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Clinical Chemistry 0: clinchem.2007.097121v1, 2007; 10.1373/clinchem.2007.097121
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Received on August 31, 2007
Accepted on October 11, 2007

Molecular Diagnostics and Genetics

Quadruplex Genotyping of F5, F2, and MTHFR Variants in a Single Closed Tube by High-Resolution Amplicon Melting

Michael T. Seipp 1*, David Pattison 1, Jacob D. Durtschi 1, Mohamed Jama 1, Karl V. Voelkerding 2, Carl T. Wittwer 3

1 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108
2 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108; Department of Pathology, University of Utah Medical School, 50 N Medical Drive, Salt Lake City, Utah 84132
3 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108; ARUP Laboratories, 500 Chipeta Way, Salt Lake City, Utah 84108; Department of Pathology, University of Utah Medical School, 50 N Medical Drive, Salt Lake City, Utah 84132

* To whom correspondence should be addressed. E-mail: seippmt{at}aruplab.com.

BACKGROUND: Multiplexed amplicon melting is a closed-tube method for genotyping that does not require probes, real-time analysis, asymmetric PCR, or allele-specific PCR; however, correct differentiation of homozygous mutant and wild-type samples by melting temperature (Tm) analysis requires high-resolution melting analysis and controlled reaction conditions.

METHODS: We designed 4 amplicons bracketing the F5 [coagulation factor V (proaccelerin, labile factor)] 1691G>A, MTHFR (NADPH) 1298A>C, MTHFR 677C>T, and F2 [coagulation factor II (thrombin)] 20210G>A gene variants to melt at different temperatures by varying amplicon length and adding GC- or AT-rich 5' tails to selected primers. We used rapid-cycle PCRs with cycles of 19–23 s in the presence of a saturating DNA dye and temperature-correction controls and then conducted a high-resolution melting analysis. Heterozygotes were identified at each locus by curve shape, and homozygous genotypes were assigned by Tm. We blinded samples previously genotyped by other methods before analysis with the multiplex melting assay (n = 110).

RESULTS: All samples were correctly genotyped with the exception of 7 MTHFR 1298 samples with atypical melting profiles that could not be assigned. Sequencing revealed that these 5 heterozygotes and 2 homozygotes contained the unexpected sequence variant MTHFR 1317T>C. The use of temperature-correction controls decreased the Tm SD within homozygotes by a mean of 38%.

CONCLUSION: Rapid-cycle PCR with high-resolution melting analysis allows simple and accurate multiplex genotyping to at least a factor of 4.




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