Analysis Overview
Lung Adenocarcinoma (Primary solid tumor)
17 April 2019  |  None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
Overview
Introduction

This is an overview of Lung Adenocarcinoma analysis pipelines from FireCloud run "17 April 2019".

Summary

Note: These results are offered to the community as an additional reference point, enabling a wide range of cancer biologists, clinical investigators, and genome and computational scientists to easily incorporate TCGA into the backdrop of ongoing research. While every effort is made to ensure that FireCloud input data and algorithms are of the highest possible quality, these analyses have not been reviewed by domain experts.

Results

  • Sequence and Copy Number Analyses

    • Analysis of mutagenesis by APOBEC cytidine deaminases (P-MACD).
      View Report | There are 108 tumor samples in this analysis. The Benjamini-Hochberg-corrected p-value for enrichment of the APOBEC mutation signature in 37 samples is <=0.05. Out of these, 25 have enrichment values >2, which implies that in such samples at least 50% of APOBEC signature mutations have been in fact made by APOBEC enzyme(s).

    • Mutation Analysis (MutSig 2CV v3.1 hg38 beta)
      View Report | 

    • Mutation Assessor
      View Report | 

    • Mutation Signature Analysis
      View Report | Our analysis idenfied 1 solution(s) of mutational signatures across 108 samples by BayesNMF method.

    • SNP6 Copy number analysis (GISTIC2)
      View Report | There were 110 tumor samples used in this analysis: 44 significant arm-level results, 27 significant focal amplifications, and 24 significant focal deletions were found.

  • Correlations to Clinical Parameters

    • Correlation between aggregated molecular cancer subtypes and selected clinical features
      View Report | Testing the association between subtypes identified by 2 different clustering approaches and 17 clinical features across 111 patients, 11 significant findings detected with P value < 0.05 and Q value < 0.25.

    • Correlation between APOBEC groups and selected clinical features
      View Report | Testing the association between APOBEC groups identified by 2 different apobec score and 17 clinical features across 108 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

    • Correlation between copy number variation genes (focal events) and selected clinical features
      View Report | Testing the association between copy number variation 51 focal events and 17 clinical features across 110 patients, 86 significant findings detected with Q value < 0.25.

    • Correlation between copy number variations of arm-level result and selected clinical features
      View Report | Testing the association between copy number variation 95 arm-level events and 17 clinical features across 110 patients, 23 significant findings detected with Q value < 0.25.

    • Correlation between gene mutation status and selected clinical features
      View Report | Testing the association between mutation status of 19 genes and 17 clinical features across 108 patients, no significant finding detected with Q value < 0.25.

    • Correlation between mRNAseq expression and clinical features
      View Report | Testing the association between 18099 genes and 17 clinical features across 111 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 13 clinical features related to at least one genes.

  • Clustering Analyses

    • Clustering of lincRNA expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 2500 most variable lincRNAs. Consensus ward linkage hierarchical clustering of 111 samples and 2500 lincRNAs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of Protein-coding gene expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 2500 most variable genes. Consensus ward linkage hierarchical clustering of 111 samples and 2500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

  • Other Analyses

    • Aggregate_Analysis_Features
      View Report | 110 samples and 200 features are included in this feature table. The figures below show which genomic pair events are co-occurring and which are mutually-exclusive.

  • Other Correlation Analyses

    • Correlation between copy number variation genes (focal events) and molecular subtypes
      View Report | Testing the association between copy number variation 51 focal events and 2 molecular subtypes across 110 patients, 31 significant findings detected with P value < 0.05 and Q value < 0.25.

    • Correlation between copy number variations of arm-level result and molecular subtypes
      View Report | Testing the association between copy number variation 95 arm-level events and 2 molecular subtypes across 110 patients, 54 significant findings detected with P value < 0.05 and Q value < 0.25.

    • Correlation between gene mutation status and molecular subtypes
      View Report | Testing the association between mutation status of 19 genes and 2 molecular subtypes across 108 patients, 12 significant findings detected with P value < 0.05 and Q value < 0.25.

Methods & Data
Input

  • Summary Report Date = Tue Jul 9 10:51:22 2019

  • Protection = FALSE

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