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This study aims to demonstrate the genomic discrepancies between pancreatic ductal adenocarcinoma (PDAC) patient tissues and model tissues during the establishment of patient-derived xenograft (PDX). We conducted whole exome sequencing and RNA sequencing on tissue samples from PDAC patients and their corresponding PDX tissues. As a result, we identified genetic alterations accumulated during PDX establishment and defined PDX model specific subtypes based on changes in gene expression profiles. This study is expected to enhance the utility of PDX models in achieving precision medicine for PDAC.