A quality control program for mutation detection in KIT and PDGFRA in gastrointestinal stromal tumours

Hostein, Isabelle; Dębiec‐Rychter, Maria; Olschwang, Sylvianne; Bringuier, Pierre Paul; Toffolati, Louisa; González, David; Forget, Sébastien; Escande, Fabienne; Morzuch, Lucyna; Tamborini, Elena; Faur, Nicolas; Pilotti, Silvana; Tos, Angelo Paolo Dei; Emile, Jean François; Coindre, Jean Michél

doi:10.1007/s00535-011-0375-0

Cited by 19 publications

(12 citation statements)

References 32 publications

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“…Mutation of KIT exons 9, 11, 13, and 17 and PDGFRA exons 12, 14, and 18 was identified by Sanger sequencing of PCR products, according to the routine protocols available in participating institutions. The institutions, which performed over 95% of mutational analysis, were included in external, international quality control programs (17,18). Mutation nomenclature followed the recommendations of the Human Genome Variation Society (www.hgvs.org).…”

Section: Translational Relevancementioning

confidence: 99%

Tumor Genotype Is an Independent Prognostic Factor in Primary Gastrointestinal Stromal Tumors of Gastric Origin: A European Multicenter Analysis Based on ConticaGIST

Woźniak

Rutkowski

Schöffski

et al. 2014

Clinical Cancer Research

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Purpose: Although the mutational status in gastrointestinal stromal tumors (GIST) can predict the response to treatment with tyrosine kinase inhibitors, the role of tumor genotype as a prognostic factor remains controversial. The ConticaGIST study sought to determine the pathologic and molecular factors associated with disease-free survival (DFS) in patients with operable, imatinib-naive GIST.Experimental Design: Clinicopathologic and molecular data from 1,056 patients with localized GIST who underwent surgery with curative intention (R0/R1) and were registered in the European ConticaGIST database were prospectively obtained and reviewed. Risk of tumor recurrence was stratified using the modified NIH criteria. The median follow-up was 52 months.Results: On testing for potential prognostic parameters, the following were associated with inferior DFS on multivariable Cox model analysis: primary nongastric site, size >10 cm, mitotic index >10 mitoses per 50 high power field, and the KIT exon 9 duplication [hazard ratio (HR), 1.47; 95% confidence interval (CI), 0.9-2.5; P ¼ 0.037] and KIT exon 11 deletions involving codons 557 and/or 558 [KITdel-inc557/558; HR, 1.45; 95% CI, 1.0-2.2; P ¼ 0.004]. Conversely, PDGFRA exon 18 mutations were indicators of better prognosis [HR, 0.23; 95% CI, 0.1-0.6; P ¼ 0.002]. KITdel-inc557/558 were an adverse indicator only in GIST localized in the stomach (P < 0.001) but not in tumors with nongastric origin. In gastric GIST, all other mutations presented remarkably superior 5-year DFS.Conclusions: In conclusion, tumor genotype is an independent molecular prognostic variable associated with gastric GIST and should be used for optimizing tailored adjuvant imatinib treatment.

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Section: Translational Relevancementioning

confidence: 99%

Tumor Genotype Is an Independent Prognostic Factor in Primary Gastrointestinal Stromal Tumors of Gastric Origin: A European Multicenter Analysis Based on ConticaGIST

Woźniak

Rutkowski

Schöffski

et al. 2014

Clinical Cancer Research

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145

112

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“…KIT (exons 9, 11, 13, and 17), PDGFRA (exons 12, 14, and 18), BRAF (exons 11 and 15), and KRAS (exons 2 and 3) genes were analyzed by Direct Sequencing on 3130 (Applied Biosystems or 3500 DX Genetic Analyzer (Applied Biosystems Life Technologies), according to the literature (14)(15)(16)(17). Each sequence reaction was carried out at least twice, starting from independent PCR reactions.…”

Section: Molecular Analysismentioning

confidence: 99%

“…All the procedures in the laboratories of Locarno (Switzerland) and Milan (Italy) are registered in external quality control audits, and the laboratory of Milan participated to quality controls for GIST molecular analyses (14).…”

Section: Molecular Analysismentioning

confidence: 99%

KRAS and BRAF Mutations Predict Primary Resistance to Imatinib in Gastrointestinal Stromal Tumors

Miranda

Nucifora

Molinari

et al. 2012

Clinical Cancer Research

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Purpose: Gastrointestinal stromal tumors (GIST) are characterized by gain-of-function mutations in KIT/ PDGFRA genes leading to a constitutive receptor activation which is well counteracted by imatinib. However, cases in which imatinib as first-line treatment has no effects are reported (primary resistance). Our purpose is to investigate alterations in downstream effectors, not reported so far in mutated GIST, possibly explaining the primary resistance to targeted treatments.Experimental Design: Two independent naive GIST cohorts have been analyzed for KIT, PDGFRA, KRAS, and BRAF mutations by direct sequencing. Cell lines expressing a constitutively activated and imatinibresponding KIT, alone or in combination with activated KRAS and BRAF, were produced and treated with imatinib. KIT receptor and its downstream effectors were analyzed by direct Western blotting.Results: In naive GISTs carrying activating mutations in KIT or PDGFRA a concomitant activating mutation was detected in KRAS (5%) or BRAF (about 2%) genes. In vitro experiments showed that imatinib was able to switch off the mutated receptor KIT but not the downstream signaling triggered by RAS-RAF effectors.Conclusions: These data suggest the activation of mitogen-activated protein kinase pathway as a possible novel mechanism of primary resistance to imatinib in GISTs and could explain the survival curves obtained from several clinical studies where 2% to 4% of patients with GIST treated with imatinib, despite carrying KIT-sensitive mutations, do not respond to the treatment.

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“…A total of 83 (72 %) cases with sufficiently preserved DNA were evaluated for KIT exons 8, 9, 11, 13, and 17, PDGFRA exons 12, 14, and 18, and exon 15 BRAF by polymerase chain reaction (PCR) amplification and direct sequencing as previously described [3,10]. Analysis of a subset of samples for presence of mutations in KIT and PDGFRA was performed in parallel by the Department of Pathology and Molecular Genetics of Treviso Hospital.…”

Section: Mutational Analysismentioning

confidence: 99%

Molecular characterization of an Italian series of sporadic GISTs

et al. 2013

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Purpose Gastrointestinal stromal tumors (GISTs) are mesenchymal tumors of the gastrointestinal tract. Most (80 %) contain activating mutations in the KIT receptor tyrosine kinase, roughly 10 % in platelet-derived growth factor receptor-alpha (PDGFRA). In a small subset, BRAF mutations are an alternative molecular pathway. GISTs respond well to imatinib, but low response is seen in patients with wild-type KIT or PDGFRA. Resistance has also been reported as a result of mutations in downstream effectors such as BRAF. Methods We provide here a molecular characterization of a series of primary GISTs from Italian patients. Of 121 GIST cases diagnosed between 2000 and 2012, 83 were evaluated by PCR amplification and direct sequencing for mutations in KIT exons 8, 9, 11, 13, and 17, PDGFRA exons 12, 14, and 18, and BRAF exon 15. Eighty-one GISTs also underwent K-RAS testing. Results Sixty-four GISTs were positive: 55 had mutations in KIT and 9 in PDGFRA; 16 patients were mutation negative. Three samples came from NF1 patients and were KIT-and PDGFRA negative. Overall, we identified six

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A quality control program for mutation detection in KIT and PDGFRA in gastrointestinal stromal tumours

Abstract: This study demonstrated that such a program was necessary for laboratories to improve the quality of the analysis, because an error rate of 4.5% may have clinical consequences for the patient.

Cited by 19 publications

References 32 publications

Tumor Genotype Is an Independent Prognostic Factor in Primary Gastrointestinal Stromal Tumors of Gastric Origin: A European Multicenter Analysis Based on ConticaGIST

Tumor Genotype Is an Independent Prognostic Factor in Primary Gastrointestinal Stromal Tumors of Gastric Origin: A European Multicenter Analysis Based on ConticaGIST

KRAS and BRAF Mutations Predict Primary Resistance to Imatinib in Gastrointestinal Stromal Tumors

Molecular characterization of an Italian series of sporadic GISTs

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