Using the DNeasy Blood and Tissue kit (Qiagen) and QIAamp DNA FFPE Tissue Kit
(Qiagen) in accordance with the manufacturer's instructions, genomic DNA was
extracted from fresh tissue and FFPE samples.29 (link) Tissue DNA was sheared
using Covaris M220 (Covaris, MA, USA), followed by end repair, phosphorylation
and adaptor ligation. Fragments between 200 and 400 bp from the sheared tissue
DNA were purified (Agencourt AMPure XP Kit, Beckman Coulter, CA, USA), followed
by hybridization with capture probes baits, hybrid selection with magnetic
beads, and PCR amplification. The quality and the size of the fragments were
assessed by high sensitivity DNA kit using Bioanalyzer 2100 (Agilent
Technologies, CA, USA). Indexed samples were sequenced on Nextseq500 (Illumina,
Inc., USA) with paired-end reads and target sequencing depth of 1,000× for
tissue samples.
(Qiagen) in accordance with the manufacturer's instructions, genomic DNA was
extracted from fresh tissue and FFPE samples.29 (link) Tissue DNA was sheared
using Covaris M220 (Covaris, MA, USA), followed by end repair, phosphorylation
and adaptor ligation. Fragments between 200 and 400 bp from the sheared tissue
DNA were purified (Agencourt AMPure XP Kit, Beckman Coulter, CA, USA), followed
by hybridization with capture probes baits, hybrid selection with magnetic
beads, and PCR amplification. The quality and the size of the fragments were
assessed by high sensitivity DNA kit using Bioanalyzer 2100 (Agilent
Technologies, CA, USA). Indexed samples were sequenced on Nextseq500 (Illumina,
Inc., USA) with paired-end reads and target sequencing depth of 1,000× for
tissue samples.
