BLT Stages

Abstract advanced bachelor of bioinformatics 2019-2020: DEVELOPMENT OF A QC WEB MODULE FOR SEQUENCING 

The Non-Invasive Prenatal Test (NIPT) is a diagnostic test used for the detection of fetal chromosome deviations such as Down syndrome, Edwards syndrome and Patau syndrome through fetal DNA extracted from the mothers blood. Since the beginning of July 2017, the Belgian government compensates the refund of the NIPT for every pregnant woman in Belgium. The refund to the patients is only applicable for tests performed by clinical laboratories that are inspected and approved by BELAC. In order to achieve and maintain an accreditation by BELAC for NIPT, the laboratory needs a detectible quality control system of the process parameters to prove that the used testing equipment is suitable for generating reliable testing results. To provide such quality control system, a database was created to monitor the process parameters throughout each testing run in order to detect and prevent system failures. The database was set with a web application that was specifically programmed for the VeriSeq NIPT by Illumine to achieve a quality control system that is both streamlined and controlled. The core of the web application is a MySQL database with a similar structure as the file structure of the data input and output of the VeriSeq NIPT.

A new SQL table was created for every quality aspect or step in the test which corresponded to the original file. To keep the database up to date with the latest parameters, several Python scripts were created. To achieve a functional web application, PHP was used as backend language for the communication with the database, this combined with HTML and CSS as the frontend languages. Additionally, Javascript was used to increase the functionality and interactivity within the application. 

To monitor the quality of the test runs, graphs were created for each QC-parameter found in the VeriSeq NIPT and were plotted out over a two week time period. The graphs made it possible to create a visual trend analysis and to perform pro-active maintenance on the pipetting robot and sequencers. The visual trend analysis was optimized with a boxplot per sequencer to achieve a visual comparison of the basic descriptive statistics between sequencers for a selected parameter. To achieve the wanted degree of quality control, the statistic comparison between the sequencers should be nearly identical since every runs needs to be performed with a high reliability with minimal process deviations to provide accurate and reproducible test results. This visual representation of the quality parameters made it possible to monitor the quality of the test runs in order to guaranty test results with high reliability as is expected by BELAC.