The genomic and transcriptional landscape of primary central nervous system lymphoma

Primary lymphomas of the central nervous system (PCNSL) are mainly diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). Despite extensive research, the molecular alterations leading to PCNSL have not been fully elucidated. In order to provide a comprehensive description of the genomic and transcriptional landscape of PCNSL, we here performed whole-genome and transcriptome sequencing and integrative analysis of 51 lymphomas presenting in the CNS, including 42 EBV-negative PCNSL, 6 secondary CNS lymphomas (SCNSL) and 3 EBV+ CNSL and matched controls. The results were compared to an independent validation cohort of 31 FFPE CNSL specimens (PCNSL, n = 19; SCNSL, n = 9; EBV+ CNSL, n = 3) and 36 systemic DLBCL cases outside the CNS. This repository contains tab separated value text files: - Radke_et_al_supplementary_somatic_CNVs.tsv (somatic copy number variations predicted by ACEseq) - Radke_et_al_supplementary_somatic_indels.tsv (somatic indels predicted by the DKFZ platypus workflow) - Radke_et_al_supplementary_somatic_indels_exonic.tsv (somatic exonic indels predicted by the DKFZ platypus workflow) - Radke_et_al_supplementary_somatic_mutations_integrated.tsv (table of gene by patients, stating which mutations were observed) - Radke_et_al_supplementary_somatic_mutations_integr_integrated_including_kataegis_counts.tsv (table of gene by patients, stating which mutations were observed, including the count of mutations falling into kataegis hotspots) - Radke_et_al_supplementary_somatic_SNVs.tsv (somatic SNVs predicted by the DKFZ mpileup workflow) - Radke_et_al_supplementary_somatic_SNVs_exonic_functional.tsv (somatic exonic SNVs predicted by the DKFZ mpileup workflow) - Radke_et_al_supplementary_somatic_SNVs_rescued_by_TiNDA (mutations initially classified as germline, but likely tumor mutations based on VAF modelling by TiNDA) - Radke_et_al_supplementary_somatic_SVs.tsv (somatic structural variations predicted by the DKFZ Sophia workflow) - Radke_et_al_supplementary_RNAseq_numReads_CNSLs.tsv (RNAseq read counts calculated by the DKFZ RNAseq workflow) This repository contains the raw unedited images from the manuscript: - Radke_et_al_Main_Figure_1c_BCL6.tif (raw unedited image for Main Figure 1c - BCL6) - Radke_et_al_Main_Figure_1c_CD10.tif (raw unedited image for Main Figure 1c - CD10) - Radke_et_al_Main_Figure_1c_MUM1.tif (raw unedited image for Main Figure 1c - MUM1) - Radke_et_al_Supplementary_Figure_1a_CD20.tif (raw unedited