Genotyping SNPs and Indels: A method to improve the scope and sensitivity of High-Resolution melt (HRM) analysis based applications

Abstract

High-resolution melt (HRM) analysis is a closed-tube technique for detecting single nucleotide polymorphisms (SNPs). However, it has limited use in high-resolution melting devices, even those with high thermal accuracy (HTA). In addition to the cost of switching to these specialized devices, the presence of nearest neighbour neutral changes (class III, IV SNPs and small indels) made HRM-based assays a challenging task due to reduced sensitivity. This study aimed to design a common modified competitive amplification of differently melting amplicons (CADMA)-based assay to address these challenges by generating allele-specific qPCR products that are detectable on most qPCR platforms.

For this study, SNPs were selected from all four classes of SNPs (class I: C/T or G/A mutation; class II: C/A or G/T mutation; class III: G/C mutation; class IV: A/T mutation). A single base pair and 19 bp indels were also chosen to simulate how CADMA primers could be designed for indels of varying lengths. The melting temperatures (Tm) were determined using IDT oligoAnalyzer. qPCR and melt data acquisition were performed on the CFX96 qPCR platform, and the melt curve data were analyzed using Precision Melt software (Bio-Rad, USA). The clusters for different genotypes were successfully identified with the aid of the control samples, and Tm predictions were carried out using the uMelt batch and Tm online tools for comparison.

Using HRM-qPCR assays based on the modified CADMA method, genotyping of various SNPs was successfully carried out. For some SNPs, similarly shaped melt curves were observed for homozygotes and heterozygotes, making shape-based genotype prediction difficult. The Tm values calculated via the Blake and Delcourts (1998) method were the closest to the experimental Tm values after adjusting for the salt concentration.

Since HRM assays usually depend on the ΔTm caused by mutations, they are prone to a high error rate due to nearest neighbour neutral changes. The technique developed in this study significantly reduces the failure rates in HRM-based genotyping and could be applied to any SNP or indel in any platform. It is crucial to have a deep understanding of the melt instrument, its accuracy and the nature of the target (SNP class or indel length and GC content of the flanking region). Furthermore, the availability of controls is essential for a high success rate.