Thursday, December 2, 2010

Article Recommendation: Glioblastoma Subtypes Defined Using Data from TCGA

After reading Verhaak et al. 2010 in Cancer Cell, and I was impressed by this very good study analyzing data from an important resource for genomics research.

The authors were able to define gene signatures to define 4 subtypes of glioblastoma.  The experimental design was pretty straightforward, and the results were quite clear.  Most importantly, their predictive model was trained an a relatively large set of 173 patient samples and validated on an even larger set of 260 patient samples (from 5 independent studies).

The study focused mostly on data provided by The Cancer Genome Atlas (TCGA).  TCGA is a database that contains various types of genomic data (gene/miRNA expression, gene/miRNA copy number, DNA sequence/polymorphism, and DNA methylation), and most or all types of genomic data are available for each patient in the database.  This provides a unique opportunity to integrate many different types of data, usually for a large number of clinical samples.  For anyone not aware of this resource, I would strongly recommend checking out the links provides above as well as the original TCGA paper (also on glioblastoma) published in Nature.
 
Creative Commons License
My Biomedical Informatics Blog by Charles Warden is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 United States License.