Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden

TLDR

Sequencing cell‑free DNA in blood offers a minimally invasive means for early cancer diagnosis, treatment monitoring, and disease assessment. The study introduces an integrated genetic/epigenetic liquid‑biopsy pipeline and applies it to 241 deep whole‑genome sequencing profiles from 126 pediatric sarcoma patients to enable analysis of tumors with few genetic aberrations. The authors benchmark fragmentation metrics, develop the LIQUORICE algorithm for chromatin‑signature‑based ctDNA detection, and combine multiple fragmentation features into a machine‑learning classifier tailored to low‑mutation pediatric sarcomas. The approach achieves highly sensitive, mutation‑independent detection and classification of circulating tumor DNA, identifies cfDNA fragmentation patterns as prognostic biomarkers in Ewing sarcoma, and provides a comprehensive, accessible liquid‑biopsy strategy for childhood cancers.

Abstract

Sequencing of cell-free DNA in the blood of cancer patients (liquid biopsy) provides attractive opportunities for early diagnosis, assessment of treatment response, and minimally invasive disease monitoring. To unlock liquid biopsy analysis for pediatric tumors with few genetic aberrations, we introduce an integrated genetic/epigenetic analysis method and demonstrate its utility on 241 deep whole-genome sequencing profiles of 95 patients with Ewing sarcoma and 31 patients with other pediatric sarcomas. Our method achieves sensitive detection and classification of circulating tumor DNA in peripheral blood independent of any genetic alterations. Moreover, we benchmark different metrics for cell-free DNA fragmentation analysis, and we introduce the LIQUORICE algorithm for detecting circulating tumor DNA based on cancer-specific chromatin signatures. Finally, we combine several fragmentation-based metrics into an integrated machine learning classifier for liquid biopsy analysis that exploits widespread epigenetic deregulation and is tailored to cancers with low mutation rates. Clinical associations highlight the potential value of cfDNA fragmentation patterns as prognostic biomarkers in Ewing sarcoma. In summary, our study provides a comprehensive analysis of circulating tumor DNA beyond recurrent genetic aberrations, and it renders the benefits of liquid biopsy more readily accessible for childhood cancers.