Molecular cytology genotyping of primary and metastatic GI stromal tumors by using a custom two-gene targeted next-generation sequencing panel with therapeutic intent.
OBJECTIVE
In an era of precision medicine, customized genotyping of GI stromal tumors by screening for driver mutations will become the standard of care. The fidelity of genotype concordance between paired cytology smears and surgical pathology specimens is unknown. In patients with either primary or metastatic sporadic disease, we sought to determine the frequency of KIT and PDGFRA pathogenic alterations within such specimens, imatinib sensitivity, and the concordance of pathogenic alterations between paired specimens.


METHODS
DNA obtained from cytology smears from 36 patients, 24 of whom had paired surgical pathology specimens, underwent targeted next-generation sequencing by using a custom panel to evaluate somatic mutations within KIT (exon 2, 9, 10, 11, 13, 14, 15, 17, 18) and PDGFRA (exon 12, 14, 15, 18) genes. Patients with KIT and PDGRFA wild-type genes completed the Qiagen Human Comprehensive Cancer GeneRead DNAseq Targeted Array V2.


RESULTS
Genotyping revealed KIT and PDGFRA mutations in 68% and 15% of patients. The wild-type population did not harbor mutations in BRAF, RAS family, SDHB, SETD2, or NF1. Imatinib sensitivity based on the oncogenic kinase mutation prevalence was estimated to be 68%. Mutational concordance between paired cytology and surgical pathology specimens was 96%.


CONCLUSIONS
Our data have demonstrated the ability to stratify either primary or metastatic gastrointestinal stromal tumors by mutational subtype using a targeted next-generation sequencing 2 gene mutation panel. We highlight the ability to use cytology specimens obtained via minimally invasive techniques as a surrogate to surgical specimens given the high mutational landscape concordance between paired specimens.
Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA.
Ferga C
FC
Gleeson
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
Sarah E
SE
Kerr
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
Benjamin R
BR
Kipp
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
Jesse S
JS
Voss
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
Douglas M
DM
Minot
Division of Biomedical Statics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.
Zheng Jin
ZJ
Tu
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
Michael R
MR
Henry
Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.
George
G
Vasmatzis
Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.
John C
JC
Cheville
Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.
Konstantinos N
KN
Lazaridis
Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA.
Michael J
MJ
Levy
D000970:Antineoplastic Agents / Q000627:therapeutic use; D017024:Chemotherapy, Adjuvant; D020732:Cytogenetic Analysis; D004273:DNA, Neoplasm / Q000032:analysis*; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D061765:Endoscopic Ultrasound-Guided Fine Needle Aspiration; D005770:Gastrointestinal Neoplasms / Q000235:genetics* / Q000473:pathology / Q000628:therapy; D046152:Gastrointestinal Stromal Tumors / Q000235:genetics* / Q000473:pathology / Q000628:therapy; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics; D006801:Humans; D000068877:Imatinib Mesylate / Q000627:therapeutic use; D025542:Neurofibromin 1 / Q000235:genetics; D057285:Precision Medicine; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics*; D015642:Radiology, Interventional; D020796:Receptor, Platelet-Derived Growth Factor alpha / Q000235:genetics*; D013385:Succinate Dehydrogenase / Q000235:genetics; D014057:Tomography, X-Ray Computed; D018631:ras Proteins / Q000235:genetics
D000970:Antineoplastic Agents; D004273:DNA, Neoplasm; D025542:Neurofibromin 1; D000068877:Imatinib Mesylate; C108095:SDHB protein, human; D013385:Succinate Dehydrogenase; D011495:Histone-Lysine N-Methyltransferase; C521636:SETD2 protein, human; D019009:Proto-Oncogene Proteins c-kit; D020796:Receptor, Platelet-Derived Growth Factor alpha; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D018631:ras Proteins