Scientific Reports

The GDC project leaders sought the advice and guidance from leading experts in clinical genomics, bioinformatics, and next generation sequencing technologies.

Comments and suggestions from the expert community that were the impetus behind the development of the GDC standards and pipelines are provided below.

ICGC Pan-cancer analysis of whole genomes: Integration of transcriptome and genome working group (PCAWG-3) 
A presentation from the Broad Institute on the analysis of whole genomes supporting their mission to characterize genomic alterations that lead to transcriptome alterations and contribute to cancer phenotypes. The presentation assisted in the design of the GDC harmonization pipeline for RNA-Seq data.

Overview of the GDC Data Model 
A report from the GDC Data Model Working Group (GDM-WG) providing an overview of the GDC Data Model and associated components.

Selecting Common Cross-Study Clinical Data Elements 
A report from the GDM-WG on the analysis of clinical data elements across studies and the selection of common clinical data elements in support of cross study comparison.

Variant Calling at the GDC
The GDC currently applies multiple somatic variant calling algorithms (or “pipelines”) to DNA-seq data. Rather than choosing a “best call” from among these, the GDC provides users with the mutations output by all pipelines. This report provides an explanation of the rationale for this decision to assist users in the interpretation of GDC variant calls.

MuTect2 Insertion Artifacts
A report describing how the GDC handles calling Indels from samples processed using Whole Genome Amplification (WGA).