The Oxford Nanopore (ONT) sequencing platform may have more modalities than a Swiss army knife. In a multimodal masterpiece of a new study, researchers now demonstrate how DNA methylation, copy number alterations, nucleosome footprinting, and fragmentation profiles derived from liquid biopsies of cancer patients can deconvolute cellular composition and identify cancer-specific methylation changes from circulating cell-free tumor DNA (ctDNA).
Researchers led by Silvestro G. Conticello (National Research Council, Pisa, Italy) and Benjamin P. Berman (Hebrew University of Jerusalem, Israel) had previously employed ONT-mediated whole-genome sequencing (WGS) to detect copy number alterations in patient-derived ctDNA, with the information carried by this component describing tissue-of-origin features and possessing diagnostic/prognostic potential. Now, the team reports the ONT-mediated detection of cancer-specific methylation changes and fragmentation signatures from ctDNA.
Let’s hear more on this polyvalent work of art from the Swiss-army-knife-wielding team of Katsman and colleagues:
- Rapid and straightforward ONT sample preparation and sequencing times combined with portability allow complete methylation analysis from a liquid biopsy in as little as a few hours
- The targeted genome coverage supports the detection of cancer-derived DNA based on DNA methylation
- ONT reports similar cancer-specific features of DNA methylation, DNA fragmentation, and copy-number alteration compared to conventional Illumina-based WGS and whole genome bisulfite sequencing methods, which entail longer, more complex sample management and a degree of degradation/input material loss
- ONT may provide a more accurate representation of DNA fragment frequencies (but involves higher error rates) and can distinguish between various DNA modifications (e.g., 5mC vs. 5hmC, 5fC, and 5CaC) when compared to bisulfite-based sequencing
- Of note, ONT does not detect cancer-associated DNA fragmentomic features in all samples, with similar results detected in Illumina-based approaches, suggesting that this derives from biological variability
- ONT provides improved specificity at very low coverage
- Short dinucleosomal sequences may represent more robust cancer markers than short mononucleosomes (which requires further validation)
These findings suggest liquid biopsy analysis using ONT may one day be a suitable strategy for clinical cancer management; however, the authors highlight the need for additional development to reduce expense and single nucleotide/indel error rates compared to Illumina. Furthermore, the authors foresee the application of the ONT platform to other urgent conditions where rapid DNA methylation analysis may provide benefits, such as myocardial infarction or COVID-19.
For more on how multimodal analysis via ONT may soon aid cancer patient management, see Genome Biology, July 2022.