Combination of Hotspot Mutations With Methylation and Fragmentomic Profiles to Enhance Multi‐Cancer Early Detection

ABSTRACT Background Multi‐cancer early detection (MCED) through a single blood test significantly advances cancer diagnosis. However, most MCED tests rely on a single type of biomarkers, leading to limited sensitivity, particularly for early‐stage cancers. We previously developed SPOT‐MAS, a multimodal ctDNA‐based assay analyzing methylation and fragmentomic profiles to detect five common cancers. Despite its potential, SPOT‐MAS exhibited moderate sensitivities for early‐stage cancers. This study investigated whether integrating hotspot mutations into SPOT‐MAS could enhance its detection rates. Method A targeted amplicon sequencing approach was developed to profile 700 hotspot mutations in cell‐free DNA and integrated into the SPOT‐MAS assay, creating a single‐blood draw workflow. This workflow, namely SPOT‐MAS Plus was retrospectively validated in a cohort of 255 non‐metastatic cancer patients (breast, colorectal, gastric, liver, and lung) and 304 healthy individuals. Results Hotspot mutations were detected in 131 of 255 (51.4%) cancer patients, with the highest rates in liver cancer (96.5%), followed by colorectal (59.3%) and lung cancer (53.7%). Lower detection rates were found for cancers with low tumor mutational burden, such as breast (31.3%) and gastric (41.9%) cancers. In contrast, SPOT‐MAS demonstrated higher sensitivities for these cancers (51.6% for breast and 62.9% for gastric). The combination of hotspot mutations with SPOT‐MAS predictions improved early‐stage cancer detection, achieving an overall sensitivity of 78.5% at a specificity of 97.7%. Enhanced sensitivities were observed for colorectal (81.36%) and lung cancer (82.9%). Conclusion The integration of genetic and epigenetic alterations into a multimodal assay significantly enhances the early detection of various cancers. Further validation in larger cohorts is necessary to support broader clinical applications.