RT Journal Article SR Electronic T1 Ultra-Rapid Somatic Variant Detection via Real-Time Threshold Sequencing JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.05.14.444172 DO 10.1101/2021.05.14.444172 A1 Jack Wadden A1 Brandon Newell A1 Joshua Bugbee A1 Robert P. Dickson A1 Carl Koschmann A1 David Blaauw A1 Satish Narayanasamy A1 Reetuparna Das YR 2021 UL http://biorxiv.org/content/early/2021/05/17/2021.05.14.444172.abstract AB 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.Competing Interest StatementThe authors have declared no competing interest.