Highly Sensitive Detection Method of CXCR4 Tumor Hotspot Mutations by Drop-Off Droplet Digital PCR in Patients with IgM Monoclonal Gammopathies

Abstract

CXCR4 mutations impact disease presentation and treatment outcomes in Waldenström macroglobulinemia. Current techniques used for CXCR4 mutation detection have a number of limitations. The aim of the present study was to develop and analytically validate a novel droplet digital PCR (ddPCR) assay for the simultaneous detection of five of the most common CXCR4 mutations in bone marrow (BM). In silico novel primers and probes designed for simultaneous detection of five hotspot mutations of CXCR4 were first performed. Experimental conditions were optimized, and the assay was analytically validated. The developed assay was further applied in 95 BM samples from patients with IgM gammopathy, 7 BM samples from patients with non-IgM gammopathy and 12 PBMCs from healthy donors, whereas a direct comparison study of Sanger sequencing and allele-specific PCR was performed by using 95 and 39 identical patient tumor DNA samples, respectively. The drop-off ddPCR assay is a robust, cost-effective, highly sensitive, and highly specific screening tool for CXCR4 mutations. Of 95 patients with IgM gammopathy samples, 27 had at least one CXCR4 mutation in their BM samples. With Sanger sequencing, 12 of the 95 samples tested positive, whereas the direct comparison of the developed assay with allele-specific PCR revealed substantial agreement. The clinical performance of the developed assay will be prospectively evaluated in a large number of patients, and the applicability of this assay will be further evaluated.