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Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting
Type of article: Brief
MedED Catalogue Reference: MCC005
MedED Cross Reference: Genomics, Critical Care
Keywords: nanopore, genome sequencing, rapid genetic diagnosis
Sources: NEJM
This article discusses the use of nanopore genome sequencing for rapid genetic diagnosis in critically ill patients. Traditional testing methods for genetic diagnoses take weeks, while rapid testing still requires days. The authors of the study implemented a workflow that combines streamlined nanopore sequencing, cloud-based bioinformatics, and a customized variant-prioritization approach to enable accurate and fast genetic diagnoses.
The study enrolled 12 patients between December 2020 and May 2021 at two hospitals in Stanford, California. They were able to obtain an initial genetic diagnosis in 5 of the patients, with the shortest time from blood sample arrival to the diagnosis being 7 hours and 18 minutes.
The sequencing workflow generated substantial amounts of data per genome, with high alignment identity and autosomal coverage. The researchers called small variants and structural variants after aligning the reads to the human reference genome and implemented a custom filtration and prioritization system to reduce the number of candidate variants for manual review.
Each initial diagnosis was reviewed and confirmed by physicians, leading to informed clinical management for the patients and their family members. The article highlights a specific case of a 3-month-old infant with status epilepticus, where a genetic variant in CSNK2B was identified, leading to a diagnosis of CSNK2B-related disorder. This result facilitated disease-specific counselling, prognostication, and management of epilepsy.
Overall, the study demonstrates the potential of nanopore genome sequencing to provide rapid and accurate genetic diagnoses in critically ill patients, leading to improved clinical management and prognosis.
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