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Cedars-Sinai Medical Center in Los Angeles, CA has filed a patent for a method for prognosticating patient survival based on the ZEB1 gene.  The application also describes methods for selecting therapies based on analysis of ZEB1 and several other genes.

Human skullGlioblastoma multiform (GBM) is an aggressive and lethal form of brain cancer and represents about 15% of all brain tumors.  Typical treatment includes chemotherapy and radiation after surgery but survival rates are still poor with a median of 15 months.  Advances in genomic research including molecular profiling to divide the cancer into subtypes has increased the understanding of GBM.    

The researchers discovered that loss of ZEB1 and LOH are common in glioblastomas and proceeded to study ZEB1 copy number and its effects on response to therapy and on survival in patients with GBM.  Their initial set of GBM samples were obtained via BioDiscovery’s TCGA Premier product which is a repository of manually curated samples from The Cancer Genome Atlas (TCGA).  TCGA is a great resource for copy number and sequence variant information along with annotations for a number of cancers.  The processed data (referred to as “Level 3” data) is freely available and has been useful in large-scale studies but has a lot more potential.  BioDiscovery has manually curated these samples to improve the quality and usefulness of the data and this data is available as TCGA Premier in conjunction with the Nexus Copy Number software

The researchers used Nexus Copy Number to analyze copy number and LOH of ZEB1 in patient samples run on the Affymetrix CytoScan HD arrays.  They also used Nexus Copy Number for downstream analysis (aggregate analysis and survival curves).  See how you can advance your research with TCGA Premier and Nexus Copy Number.  Learn more about the curated TCGA data via this webinar.