Allele-Specific Polymerase Chain Reaction for the Imatinib-Resistant KIT D816V and D816F Mutations in Mastocytosis and Acute Myelogenous Leukemia Christopher.

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Allele-Specific Polymerase Chain Reaction for the Imatinib-Resistant KIT D816V and D816F Mutations in Mastocytosis and Acute Myelogenous Leukemia Christopher L. Corless, Patina Harrell, Mario Lacouture, Troy Bainbridge, Claudia Le, Ken Gatter, Clifton White, Scott Granter, Michael C. Heinrich The Journal of Molecular Diagnostics Volume 8, Issue 5, Pages 604-612 (November 2006) DOI: 10.2353/jmoldx.2006.060089 Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Design of mutant-specific and blocking primers. The mutant-specific primer has a single mismatch (indicated by an asterisk) immediately 5′ to the 2447 T>A substitution that results in D816V but is matched to the mutant A and still allows extension. When bound to the wild-type allele, this primer is doubly mismatched at the 3′ end and makes a poor substrate for extension. The blocking oligonucleotide is designed with a reverse strategy such that it has a double mismatch to the mutant allele. In addition, the 3′ terminal nucleotide of this oligonucleotide is chemically reversed (3′ to 5′) so that it cannot serve as a primer (indicated by the X). The Journal of Molecular Diagnostics 2006 8, 604-612DOI: (10.2353/jmoldx.2006.060089) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Sensitivity of AS-PCR for D816V in paraffin-derived DNA. DNA was extracted from formalin-fixed, paraffin-embedded seminoma heterozygous for KIT D816V (50% mutant allele by denaturing HPLC and direct sequencing) and was diluted with increasing amounts of KIT wild-type DNA from a formalin-fixed, paraffin-embedded GIST before amplification by AS-PCR and detection by HPLC. The Journal of Molecular Diagnostics 2006 8, 604-612DOI: (10.2353/jmoldx.2006.060089) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 AS-PCR of wild-type and mutant KIT cDNAs. cDNA prepared from stably transfected Ba/F3 subclones expressing various isoforms of KIT cDNA was tested by AS-PCR. Positive AS-PCR signals (minimum 2 mV) were obtained from cells expressing D816V or D816F cDNA but not from cells transfected with the wild-type or D816Y forms of KIT. The Journal of Molecular Diagnostics 2006 8, 604-612DOI: (10.2353/jmoldx.2006.060089) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions