HCC Tumor cells were manually microdissected from three consecutive 10-μm sections for each sample under a dissecting microscope to obtain high-purity (>80%) tumor DNA. Fixative removal was performed twice in xylene and absolute ethanol washes. The pellets were digested with proteinase K and then processed according to the QIAamp DNA FFPE Tissue protocol (Qiagen Inc. GmbH, Germany). The concentration was determined by Nanodrop (Thermo Scientific Inc., Wilmington, DE, USA)
Label
Biotin
Label protocol
As per manufacturer (Affymetrix)
Hybridization protocol
Formalin-fixed paraffin-embedded tumor DNA was hybridized on Affymetrix GeneChip Human Mapping SNP6.0 using the Human mapping SNP6.0 assay kit (Affymetrix Inc., Santa Clara, USA) and following the manufacturer’s protocol. The only modification to the manufacturer’s protocol occurred after digestion and adaptor ligation, when the DNA was split into nine plates instead of three. Independent PCR reactions were set up using TITANIUM Taq DNA polymerase (Clontech Laboratories, Inc. Mountain View, USA), for the recommended 35 cycles. The nine PCR products were then pooled.
Scan protocol
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description
Hybridized to SNP 6.0
Data processing
CEL files (generated by Affymetrix GTYPE using the DM algorithm) were processed by Genotyping Console 3.0.1. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758.
