Mutation-Enrichment Next-Generation Sequencing for Quantitative Detection of <i>KRAS</i> Mutations in Urine Cell-Free DNA from Patients with Advanced Cancers

Abstract

<b>Purpose:</b> Tumor-derived cell-free DNA (cfDNA) from urine of patients with cancer offers noninvasive biological material for detection of cancer-related molecular abnormalities such as mutations in Exon 2 of <i>KRAS</i><b>Experimental Design:</b> A quantitative, mutation-enrichment next-generation sequencing test for detecting <i>KRAS</i>^G12/G13 mutations in urine cfDNA was developed, and results were compared with clinical testing of archival tumor tissue and plasma cfDNA from patients with advanced cancer.<b>Results:</b> With 90 to 110 mL of urine, the <i>KRAS</i>^G12/G13 cfDNA test had an analytical sensitivity of 0.002% to 0.006% mutant copies in wild-type background. In 71 patients, the concordance between urine cfDNA and tumor was 73% (sensitivity, 63%; specificity, 96%) for all patients and 89% (sensitivity, 80%; specificity, 100%) for patients with urine samples of 90 to 110 mL. Patients had significantly fewer <i>KRAS</i>^G12/G13 copies in urine cfDNA during systemic therapy than at baseline or disease progression (<i>P</i> = 0.002). Compared with no changes or increases in urine cfDNA <i>KRAS</i>^G12/G13 copies during therapy, decreases in these measures were associated with longer median time to treatment failure (<i>P</i> = 0.03).<b>Conclusions:</b> A quantitative, mutation-enrichment next-generation sequencing test for detecting <i>KRAS</i>^G12/G13 mutations in urine cfDNA had good concordance with testing of archival tumor tissue. Changes in mutated urine cfDNA were associated with time to treatment failure. <i>Clin Cancer Res; 23(14); 3657-66. ©2017 AACR</i>.