Nextseq 500 midoutput system platform

To analyze the mutational status of patient tissues, organoids, and PDOX tissues, DNA extraction and library construction were performed using the Qiagen Gentra Puregene kit (Valencia, CA, USA) and Agilent SureSelect XT library prep kit (Santa Clara, CA, USA). Deep targeted sequencing using Axen Cancer Panel 2 (170 cancer-related genes, Macrogen) and the NextSeq 500 midoutput system platform (Illumina) was conducted on tumor tissues, organoids, and PDOX samples. Libraries consisting of 150 bp paired-end reads were sequenced by high-throughput sequencing using synthesis technology to a depth coverage of approximately 2000x. An oncoplot was used for the visualization of the mutations of the tissue, organoid, and PDOX.

To analyze the mutational status of tissues and organoids, they were harvested using a cell recovery solution (Corning, Inc., Corning, NY, USA). DNA extraction and library construction were performed using the Gentra Puregene kit (Qiagen, Hilden, Germany) and SureSelect XT library prep kit (Agilent Technologies, Santa Clara, CA, USA). Deep targeted sequencing using Axen Cancer Panel 2 (170 cancer-related genes; Macrogen, Seoul, Korea) and the NextSeq 500 mid-output system platform (Illumina, San Diego, CA, USA) was conducted on 19 PDTOs. Libraries comprising 150-bp end reads were sequenced via high-throughput sequencing using synthesis technology to a depth coverage of approximately 2000×.