Genetic alteration and mutation profiling of circulating cell-free tumor DNA (cfDNA) for diagnosis and targeted therapy of gastrointestinal stromal tumors

Abstract

Gastrointestinal stromal tumors (GISTs) have been recognized as a biologically distinctive type of tumor, different from smooth muscle and neural tumors of the gastrointestinal tract. The identification of genetic aberrations in proto-oncogenes that drive the growth of GISTs is critical for improving the efficacy of cancer therapy by matching targeted drugs to specific mutations. Research into the oncogenic mechanisms of GISTs has found that these tumors frequently contain activating gene mutations in either platelet-derived growth factor receptor A (PDGFRA) or a receptor tyrosine protein associated with a mast cell growth factor receptor encoded by the KIT gene. Mutant cancer subpopulations have the potential to disrupt durable patient responses to molecularly targeted therapy for GISTs, yet the prevalence and size of subpopulations remain largely unexplored. Detection of the cancer subpopulations that harbor low-frequency mutant alleles of target proto-oncogenes through the use of molecular genetic methods, such as polymerase chain reaction (PCR) target amplification technology, is hampered by the high abundance of wild-type alleles, which limit the sensitivity of detection of these minor mutant alleles. This is especially true in the case of mutant tumor DNA derived “driver” and “drug-resistant” alleles that are present in the circulating cell-free tumor DNA (cfDNA) in the peripheral blood circulation of GIST patients. So-called “liquid biopsy” allows for the dynamic monitoring of the patients’ tumor status during treatment using minimally invasive sampling. New methodologies, such as a technology that employs a xenonucleic acid (XNA) clamping probe to block the PCR amplification of wild-type templates, have allowed improved molecular detection of these low-frequency alleles both in tissue biopsy samples and in cfDNA. These new methodologies could be widely applied for minimally invasive molecular testing in the therapeutic management of GISTs.

Diagnosis and Treatment Monitoring of a Patient with Gastrointestinal Stromal Tumor by Next-Generation Sequencing and Droplet Digital Polymerase Chain Reaction Assay of a PDGFRA Mutation in Plasma-Derived Cell-Free Tumor DNA

“…Detection of mutations in patients with GIST using liquid biopsy was reported previously [11][12][13][14][15]. These studies used sequencing as well as polymerase chain reactionbased techniques for detection of mutations in tumor and used the known tumor mutation for monitoring therapy in plasma.…”

eTumorType, An Algorithm of Discriminating Cancer Types for Circulating Tumor Cells or Cell-Free DNAs in Blood

“…However, eTumorType is capable of discriminating cancer types, which is beyond the current studies on CTC or cfDNA data, as the majority of these studies only focused on finding features ( e.g. , CNV, mutation, microRNA, methylation, and gene expression) associated with specific cancer types [25], [26], [27], [28], [29], [30]. To our best knowledge, no such algorithms have been developed so far.…”

Circulating tumor DNA (ctDNA) in the era of personalized cancer therapy

“…This is principally right in the case that in the peripheral blood circulation of GI cancers patients, the mutant form of Bdriver^genes and Bdrug-resistant^alleles of tumor are represented in the circulating cell-free tumor DNA (cfDNA) [95][96][97]. The discriminative accuracy of ctDNA the amount for diagnosis of gastrointestinal cancer contrast to the benign inflammatory diseaseshas been distinguished [98][99][100][101][102].In order to prove the comprehensive diagnostic value of ctDNA through diverse gastrointestinal tumor types, ctDNA of 640 patients evaluated by Bettegowda et al [53].…”

“…Gastric cancer is a leading cause of cancer deaths in the world with highly heterogeneous etiology and clinical characteristics [114]. The Cancer Genome Atlas (TCGA) network shed light on the heterogeneity and possible targeted therapeutics for various subtypes of gastric cancer according to comprehensive genomic platforms [95,115]. The most usual mesenchymal tumors of the gastrointestinal tract are gastrointestinal stromal tumors (GISTs) [116,117].…”