sample group: BiPN (grade 2 or higher) tissue: Peripheral blood
Treatment protocol
All patients were treated within the HOVON65/GMMG-HD4 study. Samples were untreated.
Extracted molecule
genomic DNA
Extraction protocol
DNA was extracted using salting out precipitation
Label
biotin
Label protocol
Biotin labeling according to standard protocol (Affymetrix)
Hybridization protocol
Hybridization according to protocol in hybridization ovens for 16 to 18 hours at 50 °C and 60 rpm (Affymetrix)
Scan protocol
GeneChip Scanner 3000 7G, controlled by AGCC software, was used, according to a standard protocol (Affymetrix).
Description
chips run by Aros
Data processing
Bioconductor CRLMM Out of 906,600 tagging SNPs, only the 370, 605 autosomal SNPs with a homozygosity in at least 5% of patients, a genotype call in at least 95% of patients and fulfilling a Hardy-Weinberg equilibrium P > 10^-5 were used.
