University of Twente Student Theses


Next Generation Sequencing in the UMC Groningen

Gerritsma, I. (2015) Next Generation Sequencing in the UMC Groningen.

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Abstract:Next-Generation Sequencing is becoming increasingly important in DNA diagnostic laboratories. It is expected that within a few years time nearly all traditional Sanger sequencing will be replaced by NGS. The University Medical Center Groningen (UMCG) has already transitioned most of their DNA testing to NGS. In contrast to Sanger sequencing, NGS methods require longer processing times, stressing the need of efficient planning of all procedures. This report analyses the NGS processes in the diagnostics laboratory of the UMCG, and aims to find scheduling tactics to improve the work flow. A three phase approach is designed to aid this goal. First, a weekly schedule is developed with a Mixed Integer Linear Programming (MILP) model. NGS processes can be started and executed according to this schedule. Then, a Markov Decision Problem (MDP) model finds an optimal policy for selecting NGS processes, according to a certain performance criterion. Finally, different policies are compared using a simulation model. Two policies can be identified as optimal, one for minimising the throughput time of DNA samples, the other for minimising processing costs. However, due to the simplifications made during the modelling process, the current results are not ready for implementation right away. Further research is advised.
Item Type:Essay (Master)
University Medical Center Groningen, Groningen, Netherlands
Faculty:EEMCS: Electrical Engineering, Mathematics and Computer Science
Subject:31 mathematics
Programme:Applied Mathematics MSc (60348)
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