Extraction of genomic DNA from blood was performed using the QIAamp DNA Blood Maxi Kit (Qiagen) according to the manufacturers protocol
Label
Biotin (C, G), DNP (A,T)
Label protocol
500ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using Multi-Sample Amplification Master Mix (MSM) and primer/neutralization mix (MA1 & MA2 & 0.1N NaOH). After incubation the amplified DNA was fragmented with Fragmentation solution (FMS), precipitated with isopropanol and Precipitation solution (PM1) and resuspended in hybridization buffer (RA1).
Hybridization protocol
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48℃, 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 (Illumina).
Data processing
Data processing was done using GenomeStudio (Illumina)
