Infinium hd ffpe dna restoration kit

FFPE tissues were sectioned. Archived hematoxylin and eosin-stained tissue slides were evaluated by a pathologist for the area with at least 70% tumor cells for manual macrodissection using a needle tip or scalpel. A minimum amount of 200 ng of DNA extracted from each FFPE tissue was quantified by the Qubit® 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA) and qualified using the Infinium FFPE QC Kit before being processed with the Infinium HD FFPE DNA Restoration Kit (Illumina, San Diego, CA), all according to the manufacturers’ protocols.
SNP array was performed with the HumanCytoSNP FFPE-12 v2.1 DNA Analysis BeadChip (Illumina, San Diego, CA), according to the manufacturer’s instructions. This array contains approximately 299,140 SNP markers spanning the entire genome with an average probe spacing of 72 kb. The data were analyzed with GenomeStudio Data Analysis Software v. 2011.1 (Illumina, San Diego, CA) and Nexus Copy Number v9.0 (BioDiscovery, Inc., El Segundo, CA) using the reference human genome (hg19/GRCh37).

After bisulfite conversion, the bisulfite-converted DNA was eluted, resulting in an 8 μl volume. The Infinium HD FFPE DNA restoration kit (Illumina, WG-321-1002) was then used according to the manufacturer's instructions. Following a 1-min incubation, the elution of the DNA was carried out using autoclaved ultrapure water for a 10 μl elution volume. The eluted DNA was stored at –20°C before undergoing Infinium array processing. Intermediate DNA purifications were performed using the DNA Clean and Concentrator-25 Kit (Zymo Research, D4064).