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Systematic biases in reference-based plasma cell-free DNA fragmentomic profiling.

Xiaoyi Liu1, Mengqi Yang2, Dingxue Hu3

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Summary

Cancer liquid biopsies using cell-free DNA (cfDNA) face biases from reference genomes. A new reference-free method, Freefly, offers faster, unbiased cfDNA fragmentomics for reliable cancer diagnosis.

Keywords:
CP: Systems biologycancer diagnosisend motifliquid biopsysize profile

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Area of Science:

  • Genomics
  • Biotechnology
  • Cancer Research

Background:

  • Plasma cell-free DNA (cfDNA) fragmentation patterns are key for cancer liquid biopsy.
  • Current methods rely on reference genome alignment, introducing potential biases.
  • These biases can impact diagnostic assay performance across diverse populations.

Purpose of the Study:

  • To investigate systematic biases in reference-based cfDNA fragmentomics.
  • To develop a novel, reference-free approach for cfDNA fragmentomics profiling.
  • To assess the speed, consistency, and diagnostic utility of the new approach.

Main Methods:

  • Comparative analysis of cfDNA fragmentomics using multiple reference genomes.
  • Development and implementation of Freefly, a reference-free cfDNA analysis tool.
  • Evaluation of Freefly's performance against reference-based methods in terms of speed and consistency.

Main Results:

  • Reference-based cfDNA fragmentomics exhibit systematic biases.
  • Biases are race- and sample-dependent, potentially affecting clinical assay reliability.
  • Freefly demonstrates approximately 60-fold speed improvement over reference-based methods.
  • Freefly generates highly consistent cfDNA fragmentomic features.

Conclusions:

  • Freefly provides a rapid and unbiased method for cfDNA fragmentomics.
  • The approach circumvents analytical biases inherent in reference-based methods.
  • Freefly's fragmentomic features are directly applicable to cancer diagnosis, showing translational merit.