Analysis Overview
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1F47MFD
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 Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor cohort) - 23 September 2013. Broad Institute of MIT and Harvard. doi:10.7908/C1F47MFD
Overview
Introduction

This is an overview of Lymphoid Neoplasm Diffuse Large B-cell Lymphoma 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 18 tumor samples used in this analysis: 8 significant arm-level results, 1 significant focal amplifications, and 12 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 'METHLYATION CNMF' and 3 clinical features across 16 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 9 focal events and 3 clinical features across 16 patients, no significant finding 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 9 arm-level events and 3 clinical features across 16 patients, no significant finding detected with Q value < 0.25.

- Clustering Analyses

- Clustering of Methylation: consensus NMF
  View Report | The 16037 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 18 samples and 16037 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.

- Other Correlation Analyses

- Correlation between copy number variation genes and molecular subtypes
  View Report | Testing the association between copy number variation of 9 peak regions and molecular subtype 'METHLYATION_CNMF' across 18 patients, one significant finding 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 7 arm-level results and molecular subtype 'METHLYATION_CNMF' across 18 patients, no significant finding detected with Q value < 0.25.

Methods & Data
Input

- Summary Report Date = Mon Oct 21 14:49:13 2013

- Protection = FALSE

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