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Functional Annotation Of The Non-coding Genome.


Finding The Genetic Variation That Matters.


Annogen is a biotechnology company located in Amsterdam, the Netherlands. We perform functional annotation of the non-coding genome on an unprecedented scale using our unique SuRE technology.

What we do

At Annogen we perform functional annotation of the non-coding genome on an unprecedented scale using our SuRE technology.


Our screening services enable the identification of regulatory DNA elements as well as the mutations in these elements that define traits and diseases in humans, plants and animals.

Nature Publication

This recent publication in Nature Genetics illustrates how the SuRE technology can be used to screen entire genomes or millions of sequence variants to identify non-coding variants that are most likely to play a role in traits or disease.

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The Value of Functional Genome Annotation

Having genome-specific regulatory maps can help identify functional mutations among millions of non-functional ones.


More than 95% of variants associated to traits and diseases are found in the non-coding genome.


Typically the resolution of studies trying to associate genotype with phenotype is in the order of tens of kilobases – far to low to pinpoint the causal variant or mutation.


SuRE can screen entire genomes at a resolution smaller than 300bp for mutations that affect the activity of the 2 main types of regulatory elements: promoters and enhancers


Our novel technology in 2 steps

The SuRE method is in essence a strategy to analyze millions of DNA elements for their activity as promoters or enhancers in a single experiment. By analyzing ~300 million DNA elements of ~300bp length, an entire human genome can be analyzed exhaustively at an approximate 30 fold coverage.

The only required input is DNA and once a SuRE library is established it can analyzed and compared to other DNA sources in the controlled environment of any transfectable cell type. Thus, without the requirement of invasive biopsies, any genome of interest can be analyzed in relevant cell types and under relevant (e.g. stimulatory) conditions.


Library Construction

We first construct a plasmid library containing millions of DNA elements. A human genome is randomly sheared, size-selected and cloned into a plasmid library that contains no promoter of its own. These plasmids contain a unique 20bp sequence referred to as a barcode which allows us to uniquely identify and follow each cloned DNA element. This library is characterized (i.e. barcodes are associated to their respective DNA element) by paired-end sequencing.


barcoded plasmid

Fragmented human genome

0.2 - 2 kb


barcoded plasmid


Plasmid library containing > 300 million DNA elements


Library Expression Profiling

In step 2, the plasmid library is transfected into a cell type of interest. DNA elements containing promoters or enhancers will transcribe the barcode which can now be detected in the RNA by high-throughput sequencing. By comparing these barcode frequencies with the frequencies in the plasmid library, a quantitative map of promoter and enhancer activity can be constructed for the human genome. 

Transfection plasmid library into ~1*10



Quantify expressed barcodes

Quantify all barcodes



Promoter and enhancer activity for entire genome


Introducing our experts

The management team currently consists of two seasoned professionals from the Life Sciences industry with complementary strengths and skillsets.


Recent news



Annogen and KeyGene to collaborate in research on non-coding DNA influencing gene expression

Annogen and KeyGene the Wageningen based research company developing innovative technologies for crop improvement, are to collaborate in identifying non-coding DNA fragments in plants’ genomes that influence the expression of important crop traits. This will open new possibilities to intentionally upregulate or downregulate the expression of important genes in crops.



Annogen incorporated to commercialize SuRE technology for Functional Genome Annotation.

Sister company Gen-X BV has just signed an exclusive deal for use of SuRE for gene therapy with uniQure and consequently, Annogen was incorporated with exclusive rights to commercialize the technology outside the gene therapy field.



February 1, 2020 - Annogen appoints Victor Schut as Chief Business Officer

After supporting sister company Gen-X as CBO in 2019 and following the recent execution of its exclusive deal with Dutch gene therapy company uniQure he will now focus on setting up the spin-off business around the SuRE technology outside the gene therapy field.

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