![]() (1965) observed very small double chromatin bodies during chromosome level analyses of human tumors. In addition to intact chromosomes, Cox et al. Packing of nucleosomes forms a helical structure known as the 30 nm chromatin fiber, which coils into highly condensed chromosomes during metaphase in cell division ( Annunziato, 2008). Their basic unit is the nucleosome, which consists of 146 bp of double-stranded DNA wrapped around a histone octamer. In the nucleus of eukaryotic cells, DNA is almost exclusively found in linear chromosomes, which are hierarchically organized. 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. 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. Its key step uses a graph-theoretic approach to identify putative circular fragments validated on simulated reads. The workflow is implemented based on the Snakemake workflow management system. ![]() We here describe a computational workflow for identification of DNA circles from long-read sequencing data. 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. 9Center for Bioinformatics and Department of Computer Science, Saarland University, Saarbrücken, Germany.8Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Essen, Germany.7German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany.6Berlin Institute of Health, Berlin, Germany.5Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany.4Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.3Institute for Artificial Intelligence in Medicine, IKIM, University Hospital Essen, Essen, Germany.2Algorithms for Reproducible Bioinformatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.1Laboratory of Molecular Oncology, West German Cancer Center, Department of Medical Oncology, University Hospital Essen, Essen, Germany.Alicia Isabell Tüns 1 †, Till Hartmann 2 †, Simon Magin 3, Rocío Chamorro González 4,5,6,7,8, Anton George Henssen 4,5,6,7,8, Sven Rahmann 9, Alexander Schramm 1* ‡ and Johannes Köster 2 ‡
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