By Julia Karow
Under a partnership announced earlier this month, the Covance Genomics Laboratory and the Institute for Systems Biology, both located in Seattle, will study gene expression regulation in glioblastoma multiforme, an aggressive form of brain cancer.
The project will draw on CGL's expertise in next-generation sequencing and genomics (see Q&A with Tom Turi, this issue) and ISB's experience in analyzing integrated biological networks.
According to Anup Madan, group leader for sequencing technologies at CGL, the partners will initially use RNA-seq to study the transcriptome — including non-coding RNAs — in about 20 tumor samples provided by partners of ISB, and will add more samples in the future as needed. CGL is also developing new techniques for studying methylation, which the researchers plan to add to the study later.
The scientists will then integrate the transcriptome data with existing data for glioblastoma, for example whole-genome sequencing data from the Cancer Genome Atlas.
"There is a need for developing automated platforms by which you take all these complex datasets and pass them through these various pathway analysis programs, which currently don't work on next-gen [sequencing data] very well due to the complexity of the data," Madan told Clinical Sequencing News. "We saw this as a perfect opportunity to work along with ISB to help mine these data and determine causes of glioblastoma multiforme or find biomarkers that can help develop new drugs and help the physicians to stratify patients.
"Through this process, we can learn how we can use the same approach for other diseases in which Covance's clients are interested," he added.
Madan has experience in analyzing gene expression in brain tumors by next-gen sequencing from his time as head of the genomics laboratory at the Center for Advanced Brain Tumor Treatment at the Swedish Medical Center in Seattle (IS 10/21/2008). Prior to that, he headed a DNA sequencing group at ISB.
The collaboration will further be aided by the fact that ISB will move into the same building as CGL in the near future, Madan said.
ISB announced last summer that it would relocate to a new, 140,000 square-foot facility this spring. The facility was formerly the headquarters of Merck subsidiary Rosetta Inpharmatics, which sold its gene expression group to Covance in 2009 to create the CGL.
CGL is part of the Discovery and Translational Services unit of Covance, a provider of drug discovery and development services. It offers a variety of genomics services and assays.
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