Published July 15, 2021 | Version 1.1.0
Dataset Open

The genomic and transcriptional landscape of primary central nervous system lymphoma

Authors/Creators

  • 1. Charité – Universitätsmedizin Berlin, Germany
  • 2. Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Germany
  • 3. German Cancer Research Center (DKFZ), Germany
  • 4. Vivantis Klinikum, Berlin, Germany
  • 5. , Georg-Augusts-University of Göttingen, Germany
  • 6. University Hospital Heidelberg, Heidelberg, Germany
  • 7. ICGC MMML-Seq Consortium
  • 8. Ulm University & Ulm University Medical Center, Germany

Description

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 image for Supplementary Figure 1a - CD20)
- Radke_et_al_Supplementary_Figure_1a_EBV.tif  (raw unedited image for Supplementary Figure 1a - EBV)
- Radke_et_al_Supplementary_Figure_1a_HE_(FFPE).tif  (raw unedited image for Supplementary Figure 1a - HE (FFPE))
- Radke_et_al_Supplementary_Figure_1a_HE_(frozen)_1.tif  (raw unedited image for Supplementary Figure 1a - HE (frozen) 1)
- Radke_et_al_Supplementary_Figure_1a_HE_(frozen)_2.tif  (raw unedited image for Supplementary Figure 1a - HE (frozen) 2)
- Radke_et_al_Supplementary_Figure_1a_HE_(frozen)_3.tif  (raw unedited image for Supplementary Figure 1a - HE (frozen) 3)
- Radke_et_al_Supplementary_Figure_1a_Ki67.tif  (raw unedited image for Supplementary Figure 1a - Ki67)
- Radke_et_al_Supplementary_Figure_1b_EBV_PCR.pptx  (raw unedited image for Supplementary Figure 1b - EBV PCR )
- Radke_et_al_Supplementary_Figure_1c_CDKN2A_FISH_1.jpg  (raw unedited image for Supplementary Figure 1c - CDKN2A FISH 1)
- Radke_et_al_Supplementary_Figure_1c_CDKN2A_FISH_2.jpg  (raw unedited image for Supplementary Figure 1c - CDKN2A FISH 2)
- Radke_et_al_Supplementary_Figure_7h_PD-L1_LS-033.tif  (raw unedited image for Supplementary Figure 7h - PD-L1 LS-033)
- Radke_et_al_Supplementary_Figure_7h_PD-L1_LS-031.tif  (raw unedited image for Supplemnetary Figure 7h - PD-L1 LS-031)

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Radke_et_al_Main_Figure_1c_BCL6.tif

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