BACKGROUND: Brain metastases (BMs) occur in ∼1/3 of cancer patients and are associated with poor prognosis. Genomic alterations contribute to BM development; however, mutations that predispose and promote BM development are poorly understood.OBJECTIVE: To identify differences in genomic alterations between BM and primary tumors.METHODS: A retrospective cohort of 144 BM patients were tested for genomic alterations (85 lung, 21 breast, 14 melanoma, 4 renal, 4 colon, 3 prostate, 4 others, and 9 unknown carcinomas) by a next-generation sequencing assay interrogating 315 genes. The differences in genomic alterations between BM and primary tumors from COSMIC and TCGA were evaluated by chi-square or Fisher's exact test. Overall survival curves were plotted using the Kaplan-Meier method.RESULTS: The comparison of BM and primary tumors revealed genes that were mutated in BM with increased frequency:TP53, ATR, andAPC(lung adenocarcinoma);ARID1AandFGF10(lung small-cell);PIK3CG, NOTCH3, andTET2(lung squamous);ERBB2, BRCA2, andAXL1(breast carcinoma);CDKN2A/B, PTEN, RUNX1T1, AXL, andFLT4(melanoma); andATM, AR, CDKN2A/B, TERT, andTSC1(renal clear-cell carcinoma). Moreover, our results indicate that lung adenocarcinoma BM patients withCREBBP, GPR124, orSPTA1mutations have a worse prognosis. Similarly,ERBB2, CDK12, orTP53mutations are associated with worse prognosis in breast cancer BM patients.CONCLUSION: The present study demonstrates significant differences in the frequency of mutations between primary tumors and BM and identifies targetable alterations and genes that correlate with prognosis. Identifying the genomic alterations that are enriched in metastatic central nervous system tumors could help our understanding of BM development and improve patient management.