Bibliographic Details
| Title: |
Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing |
| Authors: |
Alicia Isabell Tüns, Till Hartmann, Simon Magin, Rocío Chamorro González, Anton George Henssen, Sven Rahmann, Alexander Schramm, Johannes Köster |
| Source: |
Frontiers in Genetics, Vol 13 (2022) |
| Publisher Information: |
Frontiers Media S.A., 2022. |
| Publication Year: |
2022 |
| Collection: |
LCC:Genetics |
| Subject Terms: |
cancer, circular DNA, nanopore sequencing, algorithm, snakemake, Genetics, QH426-470 |
| More Details: |
Occurrence of extra-chromosomal circular DNA is a phenomenon frequently observed in tumor cells, and the presence of such DNA has been recognized as a marker of adverse outcome across cancer types. We here describe a computational workflow for identification of DNA circles from long-read sequencing data. The workflow is implemented based on the Snakemake workflow management system. Its key step uses a graph-theoretic approach to identify putative circular fragments validated on simulated reads. We then demonstrate robustness of our approach using nanopore sequencing of selectively enriched circular DNA by highly sensitive and specific recovery of plasmids and the mitochondrial genome, which is the only circular DNA in normal human cells. Finally, we show that the workflow facilitates detection of larger circular DNA fragments containing extrachromosomal copies of the MYCN oncogene and the respective breakpoints, which is a potentially useful application in disease monitoring of several cancer types. |
| Document Type: |
article |
| File Description: |
electronic resource |
| Language: |
English |
| ISSN: |
1664-8021 |
| Relation: |
https://www.frontiersin.org/articles/10.3389/fgene.2022.867018/full; https://doaj.org/toc/1664-8021 |
| DOI: |
10.3389/fgene.2022.867018 |
| Access URL: |
https://doaj.org/article/66e0271a213b461695eace0945899692 |
| Accession Number: |
edsdoj.66e0271a213b461695eace0945899692 |
| Database: |
Directory of Open Access Journals |
