GxL.TCGA WGS Somatic B37

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GxL.TCGA_WGS_Somatic_B37

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 [[1]] 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.


GxL.TCGA Somatic WGS B37.png


The data was downloaded from https://dcc.icgc.org/repositories/files/FI353263. Consensus calls from PCAWG were used.

Metadata

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 omicsoft.support@qiagen.com 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.