|
| Status |
Public on Aug 25, 2017 |
| Title |
Chronic lymphocytic leukemia 3 pre treatment |
| Sample type |
genomic |
| |
|
| Source name |
peripherel blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: mononuclear cells
ighv mutational status: IgHV unmutated
tp53 diruption: no TP53 disruption detected
atm disruption: no ATM disruption detected
treatment: not annotated
best clinical response: not annotated
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from mononuclear cell preparations from peripheral blood using the Qiagen® DNA Blood Mini Kit (Hilden, Germany). Immunomagnetic tumor cell enrichment was performed for a subset of samples (Midi MACS, Miltenyi Biotec®; Bergisch Gladbach, Germany) so that 98 mononuclear cell fractions, 118 CD19-positive fractions, and 52 CD19-negative fractions were used. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix®)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix® fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to GenomeWide SNP 6.0 array
|
| Data processing |
CEL-files and chp-files (generated by Affymetrix GTYPE using the DM algorithm and by the birdseed algorithm in Affymetrix Genotyping Console version 4.0, respectively) were processed by dChip and model-based expression performed using the PM/MM model.
Signal' = Summarized signal; Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
|
| |
|
| Submission date |
Jun 20, 2016 |
| Last update date |
Aug 25, 2017 |
| Contact name |
Jennifer Edelmann |
| E-mail(s) |
j.edelmann@qmul.ac.uk
|
| Phone |
0041 (0)20 7882 8780
|
| Organization name |
Barts Cancer Institute
|
| Department |
Centre for Haemato-/Oncology
|
| Lab |
3rd Floor John Vane Science Centre
|
| Street address |
Charterhouse Square
|
| City |
London |
| ZIP/Postal code |
EC1M 6BQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE83566 |
Frequent Evolution of Copy Number Alterations Following First‑line Treatment with FC(R) is Enriched with TP53 Alterations which Impact Long Term Survival – Results from the CLL8 Trial |
|
