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

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

doi:10.1038/s42003-022-03657-6

Communications Biology (Jul 2022)

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

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

Affiliations

Jack Wadden: Department of Electrical Engineering and Computer Science, University of Michigan
Brandon S. Newell: Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan
Joshua Bugbee: Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan
Vishal John: Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan School of Medicine
Amy K. Bruzek: Department of Neurosurgery, University of Michigan School of Medicine
Robert P. Dickson: Division of Pulmonary and Critical Care, Department of Internal Medicine, University of Michigan School of Medicine
Carl Koschmann: Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan School of Medicine
David Blaauw: Department of Electrical Engineering and Computer Science, University of Michigan
Satish Narayanasamy: Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan
Reetuparna Das: Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan

DOI: https://doi.org/10.1038/s42003-022-03657-6
Journal volume & issue: Vol. 5, no. 1
pp. 1 – 12

Abstract

Read online

A method for detection of somatic variants is presented for the intraoperative evaluation of tumor mutations in less than 30 min, using rapid DNA extraction, in silico optimized LAMP amplification, and a LAMP product analysis tool: LAMPrey.

Published in Communications Biology

ISSN: 2399-3642 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General)
Website: https://www.nature.com/commsbio/

About the journal