Preliminary clinical validation of a novel integrated genomic and epigenomic liquid biopsy assay (SPIRAL) in breast cancer.

Abstract

e22511 Background: Early detection of breast cancer is critical for improving patient outcomes. Liquid biopsy using circulating free DNA (cfDNA) offers a promising non-invasive approach in early detection. However, in practice, low quantity of cfDNA in blood frequently restrict comprehensive multi-analyte profiling. The SPIRAL platform allows both genomic and DNA methylation sequencing libraries to be prepared from a single low-input cfDNA sample. Here, we report the initial clinical performance of methylation sequencing via SPIRAL platform in differentiating between benign and malignant breast lesions in PERCEIVE-BREAST (NCT06979921) study. Methods: We analyzed plasma from 93 prospectively collected samples from the PERCEIVE-BREAST study, including 78 patients with breast cancer (75 invasive, 3 in situ carcinomas) and 15 with benign diseases. All samples were tested using the SPIRAL platform. The STELLA methylation analysis method was employed to determine sensitivity and specificity. Performance was also analyzed by cancer stage and molecular subtype. Results: For breast cancer detection, the sensitivity was 62% (48/78) and the specificity was 100% (15/15). Sensitivity increased with disease stage: 43% (12/28) in Stage I, 57% (16/28) in Stage II, 92% (12/13) in Stage III, and 100% (6/6) in Stage IV. For Stage 0, the sensitivity was 67% (2/3). By molecular subtype, the sensitivities were 44% (20/45) for HR+/HER2−, 88% (21/24) for HER2+, and 86% (6/7) for triple-negative breast cancer (TNBC). Conclusions: The SPIRAL assay demonstrated high specificity and clinically relevant sensitivity for detecting breast cancer using cfDNA from plasma, with performance improving at more advanced stages. These data support the utility of the SPIRAL platform for multi-modal liquid biopsy. Future work will integrate mutation detection with methylation analysis to evaluate whether this combination improves sensitivity. We also plan to validate these findings in a larger cohort to assess the assay's potential for early detection and prognosis in breast cancer. Clinical trial information: NCT06979921 .