Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Area of Science:

• Molecular Biology
• Genomics
• Oncology

Background:

• Circulating tumor DNA (ctDNA) in liquid biopsies shows promise as a biomarker for non-invasive cancer diagnostics and monitoring.
• Detecting low-abundance ctDNA is challenging due to its low proportion (<5%) in cell-free DNA.
• Highly sensitive sequencing methods are essential for identifying ctDNA based on somatic variants.

Purpose of the Study:

• To introduce CyclomicsSeq, a novel sequencing technique for highly sensitive ctDNA detection.
• To evaluate the performance of CyclomicsSeq in identifying low-frequency somatic mutations.
• To demonstrate the clinical utility of CyclomicsSeq for monitoring tumor burden in cancer patients.

Main Methods:

• CyclomicsSeq utilizes Oxford Nanopore sequencing of concatenated DNA molecules from a single source.
• Consensus calling across multiple copies of the same DNA molecule significantly improves base-calling accuracy (~60×).
• A TP53-specific assay was developed and validated using this method.

Main Results:

• CyclomicsSeq achieved high base-calling accuracy, enabling detection of TP53 mutations at frequencies as low as 0.02%.
• The method successfully monitored tumor burden in head-and-neck cancer patients during treatment.
• The technique demonstrated applicability to any genomic locus.

Conclusions:

• CyclomicsSeq offers a significant advancement in sensitive ctDNA detection for liquid biopsies.
• This method facilitates accurate real-time tumor diagnostics and monitoring.
• CyclomicsSeq is a viable approach for clinical implementation in cancer diagnostics.