4.8 Article

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

期刊

NATURE BIOTECHNOLOGY
卷 40, 期 7, 页码 1035-+

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NATURE PORTFOLIO
DOI: 10.1038/s41587-022-01221-5

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资金

  1. Stanford SystemX Alliance
  2. DARPA DSSoC
  3. National Institutes of Health [R01HG010485, U01HG010961, U24HG010262, OT2OD026682, OT3HL142481, U24HG011853]
  4. Stanford University

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This study developed an ultra-rapid nanopore whole-genome sequencing method, which efficiently identified disease-causing variants within a short period of time. The approach included optimized sample preparation, near real-time base calling and alignment, accelerated variant calling, and fast variant filtration. The results demonstrated accurate variant identification and efficient prioritization, significantly reducing the time required for clinical genome sequencing.
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. A streamlined sequencing process enables identification of disease-causing variants in the clinic within 8 hours.

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