Supplementary Table 2

Sl. no / GIST
Mutation / Gene / Primer sequence
Forward 5’-3’ / Primer sequence
Reverse 5’-3’
1 / KIT exon 9 / MAP1B / tccagagccaaacatcaaga / caacccttccaggatgttgt
2 / PDGFRA / DLK1 / atgctgcggaagaagaagaa / ttgtcacacagcagcacaaa
3 / PDGFRA / PDGFRA / tgatgctttggaagatgcag / acacacacacccacaaatgc

Forward and reverse primer sequence for generating ISH probes. T7 promoter sequence (CTAATACGACTCACTATAGGG) was added to the 5' end of either forward or reverse primer to generate sense or antisense probes.

Array-based comparative genomic hybridization

The same gene set used for expression profiling was used but now printed on Corning glass slides. This gene set represents 24,540 differentUnigene clusters with known chromosomal location. Tumor DNA was isolated from Trizol extracts; tumor DNA and reference DNA were digested with DpnIIbefore further processing. Briefly, 4 µg of tumor DNA was fluorescently labeled(Cy5) in a volume of 50 microliters, mixed with gender-matched reference DNAlabeled with Cy3, and hybridized overnight to the array. Afterwashing, the array slides were scanned on a GenePix Scanner(Axon Instruments) and fluorescence ratios (tumor/normal) calculatedusing GenePix software. Only cDNA spots with a ratio of signalover background of at least 1.4 in the Cy3 channel were includedin further analysis. Chromosomal localization of the mappedgenes was assigned as described previously (Pollack et al., 2002). For CGH data the copy numberfor each locus was based on a moving average of the five nearestcDNA clones centered on that locus (Linn et al., 2004). The amplification and deletions in chromosomes was viewed using caryoscope software (

Reference

Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL and Brown PO. (2002). Proc. Natl. Acad. Sci.,U S A. 99, 12963-12968.

Supplementary Figures legends

Supplementary Figure 1.

(a) Array CGH showing the loss of chromosome 14q region in the KIT exon 11 mutant case. (b) Array CGH showing no loss or gain in 14q region in a PDGFRA mutant case. (c) Expression pattern of DLK1 gene among the GIST mutants.

Supplementary Figure 2: Spot image of the PRKCQ gene expression among the GIST mutants.

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