Comparison of a highly sensitive, tumor-informed Illumina whole genome sequencing research assay and a tumor-informed bespoke whole exome sequencing assay for molecular residual disease detection in CheckMate-77T (NCT 04025879).

8591 Background: In CheckMate 77T (NCT 04025879), nivolumab showed clinically meaningful improvements in event free survival and pathologic complete response vs placebo in 461 patients with resectable (stage IIA-IIIB) NSCLC. Previously, circulating tumor DNA (ctDNA) clearance rates of 66% in NIVO and 38% in PBO of the neoadjuvant period (C1D1 to definitive surgery) had been reported from 130 patients by Provencio et. al. (LBA50, ESMO 2024). In this study, we aim to extend on the previous exploratory study by using a highly sensitive whole genome sequencing (WGS) minimal residual disease (MRD) assay to detect ctDNA clearance rates and compare to those measured using a tumor-informed whole exome sequencing (WES) MRD assay. Methods: Residual samples (tumor FFPE tissue/isolated DNA, normal, cfDNA) from 61 of the 130 participants previously reported comprised this study. The Illumina WGS MRD assay employs WGS of tumor and matched normal to generate tumor fingerprints which were bioinformatically monitored in plasma using low-pass WGS (lp-WGS). All samples were prepared using Illumina’s WGS Oncology Prep (research use only) and analyzed with DRAGEN MRD pipeline. A comparison of the operational complexity and turn-around-time (TAT) between tumor-informed WES MRD assays and the Illumina WGS MRD assay was performed. Results: Detection rates at C1D1 were greater in this study than previously reported, 91% for WGS vs 86% for WES, supporting the hypothesis that WGS MRD is more sensitive than WES MRD assays. Using the WES MRD results as reference, the Illumina WGS assay demonstrated a high concordance with positive percent agreement of 100%, negative percent agreement of 63% and overall percent agreement of 95%. Clearance rates of ctDNA in both study arms were calculated, summarized and compared to previous results by Provencio et. al. Compared to tumor-informed MRD assays, the Illumina WGS MRD assay significantly reduced operational complexity and TAT, as it eliminated the need for bespoke panel design, including analysis, manufacturing and assay validation. The Illumina Oncology WGS Prep uses a single streamlined workflow for all MRD sample types. The lpWGS testing of plasma cfDNA required only 2-5 ng cfDNA which can be obtained from a single tube of whole blood compared to 2 tubes of whole blood as required for many tumor-informed MRD assays. The total TAT of the WGS MRD workflow, including both tissue and plasma testing, was 1-2 weeks, substantially shorter than the 4-6 weeks required for most tumor-informed MRD assays. Conclusions: This study found the Illumina WGS MRD research assay to be highly concordant with previous tumor-informed WES MRD results for MRD positive results, with improved sensitivity, reduced TAT, lower cfDNA input requirements and decreased operational complexity. Clinical trial information: NCT04025879 .