Aggregate Analysis Features
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by Hailei Zhang (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Aggregate Analysis Features. Broad Institute of MIT and Harvard. doi:10.7908/C1S181X3
Overview
Introduction

This pipeline attempts to aggregate clinical features and significant genomic events such as copy number alterations, significant mutation genes and molecular subtypes across ALL pipelines in the GDAC Firehose analysis workflow, into a single feature table. Figures of co-occurring and mutually-exclusive pairs for all copy number and mutation events are generated from this feature table using pairwise Fisher's exact test. For more details please visit the online documentation.

Summary

942 samples and 1161 features are included in this feature table. The figures below show which genomic pair events are co-occurring and which are mutually-exclusive.

Results
Feature sample table

Table 1.  Get Full Table Part of feature table : 10 rows and 6 columns are showed below.

tcga_participant_barcode CLI_years_to_birth CLI_vital_status CLI_days_to_death CLI_days_to_last_followup CLI_tumor_tissue_site
TCGA-2K-A9WE 53 0 NA 214 kidney
TCGA-2Z-A9J1 71 0 NA 2298 kidney
TCGA-2Z-A9J2 71 0 NA 1795 kidney
TCGA-2Z-A9J3 67 1 1771 NA kidney
TCGA-2Z-A9J5 80 0 NA 3050 kidney
TCGA-2Z-A9J6 60 0 NA 1731 kidney
TCGA-2Z-A9J7 63 1 139 NA kidney
TCGA-2Z-A9J8 50 0 NA 2790 kidney
TCGA-2Z-A9J9 77 0 NA 2294 kidney
TCGA-2Z-A9JD 66 0 NA 1060 kidney

Figure 1.  Get High-res Image Co-occurring and mutually-exclusive pairs for copy number variations of arm level events. Blue means two events are co-occurring and red means two events are mutually-exclusive.

Figure 2.  Get High-res Image Co-occurring and mutually-exclusive pairs for copy number variations of focal events. Blue means two events are co-occurring and red means two events are mutually-exclusive.

Figure 3.  Get High-res Image Co-occurring and mutually-exclusive pairs for significantly mutated genes. Blue means two events are co-occurring and red means two events are mutually-exclusive.

Figure 4.  Get High-res Image Co-occurring and mutually-exclusive pairs for all copy number and mutation events. Blue means two events are co-occurring and red means two events are mutually-exclusive.

Methods & Data
Input
Description
  • Genelist : this file includes all copy number alteration genes from the copy number pancancer paper and the census genes from Cosmic .

  • Clinical file : *.merged_data.txt from Append_CustomClinical.

  • Clustering file : *.mergedcluster.txt from Aggregate_Molecular_Subtype_Clusters.

  • Copy number file : broad_values_by_arm.txt, *.conf_99.txt and broad_significance_results.txt from CopyNumber_Gistic2.

  • Mutation file : *.maf, *.sig_genes.txt, *.cosmic_sig_genes.txt and patient_counts_and_rates.txt from MutSigRun2.0/CV/2CV.

  • mRNAseq expression file : *.subclassmarkers.txt and *.log2.txt from mRNAseq_Clustering_CNMF and mRNAseq_Preprocess.

Output

A detailed description of the output files :

  • Clinical features : start with CLI_ followed by clinical feature name ex: CLI_age.

  • Clustering results : start with CLUS_ followed by platform_method ex: CLUS_mRNAseq_cHierarchical.

  • Somatic mutation genes : start with SMG_ followed by version number( mutsig2.0,cv,2cv)_gene name ex: SMG_mutsig.2CV_FAM47C.

  • Somatic mutation genes expression : start wit SMG_ followed by gene name_mRNA ex: SMG_KRT3_mRNA.

  • Marker genes in each mRNAseq clustering subtype : star with mRNA_ followed by CNMF_gene name_difference_cluster number ex: mRNA_CNMF_FAM66E_.0.6_2 (In each cluster, the top 5 up regulated and top 5 down regulated genes were selected).

  • Copy number alterations :

    • Copy number focal events : start with Amp_/Del_ followed by cytoband name ex: Amp_1q32.1/Del_1p36.32.

    • Copy number arm level events : start with CN_ followed by arm_Amp/Del ex: CN_10p_Amp/CN_10p_Del.

    • Copy number alterative gene with expression: start with Amp/Del_ followed by gene name, cytoband names which contains this alterative gene and _mRNA ex: Amp_SOX2_3q26.32_mRNA/Del_PARK2_6q24.3_mRNA.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Travis I Zack, Steven E Schumacher ..., Pan-cancer patterns of somatic copy number alteration, Nature Genetics 45:1134 (2013)