Related Experiment Video
Updated: May 17, 2025
10:36
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
11.9K
Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA
Alexandre Pellan Cheng1,2,3,4, Adam J Widman5,6, Anushri Arora5,7
1New York Genome Center, New York, NY, USA. alexandre.cheng@etsmtl.ca.
Nature Methods
|April 11, 2025
Summary
This study introduces a low-cost, deep whole-genome sequencing (WGS) method for detecting circulating tumor DNA. The duplex error-corrected WGS achieves ultra-low error rates, enabling precise disease monitoring without tumor samples.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- Distinguishing sequencing errors from true genetic variants is a critical challenge in genomics.
- Circulating cell-free DNA (ccfDNA) sequencing for cancer monitoring faces limitations due to low circulating tumor DNA abundance, high background genomic material, and preanalytical errors.
- Whole-genome sequencing (WGS) can enhance sensitivity by integrating signals across the genome, but high costs hinder widespread use.
Purpose of the Study:
- To develop and apply a cost-effective, deep WGS approach for sensitive detection of circulating tumor DNA (ctDNA).
- To establish a duplex error-corrected WGS method for ccfDNA with ultra-low error rates.
- To enable tumor-informed and tumor-uninformed ctDNA detection for disease burden assessment.
Main Methods:
- Utilized deep (~120×) whole-genome sequencing (WGS) with a lower-cost platform (Ultima Genomics).
- Developed duplex error-corrected WGS for circulating cell-free DNA (ccfDNA) to achieve exceptionally low error rates (7.7 × 10-7).
- Applied the method for tumor-informed ctDNA detection in the part-per-million range and assessed disease burden in cancer patients without matched tumor sequencing.
Main Results:
- Achieved deep (~120×) sequencing at a reduced cost, enabling sensitive ctDNA detection.
- Demonstrated duplex error-corrected WGS of ccfDNA with an error rate of 7.7 × 10-7.
- Successfully assessed disease burden in individuals with melanoma and urothelial cancer without requiring matched tumor tissue for sequencing.
Conclusions:
- Low-cost, deep WGS combined with duplex error correction provides a powerful strategy for sensitive ctDNA detection.
- This approach enables accurate assessment of disease burden, even at low variant allele frequencies, without matched tumor sequencing.
- The developed error-corrected WGS method has broad applicability in genomics for low-abundance variant detection and mapping somatic mosaicism.
