ArticleCell reports methods2024
Systematic biases in reference-based plasma cell-free DNA fragmentomic profiling.
Article in Cell reports methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Epigenomic modifications define chromatin states to regulate cell-free DNA fragmentomics.Nature communications · 2026Article
- Cancer-Like Fragmentomic Characteristics of Somatic Variants in Cell-Free DNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Fragment dispersity index analysis of cfDNA fragments reveals chromatin accessibility and enables early cancer detection.Cell reports methods · 2025Article
- Modulating cell-free DNA biology as the next frontier in liquid biopsies.Trends in cell biology · 2025Review
- Cell-free DNA end characteristics enable accurate and sensitive cancer diagnosis.Cell reports methods · 2024Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plasma cell-free DNA (cfDNA) fragmentation patterns are emerging directions in cancer liquid biopsy with high translational significance. Conventionally, the cfDNA sequencing reads are aligned to a reference genome to extract their fragmentomic features. In this study, through cfDNA fragmentomics profiling using different reference genomes on the same datasets in parallel, we report systematic biases in such conventional reference-based approaches. The biases in cfDNA fragmentomic features vary among races in a sample-dependent manner and therefore might adversely affect the performances of cancer diagnosis assays across multiple clinical centers. In addition, to circumvent the analytical biases, we develop Freefly, a reference-free approach for cfDNA fragmentomics profiling. Freefly runs ∼60-fold faster than the conventional reference-based approach while generating highly consistent results. Moreover, cfDNA fragmentomic features reported by Freefly can be directly used for cancer diagnosis. Hence, Freefly possesses translational merit toward the rapid and unbiased measurement of cfDNA fragmentomics.
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