GxL.TCGA WGS Somatic B37
From Array Suite Wiki
The Pan-Cancer Analysis of Whole Genomes (PCAWG) https://docs.icgc.org/pcawg/ brings together whole genome sequencing data from the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) projects. In GxL.TCGA_WGS_Somatic_B37 (TCGA WGS Somatic GeneticsLand), non-coding somatic variant calls from 828 TCGA subjects across 22 Tumor Types are integrated with clinical data elements as well as variant annotations [] to provide biological context. GeneticsLand serves as the main entry point for accessing somatic mutations by their frequencies, patterns of co-occurrence, etc. In addition, these data can be used to explore non-coding somatic variants in the context of gene expression when paired with OmicSoft's OncoLand Introduction_to_TCGA_Land_Content, where coding somatic variants from WES are already provided.
The data was downloaded from https://dcc.icgc.org/repositories/files/FI353263. Consensus calls from PCAWG were used.
Metadata from v1.4 of the ICGC database was used. Additional metadata from GxL.TCGA_B37 was merged with the subjects.
Using the Land
These TCGA data are protected and access requires approved authorization through dbGaP: phs000178. Please contact firstname.lastname@example.org to inquire about the co-application process with QIAGEN.
GeneticsLands can be queried by region, gene(s), and variant(s). Please refer to Using_GeneticsLand for more information on Land usage.