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Startup Genomic Expression to Contribute to $32M Danish Cancer Research Initiative


By Justin Petrone

Genomic Expression, a 2-year-old technology startup, will use its array-based digital gene-expression platform in a new cancer research initiative in Denmark.

The project, called the Danish Platform for Large-scale Sequencing and Bioinformatics, or DPLSB, was created this month with DKK170 million ($32 million) in funding and is anticipated to last five years.

The Danish National Advanced Technology Foundation contributed about DKK86 million, and a consortium of Danish universities and commercial partners provided the remaining DKK84 million, the firm said.

For its part, New York City--based Genomic Expression will contribute about $2 million to the endeavor and will work with academic partners at the University of Copenhagen, the Technical University of Denmark, Aarhus University, Ålborg University, and the Bavarian Nordic and Beijing Genome Institute Europe to accomplish several research goals.

These include developing vaccines against cancer-causing pathogens and creating an atlas of genetic variation in the Danish population.

It will also deliver both in solution kits and digital arrays to the project's researchers.

The firm's technology platform is "very similar to what is currently done when you perform digital gene expression," CEO Gitte Pedersen said. For instance, similarities include ligation and library-generation steps, the way samples are applied to the arrays, and scanning and analyzing results.

According to Genomic Expression, the initiative will have access to 15 million biological samples along with accompanying data stored in Denmark's electronic medical records system.

Pedersen told BioArray News this week that the firm will benefit from the project not only as a research partner but as the platform provider for any tests that result from the effort. The firm's long-term strategy is to see its platform adopted for clinical use.

"We would never be able to develop cancer prognostics without access to samples and clinical records, not to mention that we have some absolute star researchers in the project," Pedersen said.

She said that Genomic Expression is the initiative's "commercial diagnostic partner," which means that the firm has the option to develop tests based on "all potential diagnostic opportunities" that arise from the project.

"This is a very strategic project for us," said Pedersen. "We will utilize [our] platform going forward to service [our regular] customers … for their companion diagnostic needs, and we will develop prognostics in other therapeutic areas as well."

Digital Array Technology Analysis

Genomic Expression was founded in 2009 when it acquired global rights to IP held by Denmark-based Genomic Expression Aps.

Each member of Genomic Expression's US-based management team has worked in Denmark. Pedersen, for instance, previously worked at Novo Nordisk, while her younger brother Morten Pedersen, Genomic Expression's chief technology officer, was educated at the John F. Kennedy Institute in Glostrup and developed the technology while a postdoc at the University of Copenhagen.

Also, Chief Business Officer Jan Lomholdt formerly was CEO for North America and global vice president of sales and marketing for CLC Bio, a Danish bioinformatics company.

The firm describes its research platform, called Digital Array Technology Analysis, or DATA, as a universal digital microarray-based method to detect and quantify DNA barcodes — short, single-stranded DNA fragments of a fixed length.

The company sells its digital arrays as well as in-solution kits, designed for researchers who work with next-generation sequencing-based approaches.

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According to a poster presented at the Beyond the Genome conference in Boston last year, molecule quantification is performed on Genomic Expression's digital array by ligation of the DNA barcodes to "complementary overhang sequences of partly double-stranded probes at one end of the DNA barcodes," and ligation to the complementary overhang of another probe in solution that is coupled to a fluorochrome at the other end of the DNA barcode.

Genomic Expression's digital arrays or probes in solution are typically used to detect 8-base-pair long DNA barcodes, a product sold as DATA800. The company also sells arrays and in-solution probes designed to detect 10-base-pair long DNA barcodes, a product marketed as DATA1000.

The firm claims the DATA800 product is "well suited for profiling microorganisms based upon differences in their individual 16S RNA sequences," while DATA1000 is "well suited for expression profiling."

Pedersen said that Genomic Expression has previously ordered its arrays from third-party manufacturers, whom she declined to name. However, the company now makes its own arrays.

Pedersen said there are "pros and cons" to using the array or sequencing-based method to read the barcodes. "The choice depends on the objective of the research as well access to different technologies at the site of the researchers," she said. If they chose to use a sequencing-based approach, she said the technology "performs very similar to the existing digital gene expression kits" on the market.

Cancer Vaccines and Genome Mapping

As part of DPLSB, the consortium will build a sequencing and bioinformatics center, the University of Copenhagen said in a statement this week. Thomas Bjørnholm, the university's deputy rector, said the group's vision is to "create a Danish gene-sequencing and bioinformatics facility that will allow us to map Danes' genes, as well as to eventually create a vaccine against cancer."

The universities involved in the project hope that it will lead to partnerships with biotech and pharmaceutical firms in Europe and abroad. For instance, China's BGI Europe facility, headquartered in Copenhagen, will contribute DKK60 million to help establish the facility, the university said.

DPLSB's center will carry out two integrated studies. Eske Willerslev, a researcher at the University of Copenhagen, will lead a project to identify previously unknown pathogens that is designed to help develop and patent commercial vaccines.

In addition, Bavarian Nordic, a biotech company located in northeast Denmark just up the coast from Copenhagen, specializes in developing infectious disease treatments and will have exclusive rights to commercialize any vaccines resulting from the project.

Karsten Kristensen, also affiliated with the University of Copenhagen, will lead a second project aimed at creating a catalogue of genetic variations in the Danish population to serve as a foundation for research into the hereditary causes of diseases and how they can be prevented, the university said.

"The information yielded by the pan-genome will open the door to more ambitious projects that can use the one-of-a-kind database and blood bank to gain valuable insight into Danish DNA and prepare the ground for development of individual treatments and prevention strategies," Kristensen said in a statement.

While the project may at first glance remind some of DeCode Genetics' efforts to use Iceland's biobank to develop genetic tests and therapies, Pedersen said that the projects are not similar.

"The idea behind DeCode was that the population was [homogeneous], reducing the complexity of correlating signals with clinical outcomes," she said. "That is not a premise" for the Danish initiative, she said. "The Danish initiative is leveraging a superior healthcare informatics system, including access to samples, with state-of-the-art genomics tools."

While the academic and commercial partners prepare to create the new center, Pedersen said that Genomic Expression is ramping up manufacturing to provide the consortium with its arrays and kits at no additional cost.

"The next aim is to identify and correlate cancer-causing genetic signals and signatures with clinical outcomes," she said.

But Genomic Expression is also eyeing opportunities beyond cancer diagnostics. "Once we have established the platform, there will be other projects outside cancer for which we will apply for additional funding to perform," Pedersen said.

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