Allele-specific ligation and recombinase polymerase amplification for the detection of single nucleotide polymorphisms

Abstract A novel multiplex detection of single nucleotide polymorphisms (SNPs), with point-of-care testing as its aim, is reported for supporting pharmacogenetic-based decisions. The strategy relies on allele-specific ligation to discriminate base sequence variations at the SNP site and the extension of generated products by isothermal amplification and recombinase polymerase amplification (RPA). Having demonstrated the assay principle, the variables for the adequate integration of the ligation-amplification process were studied and compared to a conventional PCR approach. One key result was the development of RPA in a universal format using short-length primers, which enabled detection based on selective hybridisation on a barcode-DNA chip and a low-cost optical sensor. As proof of concept, we successfully discriminated genetic variants related to cardiovascular diseases and the adequate prescription of oral anticoagulant antagonists of vitamin K (genes CYP2C9 and VKROC1).