Cell-free DNA released from necrotic and/or apoptotic cells may reveal ongoing pathophysiological processes in specific tissues (e.g. adipose tissue) related to the development of important metabolic disorders, such as type 2 diabetes. Usually, a form of next-generation sequencing is needed to capture as much information as possible after extraction of cell-free DNA but this can be an costly endeavour.
Nanopore sequencing is a third-generation DNA/RNA sequencing technology, that utilises genetically engineered pore-forming proteins subjected to an electrical potential. When nucleic acids pass through the pores, each of the four bases produce a specific electrical signal, enabling high-throughput sequencing of e.g. DNA and RNA.
A number of advantages of Nanopore sequencing exists: we can track and monitor sequencing in real-time, we can sequence extremely long reads (>1 Mb) and finally, we can call methylation and base modifications directly from the recorded electrical signals. The smallest Nanopore sequencing instrument is a true in-field device requiring no advanced lab or setup and can be used in remote locations. In many ways, Nanopore (together with PacBio) sequencing are gaining ground in many scientific and diagnostic applications and represents the only serious competitors to the industry standard dominated by Illumina.
The student will gain both wet- and dry lab skills; e.g. learn how to process and work with cell-free DNA from experimental animals (mostly minipigs) and human blood samples and sequence them with Nanopore using the most modern lab facilities in the Mærsk Tower. The student will learn to analyse the high-throughput sequencing data with advanced bioinformatics tools in a highly supportive and friendly environment. Finally, the student will learn more about the use of experimental animals in metabolic disorders, including visits to our partners facilities. The end goal is to explore the vast potential of third-generation sequencing for a “liquid biopsy” test as a new clinical diagnostic or prognostic tool.
The project will be adapted to fit the ECTS needed.