|
| Status |
Public on Nov 05, 2018 |
| Title |
AK089 [tumor methylation microarray] |
| Sample type |
genomic |
| |
|
| Source name |
adult glioblastoma tumour
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 62
survival_status: dead
os (overall survival, month): 11
progression: 1
pfs (progression-free survival, month): 6
chr7_gain: 1
chr10_loss: 1
chr10q_loss: 0
chr19_gain: 1
chr20_gain: 0
idh1 mutation status: wt
idh2 mutation status: wt
egfr_amplification: 1
pten_deletion: 0
mdm2_amplification: 0
mdm4_amplification: 0
pdgfra_amplification: 0
cdkn2a_b_deletion: 1
cdk4_amplification: 0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumour DNA was extracted using either the Qiagen Allprep DNA/RNA/Protein kit, or caesium chloride (CsCl) density gradient ultracentrifugation.
|
| Label |
biotin
|
| Label protocol |
According to Illumina's protocol for methylation arrays
|
| |
|
| Hybridization protocol |
According to Illumina's protocol for methylation arrays
|
| Scan protocol |
According to Illumina's protocol for methylation arrays
|
| Data processing |
Raw signal intensities were obtained from IDAT files using the minfi Bioconductor package v.1.14.036. Each sample was individually normalized by performing a background correction (shifting of the 5% percentile of negative control probe intensities to 0) and a dye-bias correction (scaling of the mean of normalization control probe intensities to 10,000) for both colour channels. Subsequently, a correction for the type of material tissue (FFPE or frozen) was performed by fitting univariate, linear models to the log2-transformed intensity values (removeBatchEffect function, limma package v.3.24.15). Beta values were calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina).
Beta values as calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina). Due to the protected nature of this patient data, only the 358365 probes common to both 450k+EPIC platforms and that are not annotated with a SNP (IlluminaHumanMethylation450k.anno.ilmn12.hg19, dbSNP release 147) are included in the table.
|
| |
|
| Submission date |
Oct 24, 2018 |
| Last update date |
Nov 15, 2018 |
| Contact name |
Bernhard Radlwimmer |
| E-mail(s) |
b.radlwimmer@dkfz-heidelberg.de
|
| Organization name |
Deutsches Krebsforschungszentrum / German National Cancer Research Centre
|
| Department |
Department of Molecular Genetics
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE121722 |
Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - tumour methylation microarray data |
| GSE121723 |
Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype |
|
