Neuroblastoma evolution
Description
This repository contains datasets to support the manuscript: "Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome " Verena Körber1, Sabine Stainczyk2,3, Roma Kurilov4, Kai-Oliver Henrich2,3, Barbara Hero5, Benedikt Brors4, Frank Westermann2,3* and Thomas Höfer1* 1Division of Theoretical Systems Biology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany 2Hopp Children’s Cancer Center (KiTZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany 3Division of Neuroblastoma Genomics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany 4Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany 5Department of Pediatric Oncology and Hematology, University Children’s Hospital of Cologne, Medical Faculty, Cologne, Germany *Correspondence to: • Frank Westermann, Neuroblastoma Genomics, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; +49 6221 423219; f.westermann@kitz-heidelberg.de • Thomas Höfer, Theoretical Systems Biology, Im Neuenheimer Feld 580, 69120 Heidelberg; +49 6221 421980; t.hoefer@dkfz-heidelberg.de The dataset contains mutation calls (SNVs, Indels, CNVs and SVs) for each patient, stored in the folder "Data". Moreover, it contains the inferred mutational signatures for each sample, stored in the folder "Mutational_signatures". Parameter estimates for the initiation and growth of neuroblastoma tumors can be found in the folder "Processed_data". The file "Sample_sheets.pdf" contains a 1-page summary for each patient in the cohort. Keys to the individual panels are given on the first page.
Files
Steps to reproduce
All scripts necessary to reproduce the analysis can be found, together with an explanation, on https://github.com/hoefer-lab/Neuroblastoma_evolution. Each folder contains data for one tumor. For each tumor, we provide SNVs, Indels, copy number information and SVs as called by the DKFZ inhouse pipelines (https://github.com/DKFZ-ODCF/). Please refer to the manuscript for further information. To reproduce the analysis, download the data, the supplementary tables from the paper and follow the steps described on github.