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Alacris Investment Gives Qiagen Access to Modeling Tool for Cancer Biomarker Discovery

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By Uduak Grace Thomas

Qiagen recently announced its intent to purchase a stake in Alacris Theranostics, a startup that has developed a tool that creates in silico models of cancer pathways using next-generation sequence data from patients' cells that can be used to make individualized treatment recommendations.

The agreement gives Qiagen a minority stake in Berlin-based Alacris and an exclusive option to access all biomarkers that are discovered with its modeling technology. Alacris is entitled to royalties from any biomarkers that Qiagen commercializes.

The modeling system, called ModCell, was developed by researchers at the Max Planck Institute for Molecular Genetics and exclusively licensed to Alacris. Hans Lehrach, director of the vertebrate genomics group at MPI-MG and one of Alacris' founders, explained to BioInform that it generates object-oriented models that reflect biological behavior, using as input the patient's normal genomic data as well as the genomic and transcriptomic profiles of the patient's tumor.

Once the models are created, patients and oncologists can select optimal cancer treatments based on individual genomic profiles and researchers in pharmaceutical companies can test the effects of individual drugs as well as combinations of drugs on cancer. Furthermore, drug research and development companies looking to test their treatments can identify patient populations — based on the presence of relevant biomarkers — that would receive the most benefit from their therapies, Lehrach said.

Peer Schatz, Qiagen's CEO, said in a statement that investing in Alacris would expand his company's "existing broad biomarker discovery and validation initiatives" and that the Alacris' technology "complements our strategy very well since it facilitates a clinically relevant selection of molecular targets from vast amounts of genetic and clinical data."

Qiagen plans to use ModCell to identify biomarkers that it can format into real-time PCR-based assay, which it would commercialize within its pharmaceutical development assay portfolio or its TheraScreen molecular diagnostics platform (PCR Insider 01/13/2011).

Lehrach explained that ModCell is able to represent the interactions between biological objects, such as proteins and metabolites, the same way that they would interact in living cells, making its easier to spot abnormalities.

For example, he said, "if you sequence a genome... and find a mutation [in the] RAS gene ... the mutant RAS object [in the model] behaves differently than the normal RAS object in our model."

ModCell captures this biological behavior by generating systems of differential equations that quantitatively describe what happens when, for instance, epidermal growth factor is added to the system or if EGF's concentration changes. However — because reactions often require precise parameters such as specific concentration values — to solve these equations, the system "chooses parameters from probability distributions, which reflect what we know about the levels of the parameters" Lehrach said.

Using the same set of parameters, the tool creates models of all the different possible conditions — such as the interaction of the tumor with different drugs at different concentrations — that the user wants to predict in the patient. Once that’s done, the process is repeated numerous times with different sets of parameters.

After several hundred thousand iterations," we get an impression of how the whole system behaves that is independent of the parameters," Lehrach said, though he acknowledged that "each result is obviously partly determined by the parameters which we have randomly chosen."

Alacris has begun applying its technology as part of an international research project called Treat1000, which includes MPI-MG, Alacris, the Harvard Medical School, Charité University Hospital cancer center in Berlin, and CollabRx. The project, which kicked off in early 2009, aims to sequence the genomes and transcriptomes of 1,000 cancer patients and apply modeling approaches like ModCell to make personalized treatment recommendations.

The company currently relies on sequencers at the MPI-MG, but is looking to acquire its own system, Lehrach said. ModCell can accept data from different types of sequencers, including machines produced by Illumina, Roche, and Life Technologies' Applied Biosystems, and he said that he is involved in negotiations with different suppliers to determine which system his firm will deploy.

Currently, Alacris plans to market its services to oncologists in cancer clinics and pharmaceutical companies but also plans to make the technology directly available to patients in the near future.

Alacris was formally incorporated two years ago and is currently undergoing its first round of financing, Lehrach said. He added that while the firm hasn’t hired any staff, there are several potential employees who are ready to join the company as soon as the funds are available.

He also said that at its inception, the company was dubbed Alacris Pharmaceuticals because its business model at the time was focused on "pharma interactions." About a year ago, the firm was renamed because, according to Lehrach, 'theranostics' — a word that describes the combination of therapy and diagnostics — is a better representation of what the company offers.


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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