Ultra-rapid somatic variant detection via real-time targeted amplicon sequencing View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2022-07-15

AUTHORS

Jack Wadden, Brandon S. Newell, Joshua Bugbee, Vishal John, Amy K. Bruzek, Robert P. Dickson, Carl Koschmann, David Blaauw, Satish Narayanasamy, Reetuparna Das

ABSTRACT

Molecular markers are essential for cancer diagnosis, clinical trial enrollment, and some surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform due to time-consuming DNA extraction, targeted amplification, and library preparation times. In this work, we present a proof-of-principle approach for sub-1 hour targeted variant detection using real-time DNA sequencers. By modifying existing protocols, optimizing for diagnostic time-to-result, we demonstrate confirmation of a hot-spot mutation from tumor tissue in ~52 minutes. To further reduce time, we explore rapid, targeted Loop-mediated Isothermal Amplification (LAMP) and design a 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. Using LAMPrey, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes. More... »

PAGES

708

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s42003-022-03657-6

DOI

http://dx.doi.org/10.1038/s42003-022-03657-6

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1149496697

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/35840782


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