Margalit S., Tulpová Z., Zur T.D., Michaeli Y., Deek J., Nifker G., Haldar R., Gnatek Y., Omer D., Dekel B., Feldman H.B., Grunwald A., Ebenstein Y.
NAR GENOMICS AND BIOINFORMATICS 7: lqae 190, 2025

Klíčová slova:
Abstrakt: Carcinogenesis often in v olv es significant alterations in the cancer genome, mark ed b y large str uct ural variants (SVs) and copy number variations (CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not co v er features smaller than se v eral hundred kilobases. Optical genome mapping (OGM) and nanopore sequencing [Oxford Nanopore Technologies (ONT)] bridge this resolution gap and offer enhanced performance for cytogenetic applications. Additionally, both methods can capture epigenetic information as they profile native, individual DNA molecules. We compared the effectiveness of the two methods in characterizing the str uct ural, copy number and epigenetic landscape of a clear cell renal cell carcinoma tumor. Both methods provided comparable results for basic karyotyping and CNVs, but differed in their ability to detect SVs of different sizes and types. ONT outperf ormed O GM in detecting small SVs, while O GM e x celled in detecting larger SVs, including translocations. Differences were also observed among various ONT SV callers. Additionally, both methods provided insights into the tumor’s methylome and hydroxymethylome. While ONT was superior in methylation calling, hydroxymethylation reports can be further optimized. Our findings underscore the importance of carefully selecting the most appropriate platform based on specific research questions.
DOI: 10.1093/nargab/lqae190
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