Next-generation sequencing (NGS) analysis was performed on a targeted sequencing platform (CancerSCAN™) designed at Samsung Medical Center [16 (link)]. The CancerSCAN™ panel is designed to target 375 cancer-related genes. Genomic DNA (250 ng) was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn, MA, USA), and target-capture was performed with the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol.
After enriched exome libraries were multiplexed, the libraries were sequenced on a HiSeq 2500 sequencing platform (Illumina). Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation and amplification. After hybridization of the library with bait sequences for 27 h, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. The exome library was sequenced via the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).
Sequence reads were mapped to the human genome (hg19) by means of Burrows-Wheeler Aligner (BWA). Duplicate read removal was performed with Picard and SAMtools. Local alignment was optimized with the Genome Analysis Toolkit (GATK). Variant calling (SNVs, small indels, CNVs and gene fusion) was done only in regions targeted in CancerSCAN™.
After enriched exome libraries were multiplexed, the libraries were sequenced on a HiSeq 2500 sequencing platform (Illumina). Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation and amplification. After hybridization of the library with bait sequences for 27 h, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. The exome library was sequenced via the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).
Sequence reads were mapped to the human genome (hg19) by means of Burrows-Wheeler Aligner (BWA). Duplicate read removal was performed with Picard and SAMtools. Local alignment was optimized with the Genome Analysis Toolkit (GATK). Variant calling (SNVs, small indels, CNVs and gene fusion) was done only in regions targeted in CancerSCAN™.
Free full text: Click here
