Cost-effective interrogation of single nucleotide polymorphisms using the mismatch amplification mutation assay and capillary electrophoresis.
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.
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
Erin P
EP
Price
Molly A
MA
Matthews
Jodi A
JA
Beaudry
Jonathan L
JL
Allred
James M
JM
Schupp
Dawn N
DN
Birdsell
Talima
T
Pearson
Paul
P
Keim
D001408:Bacillus anthracis / Q000235:genetics; D020137:Base Pair Mismatch; D017931:DNA Primers; D019075:Electrophoresis, Capillary / Q000191:economics / Q000379:methods*; D016680:Genome, Bacterial / Q000235:genetics; D005838:Genotype; D008954:Models, Biological; D016133:Polymerase Chain Reaction / Q000191:economics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide
D017931:DNA Primers