General background
Nanopore sequencing is a new generation of DNA sequencing technology. It is only recently been optimized for commercial availability. It is the only sequencing technology that offers real-time analysis (for rapid insights), in fully scalable formats from pocket to population scale, that can analyze native DNA and sequence any length of fragment to achieve short to ultra-long read lengths.
DNA is the genetic code of life, the instructions for building and operating an organism. The total DNA code of an organism, called the genome, controls the synthesis of proteins — the building blocks of organisms. Sequencing can answer a range of biological questions, providing information on species identity, genetic disease risk or how an organism has evolved.
Considering the large amount of data obtained with sequencing of DNA with nanopore it is optimally suited to get a fast overview of the biodiversity in natural samples. Especially for microbes, with have relatively small genomes, it can even lead to a total picture of the composition of entire communities called microbiomes at the species level. This technique called metagenomics can give dep insights in many process such as symbiosis of microbes with plants and animals.
The nanopore technology offers challenges for many disciplines since: · The ethical and societal implications for research are challenging. · In the case of human DNA the legal aspects are still not well defined · The technology is still in development and can be improved. · The large data sets obtained offer challenges for bioinformatic analysis · The implications for biological questions are offering new avenues that still have not been fully explored. · The theoretical implications for modelling has only recently been recognized.
Extraordinary challenges
Nanopore sequencing is still not used in practical training in regular bachelor trajectories.
Teaching will be given by dedicated motivated teachers from many disciplines crossing the borders of teaching programs.
There is a strong link with the Leiden Bioscience Bioscience Park companies that are also involved in the teaching program.
Schedule and practicalities
The program encompasses 5 EC at level 400
It runs In summer, starting end of June to end of August
In includes 6 hours of lectures for teaching of the theoretical background including societal, ethical and legal aspects (snacks will be provided).
Based on the theory the students will write a research proposal for a team of approximately 5 students with a theme of choice of two pages. The proposal should also include societal, ethical and legal aspects of the project. It can also include exploring commercial applications. The project also which will be given feed-back on technical and financial feasibility and graded on content.
Depending on the research proposal it may include 2 weeks of experimental work in the laboratory or in the field in a collaborative project of the teams of students. The project can also be theoretical in which case it may involve data analyses or societal problems to be approached with new technology. The work will be individually supervised per project by a separate teacher for each team. Therefore the practical work will not be the same for each team.
Students are required to write a report (in a scientific note format) presenting a theoretical background based on the lectures that are relevant for this project. In addition they are required to orally present their research plan and findings for a broad public. A certificate for following this course is awarded.
There is priority placement for FWN Honours students
Schedule: · 23 June 18:00 – 19:10 (lecture ‘introduction DNA sequencing/course objectives’) · 25 June 18:00 – 19:10 (lecture ‘nanopore theory and technicalities’) · 27 June 18:00 – 19:10 (lecture ‘biophysics’) · 30 June 18:00 – 19:10 (lecture ‘ethics’) · 2 July 18:00 – 19:10 (lecture ‘symbiosis’) · 4 July 18:00 – 19:10 (lecture ‘commercial use’) · Between 14 July – 27 July (lab-/fieldwork) · 26 August 17:00 – 19:30 (presentations and pizza)
Course objective
After completion of the course the students will be able to:
Understand very basic genetic knowledge
Design a hypothesis driven independent basic research project
Write a report on their own research
Present a thought provoking research project to pears
After completion of the course the students will know:
novel technologies, bioinformatics and societal implications can be applied to formulate hypotheses
How basic life science laboratory experiments are practiced
How to handle and analyze large biological genome datasets
**Application **
Information and application via: Honourscollege@science.leidenuniv.nl. Application deadline is 13 June 2025.
Course coordination: Prof. dr. Herman P. Spaink