Truseq sbs kit v5

Four FFPE and two frozen tumors with matched normal tissue underwent DNA extraction with the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA) following manufacturer’s instructions. These six samples were subjected to whole exome sequencing. Between 1.5 and 2 μg of genomic DNA was captured by hybridization using the SureSelect XT Human All Exon V4 (Agilent Technologies). Samples were prepared according to the manufacturer’s instructions.
PCR amplification of the libraries was carried out for 6 cycles in the pre-capture step and for 10 cycles post-capture. Samples were barcoded and run on a HiSeq 2500 in 100 bp paired-end runs using the TruSeq SBS Kit v5 (Illumina). The average number of read pairs per sample was 63 million, the average duplication rate was 12%, and 94.4% of the targeted regions were sequenced at 30X or higher coverage. Sequencing data is available on the publicly accessible cBio Portal for Cancer Genomics.^{13 (link)}

Whole-genome DNA samples were prepared with DNeasy Blood and Tissue kit (Qiagen) following the manufacturer’s instructions. Normal (n =5), primary tumors (n = 5), and tumor-derived organoid or xenograft samples (n =19) were analyzed using SureSelect Human All Exon V4 (Agilent Technologies). In brief, we used 1.5 to 2 μg genomic DNA, and pre- and post-capture PCR amplification carried with six and ten cycles respectively. Samples were barcoded and run on a HiSeq 2500 instrument in 100-bp paired-end runs using TruSeq SBS kit v5 (Illumina). The average aligned reads per samples were 96 million, with 240-fold coverage on targeted regions, and the average duplication rate was 16.0%.