Analysis Overview - Breast Invasive Carcinoma (Primary solid tumor)

Analysis Overview

Breast Invasive Carcinoma (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 Breast Invasive Carcinoma 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 1094 tumor samples used in this analysis: 38 significant arm-level results, 24 significant focal amplifications, and 32 significant focal deletions were found.

Correlations to Clinical Parameters

Correlation between copy number variation genes (focal events) and selected clinical features
View Report | Testing the association between copy number variation 56 focal events and 12 clinical features across 1087 patients, 224 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 12 clinical features across 1087 patients, 148 significant findings detected with Q value < 0.25.

Clustering Analyses

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 1084 samples and 2500 lincRNAs identified 5 subtypes with the stability of the clustering increasing for k = 2 to k = 10.
Clustering of miR mature expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 273 most variable miRs. Consensus ward linkage hierarchical clustering of 1076 samples and 273 miRs identified 5 subtypes with the stability of the clustering increasing for k = 2 to k = 10.
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 1084 samples and 2500 genes identified 6 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 747 miRs and 18758 mRNAs across 1065 samples. After 2 filtering steps, the number of 97 miR:gene pairs were detected.
Methylation__HM27_Clustering_CNMF
View Report | The most robust consensus NMF clustering of 313 samples using the 2471 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 781 samples using the 9137 most variable genes 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.
Methylation__HM450_Clustering_Consensus_Plus
View Report | Median absolute deviation (MAD) was used to select 2500 most variable genes. Consensus ward linkage hierarchical clustering of 780 samples and 2500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Methods & Data

Input

Summary Report Date = Thu Dec 14 13:41:01 2017
Protection = FALSE

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