Analysis Overview
Lung Adenocarcinoma (Primary solid tumor)
17 October 2017  |  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 October 2017".

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

    • SNP6 Copy number analysis (GISTIC2)
      View Report | There were 518 tumor samples used in this analysis: 33 significant arm-level results, 27 significant focal amplifications, and 36 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 9 different clustering approaches and 15 clinical features across 519 patients, 51 significant findings 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 63 focal events and 15 clinical features across 517 patients, 22 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 82 arm-level events and 15 clinical features across 517 patients, 4 significant findings detected with Q value < 0.25.

  • Clustering Analyses

    • Clustering of copy number data by focal peak region with absolute value: consensus NMF
      View Report | The most robust consensus NMF clustering of 517 samples using the 63 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of copy number data by peak region with threshold value: consensus NMF
      View Report | The most robust consensus NMF clustering of 517 samples using the 63 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • 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 512 samples and 2500 lincRNAs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of lincRNA expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 513 samples using the 2500 most variable lincRNAs was identified for k = 7 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of miR mature expression: consensus hierarchical
      View Report | Median absolute deviation (MAD) was used to select 288 most variable miRs. Consensus ward linkage hierarchical clustering of 512 samples and 288 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

    • Clustering of miR mature expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 513 samples using the 288 most variable miRs was identified for k = 5 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Clustering of protein coding gene expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 513 samples using the 2500 most variable genes was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • 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 512 samples and 2500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

  • Other Analyses

    • Identification of putative miR direct targets by sequencing data
      View Report | The CLR algorithm was applied on 780 miRs and 18785 mRNAs across 507 samples. After 2 filtering steps, the number of 175 miR:gene pairs were detected.

    • Methylation__HM27_Clustering_CNMF
      View Report | The most robust consensus NMF clustering of 126 samples using the 1281 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

    • Methylation__HM450_Clustering_CNMF
      View Report | The most robust consensus NMF clustering of 457 samples using the 1926 most variable genes was identified for k = 6 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

  • Other Correlation Analyses

    • Correlation between copy number variation genes (focal events) and molecular subtypes
      View Report | Testing the association between copy number variation 63 focal events and 9 molecular subtypes across 517 patients, 459 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 82 arm-level events and 9 molecular subtypes across 517 patients, 437 significant findings detected with P value < 0.05 and Q value < 0.25.

Methods & Data
Input

  • Summary Report Date = Thu Dec 14 13:59:27 2017

  • Protection = FALSE

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