title: Impact of mutation type and amplicon characteristics on genetic diversity measures generated using a high-resolution melting diversity assay.
abstract: We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology.
authors.affiliation: Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Matthew M
authors.initials: MM
authors.lastname: Cousins
authors.forename: Deborah
authors.initials: D
authors.lastname: Donnell
authors.forename: Susan H
authors.initials: SH
authors.lastname: Eshleman
mesh_terms: D001482:Base Composition; D004252:DNA Mutational Analysis / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D014644:Genetic Variation; D016679:Genome, Viral; D006678:HIV / Q000235:genetics*; D006801:Humans; D009154:Mutation; D010957:Plasmids; D016133:Polymerase Chain Reaction; D013696:Temperature
chemical_list: D017931:DNA Primers; D004279:DNA, Viral