Highly Accurate Detection of Circulating Tumor DNA for Monitoring Minimal Residual Disease in Solid Tumors: Analytical and Clinical Validation of the Haystack MRD Assay
- Author(s)
- CLARK, M; Prathapam, R; Bramlett, KS; Helfrich-Kröger, A; Sussman, RT; Hwang, HJ; Querfurth, R; Champion, KJ; Holtrup, F; Slavin, TP; Küntzlin-Schierloh, D; Koenig, A; Frame, IJ; Maramica, I; Quinn, H; Kaplan, JB; Mehnert, DH; Sass, C; Cleveland, CL; Elzinga, C; DeGrazia, J; Angeloni, T; Goos-Root, D; Powers, S; Carbonell, JI; Stirzaker, R; Debrincat, MA; Chapman, M; Brown, E; Ryder, M; Gibbs, P; Sloane, HS; Edelstein, D; Tie, J;
- Journal Title
- Journal of Molecular Diagnosis
- Publication Type
- Aug 20
- Abstract
- Advances in cell-free DNA (cfDNA) processing and error-suppressed next-generation sequencing (NGS) have enabled detection of circulating tumor DNA (ctDNA) at low abundance for assessment of minimal residual disease (MRD). MRD testing requires high analytical specificity near the stochastic limit of rare-molecule sampling amid wild-type cfDNA background, i.e., the "needle-in-a-haystack" analytical challenge. This study reports the analytical and clinical validation of Haystack MRD, a tumor-informed ctDNA MRD assay that tracks patient-specific somatic mutations with background-noise suppression architecture to improve discrimination of ctDNA signal from technical and biological interferences. Analytical validation used reference materials and clinical specimens across 23 solid tumor types, followed by clinical validation in stage II-III colorectal cancer (CRC) patients from trial cohorts and real-world evaluation across 27 cancer types. Haystack MRD demonstrated a 95% limit of detection of 0.063 mean ctDNA molecules/mL and an analytical measurement range of 0.25-1,000 mean ctDNA molecules/mL. Concordance of tested samples with expected MRD status yielded 99% agreement (95% CI: 94.2%-99.9%). Quantitative mean ctDNA molecules/mL concentrations were highly concordant with an orthogonal method (R(2)=0.9998; slope=1.053), supporting accuracy and linearity. In early-stage CRC patients, post-treatment MRD status was highly associated with recurrence, demonstrating 100% sensitivity (72.3%-100.0%) and 100% specificity (92.9%-100.0%) at 3-year follow-up, and 83.3% sensitivity (55.2%-97.0%) and 100% specificity (92.6%-100.0%) at 5-year follow-up, outperforming CEA.
- Publisher
- Elsevier
- Research Division(s)
- Personalised Oncology
- PubMed ID
- 42624249
- Publisher's Version
- https://doi.org/10.1016/j.jmoldx.2026.07.006
- Open Access at Publisher's Site
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Creation Date: 2026-08-28 10:52:04
Last Modified: 2026-08-28 10:56:27