Qiagen AllPrep extraction kit was used according to the manufacturer's instructions
Label
biotin
Label protocol
Affymetrix Genome-Wide SNP Nsp/Sty Assay Kit 5.0/6.0
Hybridization protocol
Affymetrix Genome-Wide SNP Nsp/Sty Assay Kit 5.0/6.0
Scan protocol
Affymetrix user manual (GeneChip scanner 3000)
Description
none
Data processing
Raw intensity data from the Affymetrix SNP 6.0 array was obtained for the tumor sample and matched normal. These data were normalized using a method first described for Illumina genotyping arrays. Specifically, we followed an adaptation of the Illumina method adapted for Affymetrix arrays normalization protocol implemented in the PennCNV package (http://www.openbioinformatics.org/penncnv/penncnv_tutorial_affy_gw6.html) to obtain normalized B-allele Frequency (BAF) and LogR Ratio (LRR) values for each probeset. BAF represents the raw proportion of signal coming from allele B (Theta) normalized using Theta values from a pool of normal samples with pre-determined AA, AB, or BB genotypes at that probe position. LRR represents the log of the ration of the total signal from A and B alleles for a sample divided by expected total signal from a pool of normal samples given the same value of Theta. In brief, the raw intensity values (CEL files) were processed to obtain normalized allele-specific values for each probe using the Affymetrix Power Tools version 1.10 (http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx#1_1) tools apt-probeset-genotype and apt-probeset-summarize. A reference probe-intensity distribution obtained from the HapMap project samples was used for the quantile normalization step. BAF and LRR values were calculated with the script “normalize_affy_geno_cluster.pl” from the PennCVN-Affy package. This script additionally implements a correction for GC-content bias in the LRR values. Data from the HapMap project were used for the reference clusters of AA, AB, and BB genotype signal intensity values. LRR values for somatic CNVs were calculated as the difference of the Tumor and Normal LRR values.
