|
| Status |
Public on Nov 30, 2017 |
| Title |
03PB938_01-454_ |
| Sample type |
genomic |
| |
|
| Source name |
PATIENT_ID: 03PB938_01-454_
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: T-PLL
tcl1a: POS
mtcp1: NA
os_diagnosis_to_last_fu: NA
os_treatment_to_last_fu: 452
os_scoring: DOD
pfs: NA
pfs_scoring: death; relapse or progression; primary treatment failure
wbc_diagn: NA
wbc_sample: NA
description: NA
cell type: T cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Human T-PLL cells. Sample preparation: DNAs were isolated from PBMCs of T-PLL patients (n=83, >95% purity of T-cells) that included 13 CD4/CD8-enriched/depleted tumor/germline (t/g) pairs (see chapter “Magnetic-bead based cell enrichment” for details on cell purification) using the QIAamp DNA Kit (Qiagen). SNP-array analyses were conducted using Affymetrix SNP 6.0 chips according to manufacturer’s instructions.
|
| 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.
|
| Data processing |
Bioinformatics: To globally infer on sCNAs across the T-PLL genome, the T-PLL data sets were compared to the pooled controls (non-tumor hematopoietic cell DNA as ‘germline’ from T-PLL patients, n=13) obtained by the Affymetrix Power Tools, version 1.14.2 with duplicate SNP/CN markers (by identical position) removed. We segmented the called SNP / copy number (CN) markers by the Circular binary segmentation (CBS) algorithm (default options, p<0.01) within the DNAcopy R-package and converted the output files to .seg files to view them in the “Integrative Genome Viewer”. Since the CBS algorithm only reports significantly altered segments/regions and therefore disregards gene structure (perhaps splits them in two or more segments), we mapped regions on gene CDS (based on version 75 of the Ensembl annotation) within the GenomicRanges R package, version 1.16.4, and clustered CNs by gene names and 100kb regions with the gplots R package.
Globally, we identified gains (CN>2.5) in 19,590 genes and losses (CN<1.5) in 27,193 genes (Supplementary Data7). The number of sCNA-affected genes (median 3354) varied inter-individually (e.g. 13,862 in TP038 vs. 42 in TP033).
|
| |
|
| Submission date |
Nov 29, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Giuliano Crispatzu |
| Organization name |
University of Cologne (UoC), Germany
|
| Department |
CECAD
|
| Street address |
Joseph-Stelzmann-Straße 26
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE107507 |
The molecular basis of T-PLL is an actionable perturbation of TCL1/ATM- and epigenetically instructed damage responses [human SNP array] |
| GSE107513 |
The molecular basis of T-PLL is an actionable perturbation of TCL1/ATM- and epigenetically instructed damage responses |
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