Arrays after staining with a fluorescent detection stain.
|
| Description |
Hybridized to Affymetrix OncoScan FFPE Express
45T
|
| Data processing |
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, El Segundo, CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb. CNAs were considered germinal CNAs by analyzing the corresponding constitutional DNA of each sample. In cases in which normal DNA was not available, alterations were cross checked in copy number variation database (http://dgv.tcag.ca/dgv/app/). Physiological deletions of the immunoglobulin heavy and light chain loci (IGH@14q32, IGK@2p11, and [email protected]) were excluded from the analysis. Results on both arrays were integrated in a unique database.
|
| |
|
| Submission date |
Jul 27, 2015 |
| Last update date |
Jan 22, 2016 |
| Contact name |
Elena Sebastián |
| Organization name |
Hospital Universitario de Salamnca
|
| Department |
Hematology
|
| Lab |
Molecular Biology
|
| Street address |
Paseo de San Vicente
|
| City |
Salamanca |
| ZIP/Postal code |
38007 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18602 |
| Series (2) |
| GSE71386 |
Paired copy number analysis of Diffuse Large B Cell Lymphoma [OncoScan] |
| GSE71394 |
Paired copy number analysis of Diffuse Large B Cell Lymphoma |
|
