|
| Status |
Public on Oct 12, 2012 |
| Title |
Primary Plasma Cell Leukemia PCL-020 Copy number |
| Sample type |
genomic |
| |
|
| Source name |
Primary Plasma Cell Leukemia PCL-020
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: plasma cell
disease state: plasma cell leukemia
genome variation: translocation none
|
| Treatment protocol |
Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction was performed using Wizard® Genomic DNA Purification kit according to the manufacturer's instructions (Promega).
|
| Label |
biotin
|
| Label protocol |
Biotinylated DNA were prepared according to the standard Affymetrix protocol starting from 250 nanograms of genomic DNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 90 micrograms of biotin-labeled DNA were hybridized for 16 hr at 49°C on GeneChip Human Mapping 250K NspI Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Human Mapping 250K NspI arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-020
|
| Data processing |
Images were acquired using Affymetrix GeneChip® Operating System (GCOS 1.4). The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS), (Olshen et al., Biostatistics 2004) and the median of the estimated probes was scaled back to a nominal multiplicity of two. After scaling, a k-means clustering algorithm was used on the cumulative profile of all the data to determine the thresholds for inferring discrete CN values. Inferred CN higher than 2.2, 2.5 and 3.4 corresponded to 3, 4 and 5 or more copies whereas CN below 1.7 and 1.3 to loss and biallelic deletion, respectively.
|
| |
|
| Submission date |
Jul 16, 2012 |
| Last update date |
Oct 13, 2012 |
| Contact name |
Luca Agnelli |
| E-mail(s) |
luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com
|
| Phone |
+390223903581
|
| Organization name |
IRCCS Istituto Nazionale dei Tumori
|
| Department |
Department of Advanced Diagnostics
|
| Street address |
Venezian 1
|
| City |
MILAN |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL3718 |
| Series (2) |
| GSE39380 |
Genome-wide analysis of primary plasma cell leukemia identifies recurrent imbalances associated with transcriptional Profile alterations (Copy number) |
| GSE39383 |
Genome-wide analysis of primary plasma cell leukemia identifies recurrent imbalances associated with transcriptional Profile alterations |
|
