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Clinical Chemistry 45: 1133-1140, 1999;
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(Clinical Chemistry. 1999;45:1133-1140.)
© 1999 American Association for Clinical Chemistry, Inc.

Articles

Optimal Temperature Selection for Mutation Detection by Denaturing HPLC and Comparison to Single-Stranded Conformation Polymorphism and Heteroduplex Analysis

Alistair C. Jones2, Jehannine Austin1, Nancy Hansen3, Bastiaan Hoogendoorn1, Peter J. Oefner3,1, Jeremy P. Cheadle2 and Michael C. O'Donovan1,a

Divisions of
1 Psychological Medicine and
2 Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff CF4 4XN, UK.
3 Stanford DNA Sequencing and Technology Center, Palo Alto, CA 94304.
a Address correspondence to this author at: Department of Psychological Medicine, University of Wales College of Medicine, Heath Park, Cardiff CF4 4XN, UK. Fax 44 (0)1222 747839; e-mail odonovanmc{at}cardiff.ac.uk

Background: Denaturing HPLC (DHPLC) is a semi-automated method for detecting unknown DNA sequence variants. The sensitivity of the method is dependent on the temperature at which the analysis is undertaken, the selection of which is dependent on operator experience. To circumvent this, software has been developed for predicting the optimal temperature for DHPLC analysis. We examined the utility of this software.

Methods: To maximize the relevance of our data for other investigators, we have screened 42 different amplimers from CFTR, TSC1, and TSC2. The samples consisted of 103 unique sequence heterozygotes and 126 wild-type homozygous controls.

Results: At the temperature recommended by the software, 96% (99 of 103) of heterozygotes and all of the wild-type controls were correctly classified. This compares favorably with sensitivities of 85% for single-stranded conformation polymorphism and 82% for gel-based heteroduplex analyses of the same fragments.

Conclusions: Software-optimized DHPLC is a highly sensitive method for mutation detection. However, where sensitivity >96% is required, our data suggest that in addition to the recommended temperature, fragments should also be run at the recommended temperature plus 2 °C.© 1999 American Association for Clinical Chemistry




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