Superior Multiplexing Capacity of PlexPrimers Enables Sensitive and Specific Detection of SNPs and Clustered Mutations in qPCR
| Autor: | Alison V. Todd, Tina Lonergan, Elisa Mokany, Samantha Walker, Nicole E. Lima, Lit Yeen Tan |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Gene Identification and Analysis lcsh:Medicine Artificial Gene Amplification and Extension medicine.disease_cause Genetic analysis Polymerase Chain Reaction Biochemistry Multiplexing 0302 clinical medicine Multiplex lcsh:Science Genetics Mutation Multidisciplinary Hydrolysis Chemical Reactions Nucleic acids Chemistry Deletion Mutation Ribosomal RNA 030220 oncology & carcinogenesis Physical Sciences Telecommunications Engineering and Technology Research Article medicine.medical_specialty Cell biology Cellular structures and organelles Single-nucleotide polymorphism Biology Research and Analysis Methods Polymorphism Single Nucleotide Sensitivity and Specificity 03 medical and health sciences Molecular genetics medicine Humans Point Mutation Allele Non-coding RNA Molecular Biology Techniques Gene Mutation Detection Molecular Biology Alleles DNA Primers Point mutation lcsh:R Biology and Life Sciences 030104 developmental biology Genetic Loci RNA lcsh:Q Amplification-Refractory Mutation System Analysis Ribosomes |
| Zdroj: | PLoS ONE, Vol 12, Iss 1, p e0170087 (2017) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | 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. Method 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%. Conclusion 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. |
| Databáze: | OpenAIRE |
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