title: Superior Multiplexing Capacity of PlexPrimers Enables Sensitive and Specific Detection of SNPs and Clustered Mutations in qPCR.
abstract: BACKGROUND
  Whilst qPCR provides an extremely powerful tool for genetic analysis, some applications such as multiplexing variant alleles (eg SNPs, point mutations or deletions), remain challenging using current primer/probe systems. The novel design features of PlexPrimers allow sensitive, multiplexed analysis of variant alleles even when these are tightly clustered.
  
  
  METHODS
  PlexPrimers were combined with PlexZymes in qPCR assays for the detection of SNPs in human absorption, distribution, metabolism, and excretion (ADME) genes; clustered mutations in the 23S rRNA gene which confer antibiotic resistance to Mycoplasma genitalium; and deletions within the human epidermal growth factor receptor (EGFR) gene.
  
  
  RESULTS
  The combination of PlexPrimers and PlexZymes allowed robust multiplexing of targets which resulted in 100% concordance with results obtained using hydrolysis probe kits for 14 SNPs in the ADME genes. A 7-plex qPCR assay targeting M. genitalium, 5 clustered mutations associated with macrolide resistance and an internal control, allowed efficient amplification of all targets, with all 5 mutations detected in a single channel. Finally, the strategy was employed to analyse common EGFR mutants with high sensitivity, detecting deletions present at only 0.01%.
  
  
  CONCLUSIONS
  PlexPrime is a novel technology for the detection of genetic variants. Unlike previous strategies, the combination of PlexPrimers with PlexZymes enables both allele-specific detection and allele-specific amplification in qPCR. The study demonstrated highly sensitive and specific detection of mutations and SNPs, and superior multiplexing capacity. The ability to multiplex clustered genetic variants reduces the time to result providing more actionable information.
authors.affiliation: SpeeDx Pty Ltd, Eveleigh, NSW, Australia.
authors.forename: Lit Yeen
authors.initials: LY
authors.lastname: Tan
authors.affiliation: SpeeDx Pty Ltd, Eveleigh, NSW, Australia.
authors.forename: Samantha Michelle
authors.initials: SM
authors.lastname: Walker
authors.affiliation: SpeeDx Pty Ltd, Eveleigh, NSW, Australia.
authors.forename: Tina
authors.initials: T
authors.lastname: Lonergan
authors.affiliation: SpeeDx Pty Ltd, Eveleigh, NSW, Australia.
authors.forename: Nicole Elizabeth
authors.initials: NE
authors.lastname: Lima
authors.affiliation: SpeeDx Pty Ltd, Eveleigh, NSW, Australia.
authors.forename: Alison Velyian
authors.initials: AV
authors.lastname: Todd
authors.affiliation: SpeeDx Pty Ltd, Eveleigh, NSW, Australia.
authors.forename: Elisa
authors.identifier: http://orcid.org/0000-0002-6380-9662
authors.initials: E
authors.lastname: Mokany
mesh_terms: D017931:DNA Primers; D006801:Humans; D009154:Mutation; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity
chemical_list: D017931:DNA Primers