DNA from the paired-WGS set was extracted from frozen tumor tissue and blood using the Puregene DNA purification kit (Gentra Systems, Minneapolis, MN, USA). DNA was amplified using Multiple Displacement Amplification (MDA) (Illustra GenomiPhi V2 DNA Amplification Kit, GE Healthcare)
Label
C-Bio and A-DNP
Label protocol
500 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
Hybridization protocol
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
Scan protocol
After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a iScan Reader (Illumina).
Description
Genomic DNA extracted from bladder tumors was genotyped using Infinium HumanOmni 1-Quad BeadChip (Illumina, San Diego, CA, USA)
Data processing
Genomic DNA extracted from bladder tumors was genotyped using Infinium HumanOmni 1-Quad BeadChip (Illumina, San Diego, CA, USA).
