Analysis Overview
Sarcoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1707ZT7
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Analysis Overview for Sarcoma (Primary solid tumor cohort) - 23 September 2013. Broad Institute of MIT and Harvard. doi:10.7908/C1707ZT7
Overview
Introduction

This is an overview of Sarcoma analysis pipelines from Firehose run "23 September 2013".

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 Firehose 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 83 tumor samples used in this analysis: 11 significant arm-level results, 13 significant focal amplifications, and 35 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 8 different clustering approaches and 3 clinical features across 66 patients, one 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 48 focal events and 3 clinical features across 57 patients, 2 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 78 arm-level events and 3 clinical features across 57 patients, 5 significant findings detected with Q value < 0.25.

    • Correlation between gene methylation status and clinical features
      View Report | Testing the association between 19721 genes and 3 clinical features across 54 samples, statistically thresholded by Q value < 0.05, 1 clinical feature related to at least one genes.

    • Correlation between miRseq expression and clinical features
      View Report | Testing the association between 493 genes and 3 clinical features across 66 samples, statistically thresholded by Q value < 0.05, no clinical feature related to at least one genes.

    • Correlation between mRNAseq expression and clinical features
      View Report | Testing the association between 17825 genes and 3 clinical features across 50 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.

  • Clustering Analyses

    • Clustering of copy number data by focal peak region with log2 ratio: consensus NMF
      View Report | The most robust consensus NMF clustering of 83 samples using the 48 copy number focal regions was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

    • Clustering of Methylation: consensus NMF
      View Report | The 13597 most variable methylated genes were selected based on variation. The variation cutoff are set for each tumor type empirically by fitting a bimodal distriution. For genes with multiple methylation probes, we chose the most variable one to represent the gene. Consensus NMF clustering of 83 samples and 13597 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of miRseq mature expression: consensus hierarchical
      View Report | We filtered the data to 238 most variable miRs. Consensus average linkage hierarchical clustering of 97 samples and 238 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of miRseq mature expression: consensus NMF
      View Report | We filtered the data to 238 most variable miRs. Consensus NMF clustering of 97 samples and 238 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of miRseq precursor expression: consensus hierarchical
      View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 97 samples and 150 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of miRseq precursor expression: consensus NMF
      View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 97 samples and 150 miRs identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of mRNAseq gene expression: consensus hierarchical
      View Report | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 75 samples and 1500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of mRNAseq gene expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 75 samples using the 1500 most variable genes was identified for k = 6 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

  • Pathway Analyses

    • PARADIGM pathway analysis of mRNASeq expression and copy number data
      View Report | There were 54 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNASeq expression data
      View Report | There were 56 significant pathways identified in this analysis.

  • Other Correlation Analyses

    • Correlation between copy number variation genes and molecular subtypes
      View Report | Testing the association between copy number variation of 48 peak regions and 8 molecular subtypes across 83 patients, 34 significant findings detected with 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 77 arm-level results and 8 molecular subtypes across 83 patients, 7 significant findings detected with Q value < 0.25.

    • Correlation between mRNA expression and DNA methylation
      View Report | The top 25 correlated methylation probes per gene are displayed. Total number of matched samples = 75. Number of gene expression samples = 75. Number of methylation samples = 83.

    • Correlations between copy number and mRNAseq expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 1167, 2018, 2694.6, 3326, 3942, 4577.2, 5245, 5937, 6759.8, respectively.

Methods & Data
Input

  • Summary Report Date = Mon Oct 21 15:29:21 2013

  • Protection = FALSE

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