Analysis of relevant planning parameters for a molecular genetic laboratory in a hospital

Abstract

Genetic sequencing technology has advanced significantly in recent decades. This has opened new avenues for clinical applications and thereby increased both the feasibility of genetic testing and the demand for it. The aim of this thesis was to support the planning of a clinical genetics laboratory within a hospital setting.The laboratory was planned around an PromethION 24 nanopore sequencer, utilizing the flexibility of this next generation sequencing technology to increase throughput and accelerate processing of genetic tests. The laboratory workflow from blood sample arrival to reporting of test results was modelled as a discrete event simulation in AnyLogic. The model was designed to account for different test types and their paths through the laboratory. Sequencer flow cells and personnel were both represented as resources to examine their use and potential scarcity.Given the expected quantities of tests the simulation confirmed that most of the performance targets could be fulfilled. The desired average turnaround time of three to four weeks was met with a mean duration of 8.78 days. With 25.56 days, the 95%-quantile was also well below the goal of six weeks. High priority tests of the two core test categories, which should be completed within one week, met this target in 93.9% and 91.7% of cases respectively.Additionally, behaviour under increased load was investigated. This analysis showed the suitability of the intended sequencer even for high test quantities and revealed the potential bottleneck to be staffing levels. Turnaround times increased for all test categories. Starting at a test quantity of 170% of expected levels, this increase was especially pronounced for those categories of low priority tests that needed a barcoding step. Besides barcoding, shared pre-analytic steps and data analysis contributed substantially to increases in turnaround time.