Improved Detection of KIT Exon 11 Duplications in Formalin-Fixed, Paraffin-Embedded Gastrointestinal Stromal Tumors Jerzy Lasota, Bartosz Wasag, Sonja.

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Improved Detection of KIT Exon 11 Duplications in Formalin-Fixed, Paraffin-Embedded Gastrointestinal Stromal Tumors Jerzy Lasota, Bartosz Wasag, Sonja E. Steigen, Janusz Limon, Markku Miettinen The Journal of Molecular Diagnostics Volume 9, Issue 1, Pages 89-94 (February 2007) DOI: 10.2353/jmoldx.2007.060104 Copyright © 2007 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Genomic sequences of mutated KIT alleles identified in this study. Part of the genomic and amino acid sequence of WT KIT exon 11 is shown above. Duplicated sequences are boxed. Nomenclature of the mutations identified at the DNA level and deduced mutations at the protein level are shown in the second column. The Journal of Molecular Diagnostics 2007 9, 89-94DOI: (10.2353/jmoldx.2007.060104) Copyright © 2007 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 DHPLC analyses of 271-bp (A), 234-bp (B), and 129-bp (C) PCR products amplified from GISTs 1, 2, and 3. Left and right peaks represent products amplified from WT and mutant KIT alleles, respectively. A: Note the presence of WT and mutant KIT peaks in case 1, no indication of mutation (one WT peak) in case 2, and the lack of PCR amplification products in case 3. B: Note the presence of WT and mutant KIT peaks in case 1 and 2 and no indication of mutation (one WT peak) in case 3. C: Note the presence of WT and mutant KIT peaks in all three cases. The Journal of Molecular Diagnostics 2007 9, 89-94DOI: (10.2353/jmoldx.2007.060104) Copyright © 2007 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Direct sequencing of 234-bp (A and B) and 129-bp (C) PCR products from GIST 2. Note the hardly visible (A) and artificially elevated (B) “tail sequence” of mutant KIT allele. Elevated peaks of mutant KIT allele could not be easily distinguished from the elevated background. C: A shift of sequence detected in 129-bp PCR assay indicating duplication is emphasized by an arrow. WT and mutant KIT allele codons demarcating beginning of duplication are indicated by codon numbers. The Journal of Molecular Diagnostics 2007 9, 89-94DOI: (10.2353/jmoldx.2007.060104) Copyright © 2007 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Direct sequencing of 234-bp (A) and 129-bp (B) PCR products from GIST 3. A: Note the lack of mutant KIT allele sequence in the products from 234-bp PCR assay. B: A shift of sequence detected in 129-bp PCR assay indicating duplication is emphasized by an arrow. WT and mutant KIT allele codons demarcating beginning of duplication are indicated by codon numbers. The Journal of Molecular Diagnostics 2007 9, 89-94DOI: (10.2353/jmoldx.2007.060104) Copyright © 2007 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions