Cost-effective interrogation of single nucleotide polymorphisms using the mismatch amplification mutation assay and capillary electrophoresis

Erin P. Price, Molly A. Matthews, Jodi A. Beaudry, Jonathan L. Allred, James M. Schupp, Dawn N. Birdsell, Talima R Pearson, Paul S Keim

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

The ability to characterize SNPs is an important aspect of many clinical diagnostic, genetic and evolutionary studies. Here, we designed a multiplexed SNP genotyping method to survey a large number of phylogenetically informative SNPs within the genome of the bacterium Bacillus anthracis. This novel method, CE universal tail mismatch amplification mutation assay (CUMA), allows for PCR multiplexing and automatic scoring of SNP genotypes, thus providing a rapid, economical and higher throughput alternative to more expensive SNP genotyping techniques. CUMA delivered accurate B. anthracis SNP genotyping results and, when multiplexed, saved reagent costs by more than 80% compared with TaqMan real-time PCR. When real-time PCR technology and instrumentation is unavailable or the reagents are cost-prohibitive, CUMA is a powerful alternative for SNP genotyping.

Original languageEnglish (US)
Pages (from-to)3881-3888
Number of pages8
JournalElectrophoresis
Volume31
Issue number23-24
DOIs
StatePublished - Dec 2010

Fingerprint

Capillary electrophoresis
Capillary Electrophoresis
Polymorphism
Single Nucleotide Polymorphism
Amplification
Assays
Nucleotides
Costs and Cost Analysis
Mutation
Bacilli
Multiplexing
Costs
Bacteria
Genes
Bacillus anthracis
Throughput
Real-Time Polymerase Chain Reaction
Genotyping Techniques
Genotype
Genome

Keywords

  • Bacillus anthracis
  • CE
  • CE universal tail mismatch amplification mutation assay
  • Genotyping
  • SNP

ASJC Scopus subject areas

  • Biochemistry
  • Clinical Biochemistry

Cite this

Cost-effective interrogation of single nucleotide polymorphisms using the mismatch amplification mutation assay and capillary electrophoresis. / Price, Erin P.; Matthews, Molly A.; Beaudry, Jodi A.; Allred, Jonathan L.; Schupp, James M.; Birdsell, Dawn N.; Pearson, Talima R; Keim, Paul S.

In: Electrophoresis, Vol. 31, No. 23-24, 12.2010, p. 3881-3888.

Research output: Contribution to journalArticle

Price, Erin P. ; Matthews, Molly A. ; Beaudry, Jodi A. ; Allred, Jonathan L. ; Schupp, James M. ; Birdsell, Dawn N. ; Pearson, Talima R ; Keim, Paul S. / Cost-effective interrogation of single nucleotide polymorphisms using the mismatch amplification mutation assay and capillary electrophoresis. In: Electrophoresis. 2010 ; Vol. 31, No. 23-24. pp. 3881-3888.
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