Input dataset for CNSistent integration and feature extraction from somatic copy number profiles

Description

The pre-processed input datasets for the article CNSistent integration and feature extraction from somatic copy number profiles

Source Data Accession and Attribution

The data have been obtained from the following sources, accessed in December 2023.

TCGA data obtained from ASCATv3 at: https://github.com/VanLoo-lab/ascat/tree/master/ReleasedDataCite: https://www.pnas.org/doi/full/10.1073/pnas.1009843107The results published here are in part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.

PCAWG data obtained from: https://dcc.icgc.org/releases/PCAWG/consensus_cnv Cite: https://www.nature.com/articles/s41587-019-0055-9

TRACERx data obtained from: https://zenodo.org/records/7649257Cite: https://www.nature.com/articles/s41586-023-05729-x

COSMIC cancer set obtained from: https://cancer.sanger.ac.uk/censusCite: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450507

Human genome gene set obtained using PyENSEMBL (2023). Cite: https://academic.oup.com/nar/article/51/D1/D933/6786199

Cytoband, Gap data obtained from: https://genome.ucsc.edu Cite: https://www.nature.com/articles/35057062

Archive Structure:

Input data for datasets TRACERx (primary only, primary with metastatic, and combined), PCAWG, and TCGA are always a pair copy-number segments, samples.

Gene locations based on COSMIC and ENSEMBL are in bed file format.