R&D PROJECTS

At Amplexa Genetics, we are committed to advancing the field of genetic research by developing and refining sequencing-based methodologies. Our dedication to innovation drives us to explore new scientific frontiers, ensuring precise and groundbreaking interpretations of genetic data.

Our focus is on non-routine, pioneering projects that address specific, field-related research questions.

We use state-of-the-art platforms both within molecular biology (specifically scRNAseq), microbiology, and bioinformatics to facilitate novel biological discoveries and enhance our understanding of disease-causing pathogens in the industry and clinic.

As we continue to expand the scope of our research capabilities, we invite collaboration from both industry and academic partners. If you are interested in discussing potential research collaborations or wish to propose a project, please do not hesitate to contact us.

Read here about current out research projects here.

INDUSTRIAL PhD PROJECTS

Construction of bioinformatic infrastructure for transcriptomic analysis to improve induced pluripotent stem cell systems

In this project we are using computational methods to reform the inadequate attempts to fully mature pluripotent stem cells for clinical use.

Specifically, we are focusing on patients who have suffered from a heart attack. After a heart attack, damaged tissue cannot be regenerated, however, recent advancements in maturating induced pluripotent stem cells (iPSCs) to the functional cells of the heart, cardiomyocytes (CMs), have raised the potential of replacing lost CMs with iPSC-CMs.

The relative immaturity of iPSC-CMs that is a consequence of missing factors in a delicate regulatory network and inappropriate oxygen tension during maturation, is currently a challenge to be solved before the method can be used therapeutically.

The state-of-art technology single cell RNA sequencing (scRNAseq) provides a complete depiction of ongoing processes at single cell level. scRNAseq is being applied to discover critical biological factors present during maturation in order to dissect the missing gap between iPSC-CMs and fully mature, adult CMs.

Discoveries are expected to push maturation of iPSC-CMs towards relevant physiological and therapeutic CMs and to be applicable to other fields of iPSC maturation.

PhD candidate Frederik A. Bjerre

In collaboration with Prof. Ditte C. Andersen at University of Southern Denmark.

Financed by Innovation Fund Denmark.

Development of a single cell RNA sequencing platform for bacteria to delineate antibiotic hetero-resistance

The aim of this project is to demonstrate how the revolutionizing molecular method single cell RNA sequencing (scRNAseq) can be used to describe bacteria displaying so-called heterogenous antibiotic resistance and subsequently identify biomarkers for designing a diagnostic kit.

Heterogeneously resistant bacteria are characterized by subpopulations of cells with different antibiotic resistance levels arising from variability in gene expression. Hence, infections with such heterogeneous populations are associated with increased morbidity and mortality compared to other infections, as this type of resistance is difficult to determine using traditional diagnostic methods, thus emphasizing an urgent need for methods to detect hetero-resistant subpopulations.

We propose to apply scRNAseq to map the molecular patterns behind heterogeneous infections, first by establishing protocols for stabilization of RNA and isolation of single bacterial cells in vitro and next apply this pipeline to clinically isolated cultures.

This will result in commercial establishment of the highly compatible service scRNAseq of bacteria in addition to enable identification of biomarkers for development of diagnostic kits.

The nontrivial application of scRNAseq to bacteria has been demonstrated in E. coli which will be used as proof-of-concept, complemented by the highly clinically relevant S. aureus.

PhD candidate Freja C. Mikkelsen

In collaboration with Prof. Hanne Ingmer at University of Copenhagen.

Financed by Innovation Fund Denmark.

OTHER PROJECTS

sBACseqFOOD

This project will advance the analysis of bacterial growth patterns in an industrial context, ultimately reducing contamination and spoilage. By reforming the technical approach to studying bacterial cultures, we will enable important insight into bacterial growth at a single cell resolution. This will allow access to previously inaccessible knowledge on the growth patterns of pathogenic bacteria in food production chains with potential expansion to other fields. Based on this, we will design a highly sensitive biomarker kit that the food industry can use to detect and prevent bacterial contamination. Our innovative approach will significantly impact public health by reducing contamination.

In collaboration with Prof. Hanne Ingmer at University of Copenhagen and Matìs in Iceland.

Financed by Eurostars

Understanding focal cortical dysplasia: A path to novel treatments

This project seeks to advance understanding and treatment of Focal Cortical Dysplasia (FCD), a major cause of drug-resistant epilepsy linked to mutations in mTOR pathway genes. By examining tissue from epilepsy surgeries, we aim to detect these mutations and explore their presence in circulating DNA in the blood. This study aims at developing new diagnostic tools and treatment options, offering hope for rapid application to clinical practice. Ultimately, this could transform the management of epilepsy, providing relief and new solutions for those affected by this challenging condition.

Press: https://www.kcl.ac.uk/news/1.1-million-nihrmrc-node-mtor-pathway-rare-diseases

In collaboration with Professor Joseph Bateman from the Department of Basic and Clinical Neuroscience (BCN), Professor Deb Pal (BCN), Dr Frances Elmslie (St George's), Dr Laura Mantoan (BCN), and Dr Charlotte Tye (Psychology).

Financed by Epilepsy Research UK and NHS

Enhancing fertility treatment through advanced non-invasive preimplantation genetic testing for aneuploidy (niPGT-A)

This project will introduce a non-invasive method for selecting embryos with the highest potential for successful pregnancy. Currently, embryo selection largely relies on morphological evaluation, which is not a reliable indicator of chromosomal normality. Our approach leverages recent discoveries that fertilized eggs release DNA into their culture medium. By analyzing this DNA with advanced molecular techniques, we can assess the chromosomal makeup of embryos without the need for biopsy. Our innovative non-invasive PGT-A (niPGT-A) could significantly reduce the physical and emotional strain on women undergoing IVF, decrease the need for repeated treatments, and lower overall treatment costs. This method has the potential to improve the IVF success rate by better identifying viable embryos, thus reducing unwanted abortions and the emotional and financial burden associated with repeated IVF cycles. By differentiating DNA origins — whether from the trophoblast (which becomes the placenta) or the inner cell mass (which develops into the embryo) — we anticipate establishing a correlation that enhances our understanding and implementation of niPGT-A. This project not only aims to optimize reproductive outcomes but also addresses social and economic disparities in reproductive health, making IVF more accessible and equitable. If successful, our findings could shift IVF practices globally towards a less invasive, more cost-effective approach, benefiting more clinics and couples facing fertility issues. This could lead to a paradigm shift in how embryos are assessed, significantly impacting the IVF industry by providing a gentler, more affordable, and optimized treatment alternative.

In collaboration with Steen Broch Laursen from IVF-Syd and Marie Louise Grøndahl at Herlev and Gentofte Hospital

Financed by Danish Life Science Cluster Videnbro grant.