Multivariate Cox proportional hazard analysis demonstrated a significant 3.24-fold increased risk of progression with 6p CN-LOH/homozygous deletion or BTG1/ETV6 mutations….We identify CN-LOH and homozygous deletions involving the HLA region at 6p21 as well as BTG1 and ETV6 mutations as candidate genomic biomarkers that correlate with accelerated disease progression with MTR-based chemotherapy in PCNSL.