Published online before print April 26, 2007

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Journal of Molecular Diagnostics 2007, Vol. 9, No. 3
Copyright © 2007 American Society for Investigative Pathology & Association for Molecular Pathology
DOI: 10.2353/jmoldx.2007.060136

Technical Advance

Unlabeled Oligonucleotides as Internal Temperature Controls for Genotyping by Amplicon Melting

Michael T. Seipp^*, Jacob D. Durtschi^*, Michael A. Liew^*, Jamie Williams, Kristy Damjanovich^*, Genevieve Pont-Kingdon^*, Elaine Lyon^*, Karl V. Voelkerding^* and Carl T. Wittwer^*

From the ARUP Institute for Clinical and Experimental Pathology * and ARUP Laboratories, Salt Lake City; and the Department of Pathology, University of Utah Medical School, Salt Lake City, Utah

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 (T_m) requires high-resolution melting and closely controlled reaction conditions. When three different DNA extraction methods were used to isolate DNA from whole blood, amplicon T_m differences of 0.03 to 0.39°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 T_m 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.

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