Automating the Design of Cancer Specific DNA Probes Using Computational Algorithms

Abstract

This paper introduces a novel Python script which automates the design process of cancer variant-specific DNA probes, based on the amplification method LAMP (Loop-Mediated Isothermal Amplification). With just an input of the DNA sequence and the mutation base location, the script outputs suggestions of two best fitting primer sets for a given target, together with an estimated working efficiency. The script also implements a feature of 'script training', using experimentally-validated primers as a benchmark for primer design optimisation. The proposed script has been tested using the gene sequences of ESR1 p.E380Q and ESR1 p.Y537S cancer specific mutations, with the results to closely resemble the experimentally validated primer sets. Creating a rapid LAMP primer design utility allows LAMP to be more easily used as a molecular method for assay development in Lab-on-Chip (LoC) systems to track mutational profiles of variant-specific assays.