Subject(s)
Critical Care , Nanopore Sequencing/methods , Neurodevelopmental Disorders/diagnosis , Adolescent , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Mutation , Nanopore Sequencing/economics , Neurodevelopmental Disorders/genetics , Sequence Analysis, DNA/methods , Status Epilepticus/geneticsABSTRACT
Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we develop an approach for ultra-rapid nanopore WGS that combines an optimized sample preparation protocol, distributing sequencing over 48 flow cells, near real-time base calling and alignment, accelerated variant calling and fast variant filtration for efficient manual review. Application to two example clinical cases identified a candidate variant in <8 h from sample preparation to variant identification. We show that this framework provides accurate variant calls and efficient prioritization, and accelerates diagnostic clinical genome sequencing twofold compared with previous approaches.