Genomic Characterization of Chordoma: Insights from the AACR Project GENIE Database

<b>Background:</b> Chordoma is a rare primary tumor originating from embryonic notochord remnants, with limited systemic therapeutic options due to a poor understanding of its genomic landscape. This study aims to characterize the genetic alterations in chordoma using a large national patient-level genomic repository, the AACR Project GENIE, to identify potential therapeutic targets and improve disease modeling. <b>Methods:</b> A retrospective analysis of chordoma samples was conducted using the AACR Project GENIE database. Targeted sequencing data were analyzed for recurrent somatic mutations, tumor mutational burden, and chromosomal copy number variations, with significance set at <i>p</i> < 0.05. <b>Results:</b> Frequent mutations were observed in genes associated with SWI/SNF complex affecting chromatin remodeling (<i>SETD2</i>, <i>PBRM1</i>, <i>ARID1A</i>). Mutations were also common among the <i>TERT</i> promoter regions, and cell cycle regulation (<i>CDKN2A</i>). Significant co-occurrences were identified among <i>PBRM1</i>, <i>BRCA2</i>, and <i>KMT2D</i> mutations. <i>CDKN2A/B</i> deletions were enriched in metastatic tumors, and pediatric cases demonstrated distinct mutation profiles compared to adults. <b>Conclusions:</b> This study provides a genomic profile of chordoma, identifying key mutations and potential therapeutic targets. These findings highlight the roles of chromatin remodeling and cell cycle pathways in chordoma biology, offering insights for future precision medicine approaches and therapeutic interventions.