Analysis Overview for Thyroid Adenocarcinoma
(other cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This is the analysis overview for Firehose run "18 March 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

- Copy number analysis (GISTIC2)
  View Report | There were 20 tumor samples used in this analysis: 15 significant arm-level results, 0 significant focal amplifications, and 0 significant focal deletions were found.

- Mutation Analysis (MutSig vS2N)
  View Report |

- Clustering Analyses

- Clustering of Methylation: consensus NMF
  View Report | The 7423 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 20 samples and 7423 genes identified 2 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 20 samples and 150 miRs identified 2 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 20 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 molecular subtypes
  View Report | Testing the association between copy number variation 11 arm-level results and 3 molecular subtypes across 20 patients, no significant finding detected with Q value < 0.25.

Methods & Data
Input

- Run Prefix = awg_thca__2013_03_18

- Summary Report Date = Thu Apr 4 15:44:33 2013

- Protection = FALSE

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