Analysis Overview for Skin Cutaneous Melanoma (Primary and Metastases)
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)


NOTICE: These results were produced using all sample types (primary and metastases).


Unique Tumor Sample Counts

TumorBCRClinicalCNLowPMethylationmRNAmRNAseqmiRmiRseqRPPAMAF
SKCM28813827510125302470240164253


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Task Dashboard
Overview
Introduction

This is the analysis overview for Firehose run "21 December 2012" in support of the SKCM analysis working group.

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

    • Copy number analysis (GISTIC2)
      View Report | There were 275 tumor samples used in this analysis: 23 significant arm-level results, 23 significant focal amplifications, and 28 significant focal deletions were found.

    • Mutation Analysis (MutSig vS2N)
      View Report | 

  • Clustering Analyses

    • Clustering of copy number data: consensus NMF
      View Report | The most robust consensus NMF clustering of 275 samples using the 51 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 10932 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 255 samples and 10932 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 RPPA data: consensus NMF
      View Report | The most robust consensus NMF clustering of 165 samples using the 150 most variable proteins was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

    • Clustering of RPPA data: consensus hierarchical
      View Report | The 150 most variable proteins were selected. Consensus average linkage hierarchical clustering of 165 samples and 150 proteins 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 249 samples using the 1500 most variable genes 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 mRNAseq gene expression: consensus hierarchical
      View Report | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 249 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 miRseq expression: consensus NMF
      View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 241 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 expression: consensus hierarchical
      View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 241 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.

  • Correlation Analyses

    • Correlation between copy number variations of arm-level result and selected clinical features
      View Report | Testing the association between copy number variation 72 arm-level results and 3 clinical features across 138 patients, no significant finding detected with Q value < 0.25.

    • Correlation between copy number variation genes and selected clinical features
      View Report | Testing the association between copy number variation of 51 peak regions and 3 clinical features across 138 patients, no significant finding detected with Q value < 0.25.

    • Correlation between gene methylation status and clinical features
      View Report | Testing the association between 17147 genes and 3 clinical features across 131 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.

    • Correlation between 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 138 patients, no significant finding detected with P value < 0.05.

    • Correlation between RPPA expression and clinical features
      View Report | Testing the association between 175 genes and 3 clinical features across 99 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 18108 genes and 3 clinical features across 134 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 614 genes and 3 clinical features across 133 samples, statistically thresholded by Q value < 0.05, no clinical feature related to at least one genes.

    • Correlations between copy number and mRNAseq expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 990, 1697, 2241, 2805.8, 3413, 4062.2, 4700, 5395.6, 6173, respectively.

    • Correlation between mRNA expression and DNA methylation
      View Report | The top 25 correlated methylation probes per gene are displayed. Total number of matched samples = 247. Number of gene expression samples = 249. Number of methylation samples = 249.

  • Other Analyses

    • PARADIGM pathway analysis of mRNASeq expression data
      View Report | There were 58 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNASeq expression and copy number data
      View Report | There were 57 significant pathways identified in this analysis.

Methods & Data
Input

  • Run Prefix = awg_skcm__2012_12_21

  • Summary Report Date = Tue Jan 8 12:54:56 2013

  • Protection = FALSE

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