Confirmation of a BRAF mutation-associated gene expression signature in melanoma

Johansson, Peter, Pavey, Sandra and Hayward, Nicholas (2007) Confirmation of a BRAF mutation-associated gene expression signature in melanoma. Pigment Cell and Melanoma Research, 20 3: 216-221. doi:10.1111/j.1600-0749.2007.00375.x


Author Johansson, Peter
Pavey, Sandra
Hayward, Nicholas
Title Confirmation of a BRAF mutation-associated gene expression signature in melanoma
Journal name Pigment Cell and Melanoma Research   Check publisher's open access policy
ISSN 1755-1471
1755-148X
Publication date 2007-06-01
Year available 2007
Sub-type Article (original research)
DOI 10.1111/j.1600-0749.2007.00375.x
Open Access Status Not yet assessed
Volume 20
Issue 3
Start page 216
End page 221
Total pages 6
Editor C.R. Godling
Place of publication Malden, MA, United States
Publisher Wiley-Blackwell Publishing
Language eng
Subject 730108 Cancer and related disorders
C1
321015 Oncology and Carcinogenesis
Abstract Mutations in the BRAF oncogene occur in the majority of melanomas, leading to the activation of the mitogen-activated protein kinase pathway and the transcription of downstream effectors. As BRAF and its effectors could be good melanoma therapy targets, defining the repertoire of genes that are differentially regulated because of BRAF mutational activation is an important objective. Towards this goal, we and others have attempted to determine whether a BRAF mutation-associated gene expression profile exists. Results have been mixed, with some groups reporting a BRAF-signature and another group not. Here we resolve this issue and confirm that while gene-by-gene correlations fail to reveal a specific gene(s) whose expression correlates with BRAF status, a BRAF signature can be distinguished by analysis of global expression patterns. Specifically, we have here applied support vector machine (SVM) analysis to Affymetrix microarray data from a panel of 63 melanoma cell lines. SVMs found a BRAF signature in training samples and predicted BRAF mutation status with high accuracy (AUC = 0.840) in the remaining samples. We verified this is a generalized BRAF signature by repeating the analysis in three published microarray datasets, and again found that SVMs predicted BRAF mutation well (Philadelphia: AUC = 0.788; Zurich: AUC = 0.688; Mannheim: AUC = 0.686). An ensemble of 300 SVMs trained on our data also predicted BRAF mutation status in two of the three published datasets (Philadelphia AUC = 0.778; Zurich AUC = 0.719; Mannheim AUC = 0.564). Taken together, these data support the existence of a BRAF mutation-specific expression signature.
Formatted abstract
Summary
Mutations in the BRAF oncogene occur in the majority of melanomas, leading to the activation of the mitogen-activated protein kinase pathway and the transcription of downstream effectors. As BRAF and its effectors could be good melanoma therapy targets, defining the repertoire of genes that are differentially regulated because of BRAF mutational activation is an important objective. Towards this goal, we and others have attempted to determine whether a BRAF mutation-associated gene expression profile exists. Results have been mixed, with some groups reporting a BRAF-signature and another group not. Here we resolve this issue and confirm that while gene-by-gene correlations fail to reveal a specific gene(s) whose expression correlates with BRAF status, a BRAF signature can be distinguished by analysis of global expression patterns. Specifically, we have here applied support vector machine (SVM) analysis to Affymetrix microarray data from a panel of 63 melanoma cell lines. SVMs found a BRAF signature in training samples and predicted BRAF mutation status with high accuracy (AUC = 0.840) in the remaining samples. We verified this is a generalized BRAF signature by repeating the analysis in three published microarray datasets, and again found that SVMs predicted BRAF mutation well (Philadelphia: AUC = 0.788; Zurich: AUC = 0.688; Mannheim: AUC = 0.686). An ensemble of 300 SVMs trained on our data also predicted BRAF mutation status in two of the three published datasets (Philadelphia AUC = 0.778; Zurich AUC = 0.719; Mannheim AUC = 0.564). Taken together, these data support the existence of a BRAF mutation-specific expression signature.
Keyword BRAF
Expression
Microarray
Mutation
Signature
SVM
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
2008 Higher Education Research Data Collection
School of Medicine Publications
 
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Created: Tue, 29 Apr 2008, 23:06:09 EST by Sarah Elliott on behalf of Medicine - Royal Brisbane and Women's Hospital