Abstract 6641: Inclusion of INDEL somatic variants in MRD panels improves confidence in ctDNA residual disease detection
Authors: Ravi Patel, Elise Buser, Nafei Xu, Matthew LaBella, Kyle Trettin, Long Tian, Ashley Acevedo, Christopher Battey, Genevieve Gould, Dale Muzzey
Journal: Cancer Research (2025)

Abstract Molecular residual disease (MRD) tests detect residual tumor in a patient by identifying the presence of circulating tumor DNA (ctDNA) in cell free DNA (cfDNA). We have developed a highly sensitive MRD test that utilizes panels of hybridization probes targeting somatic variants specific to each patient’s tumor. Our tumor-informed MRD assay utilizes whole genome sequencing (WGS) of tumor and normal tissue followed by a somatic calling pipeline to identify tumor variants and generate a panel targeting these variants. The sensitivity of bespoke MRD tests, like ours, is a function of each patient’s panel content. A major challenge of ctDNA detection at low tumor concentrations is differentiation of true tumor variants from technical errors. The variants that are most informative for detection of low tumor fraction residual disease are those that are the least likely to occur due to PCR errors or other artifacts during sample preparation. Here we assessed the technical error rates of single nucleotide variants (SNVs) and insertions and deletions (INDELs). In our experiments, many INDELs were less likely to occur due to PCR errors compared to many SNVs, though the error rates of individual variants depended on their genomic context. Several features impacted the error rate of individual INDEL variants in cfDNA including the number of bases inserted or deleted in the INDEL variant and the proximity of the INDEL variant to homopolymer regions. The lower error rate from many INDEL variants resulted in more signal to noise when detecting the presence of the tumor variant. We identified INDEL somatic variants using an ensemble of somatic callers with 99.8% confirmation rate. INDELs were typically less prevalent than SNVs but we observed that INDELs made up as much as 26.4% of a 1000 variant panel. To assess the impact of INDELs on our ability to detect residual tumor, we ran our MRD assay on patients with residual disease. Our detection pipeline was run using a 1000 probe panels that included both INDELs and SNVs or just SNVs alone. INDELs improved the sensitivity of our assay; we observed 60-90%lower error rates for INDELs with more than a single base inserted or deleted compared to SNVs in cfDNA. In conclusion, the likelihood of detecting low abundance ctDNA is higher for panels with INDELs included than for panels without INDELs. Overall, our assay achieved high sensitivity at low tumor concentrations by prioritizing the inclusion of low error rate variants including INDELs in bespoke patient panels. Citation Format: Ravi Patel, Elise Buser, Nafei Xu, Matthew LaBella, Kyle Trettin, Long Tian, Ashley Acevedo, Christopher Battey, Genevieve Gould, Dale Muzzey. Inclusion of INDEL somatic variants in MRD panels improves confidence in ctDNA residual disease detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6641.