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- W3162945637 abstract "Abstract Molecular markers are becoming increasingly important for cancer diagnosis, proper clinical trial enrollment, and even surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform. In this work, we present Threshold Sequencing, a methodology for designing protocols for targeted variant detection on real-time sequencers with a minimal time to result. Threshold Sequencing analytically identifies a time-optimal threshold to stop target amplification and begin sequencing. To further reduce diagnostic time, we explore targeted Loop-mediated Isothermal Amplification (LAMP) and design a LAMP-specific bioinformatics tool—LAMPrey—to process sequenced LAMP product. LAMPrey’s concatemer aware alignment algorithm is designed to maximize recovery of diagnostically relevant information leading to a more rapid detection versus standard read alignment approaches. Coupled with time-optimized DNA extraction and library preparation, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes." @default.
- W3162945637 created "2021-05-24" @default.
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- W3162945637 date "2021-05-17" @default.
- W3162945637 modified "2023-09-27" @default.
- W3162945637 title "Ultra-Rapid Somatic Variant Detection via Real-Time Threshold Sequencing" @default.
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- W3162945637 doi "https://doi.org/10.1101/2021.05.14.444172" @default.
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