This week, the Journal of Medical Genetics will publish a paper on Rapid Paediatric Sequencing (RaPS), a real-life workflow for rapid diagnosis of critically ill children.
Researchers from UCL have designed RaPS for the growing number of critically ill patients in paediatric intensive care units (PICU) suffering from a rare genetic condition. The clinical decision making process for these patients is complex and often introduces a diagnosis odyssey for the family. Genetic testing has the potential to reduce this complexity and help families to get an early grip on the condition of their child. As a consequence, genetic testing can help to reduce the time spent in PICU, which has a positive financial and capacity impact on the healthcare system as well.
One of the biggest barriers in reaching a genetic diagnosis used to be the unacceptable long turn-around-times of data processing. In practice this means routine genetic testing can take weeks before a diagnosis is reached. Data processing of full genome NGS data alone takes 45 hours per using conventional open-source solutions on the computing facility of UCL. In this specific case a child, father and mother sample must be processed.
In order to reach the target time frame for RaPS, the team implemented the Genalice solution in the workflow. Running on commodity Intel hardware, Genalice was able to drastically reduce the processing of NGS data to 20 minutes per full genome sample. This allowed the team to process a full trio (mother-father-child data) in just one hour. In addition to this acceleration, the Genalice technology delivered a pure observational calling of the genomes which fitted the purpose of finding rare variants perfectly.
Hywel Williams, Senior Research Associate UCL – “This important research shows that this method is cost effective and technically possible within an NHS setting. Sequencing one genome using this approach only costs slightly greater than the cost of spending one day in intensive care. RaPS has the potential to transform care for some of the sickest children not just at GOSH but across the NHS, as well as delivering significant savings by reducing the length of stays in ICU.”
Hans Karten, CTO Genalice – “Working with the UCL team on this project touches the heart of what Genalice is about. We see the demand for acceleration and increased accuracy of NGS data processing in many fields, but it is here where we see immediate life changing impact – helping to diagnose critically ill children in PICU! RaPS is designed to be implemented in a standard NHS diagnostic setting, which means that many more children can benefit from this workflow.”