Single molecule-overlapping read analysis for minor variant mutation detection in pathogen samples

US10508311B2 · kind B2 · utility

Assignees

• The Translational Genomics Research Institute · US
• Arizona Board of Regents on Behalf of Northern Arizona University · US
• The Regents of the University of California · US

Inventors

• Rebecca E. Colman · Flagstaff, US
• David Engelthaler · Flagstaff, US
• James M. Schupp · Flagstaff, US
• Paul Keim · Flagstaff, US
• David I. Smith · Royal Oak, US
• Antonino Catanzaro · San Diego, US
• Timothy Rodwell · San Diego, US

Key dates

• Filing date: Aug 26, 2014
• Grant date: Dec 17, 2019
• Expiry date: Jul 15, 2036

Classification

• Technology area (CPC C): Chemistry; Metallurgy
• CPC primary: C12Q2600/156
• WIPO field: Biotechnology
• WIPO sector: Chemistry

Abstract

The present invention provides a method of detecting a heteroresistant population of a pathogen in a sample, the method comprising: a) providing a sample comprising a population of a pathogen; b) extracting nucleic acids from the sample; c) amplifying a target locus of the genome of the pathogen in the extracted nucleic acids, wherein the target locus comprises at least one minor variant associated with drug resistance in the pathogen; d) consecutively sequencing both overlapping nucleic acid strands from a single DNA molecule amplified from the target locus on a Next Generation Sequencing (NGS) platform; e) applying an alignment algorithm to sequencing data from the overlapping nucleic acid strands; and f) performing an analysis of the aligned sequencing data to detect the at least one minor variant and heteroresistant population of the pathogen.