title: Unlabeled oligonucleotides as internal temperature controls for genotyping by amplicon melting.
abstract: Amplicon melting is a closed-tube method for genotyping that does not require probes, real-time analysis, or allele-specific polymerase chain reaction. However, correct differentiation of homozygous mutant and wild-type samples by melting temperature (Tm) requires high-resolution melting and closely controlled reaction conditions. When three different DNA extraction methods were used to isolate DNA from whole blood, amplicon Tm differences of 0.03 to 0.39 degrees C attributable to the extractions were observed. To correct for solution chemistry differences between samples, complementary unlabeled oligonucleotides were included as internal temperature controls to shift and scale the temperature axis of derivative melting plots. This adjustment was applied to a duplex amplicon melting assay for the methylenetetrahydrofolate reductase variants 1298A>C and 677C>T. High- and low-temperature controls bracketing the amplicon melting region decreased the Tm SD within homozygous genotypes by 47 to 82%. The amplicon melting assay was 100% concordant to an adjacent hybridization probe (HybProbe) melting assay when temperature controls were included, whereas a 3% error rate was observed without temperature correction. In conclusion, internal temperature controls increase the accuracy of genotyping by high-resolution amplicon melting and should also improve results on lower resolution instruments.
authors.affiliation: ARUP Institute for Clinical and Experimental, Pathology, Salt Lake City, UT 84108, USA. seippmt@aruplab.com
authors.forename: Michael T
authors.initials: MT
authors.lastname: Seipp
authors.forename: Jacob D
authors.initials: JD
authors.lastname: Durtschi
authors.forename: Michael A
authors.initials: MA
authors.lastname: Liew
authors.forename: Jamie
authors.initials: J
authors.lastname: Williams
authors.forename: Kristy
authors.initials: K
authors.lastname: Damjanovich
authors.forename: Genevieve
authors.initials: G
authors.lastname: Pont-Kingdon
authors.forename: Elaine
authors.initials: E
authors.lastname: Lyon
authors.forename: Karl V
authors.initials: KV
authors.lastname: Voelkerding
authors.forename: Carl T
authors.initials: CT
authors.lastname: Wittwer
mesh_terms: D001483:Base Sequence; D002138:Calibration; D005838:Genotype; D006801:Humans; D042965:Methylenetetrahydrofolate Reductase (NADPH2) / Q000235:genetics; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D015345:Oligonucleotide Probes / Q000032:analysis*; D016133:Polymerase Chain Reaction / Q000379:methods*; D011786:Quality Control; D013696:Temperature; D044366:Transition Temperature
chemical_list: D015345:Oligonucleotide Probes; D042965:Methylenetetrahydrofolate Reductase (NADPH2)