Northern Arizona University

The Translational Genomics Research Institute

University of California

Rebecca E Colman

Paul S Keim

David Engelthaler

James M Schupp

Antonino Catanzaro

Timothy Rodwell

David R Smith

John D Gillece

Nathan Hicks

Antonio Catanzaro

David Smith

David M Engelthaler

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.

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

Some embodiments of the invention include a method of preparing a sample for sequencing that includes receiving a sample and amplifying at least one marker within the sample. In some embodiments, amplification of the first marker may include mixing the sample with a first oligonucleotide that comprises a first universal tail sequence and a second oligonucleotide that comprises a second universal tail sequence. In some aspects of the invention, the first universal tail sequence and the second universal tail sequence are different sequences.

Systems and methods for universal tail-based indexing strategies for amplicon sequencing

Growing community of inventors

Phoenix, AZ, United States of America

Rebecca E Colman