Carcinogenesis often involves significant alterations in the cancer genome, marked by large structural 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 cover features smaller than several 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 structural, 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 outperformed OGM in detecting small SVs, while OGM excelled 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.

Department of Biomedical Engineering Tel Aviv University 6997801 Tel Aviv Israel

Institute of Experimental Botany of the Czech Academy of Sciences Olomouc Czech Republic

Pediatric Nephrology Unit The Edmond and Lily Safra Children's Hospital Sheba Medical Center 52621 Ramat Gan Israel

Pediatric Stem Cell Research Institute Edmond and Lily Safra Children's Hospital Sheba Medical Center 52621 Ramat Gan Israel

School of Chemistry Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University 6997801 Tel Aviv Israel

School of Medicine Faculty of Medical and Health Sciences Tel Aviv University 6997801 Tel Aviv Israel

The Genetics Institute and Genomics Center Tel Aviv Sourasky Medical Center Tel Aviv Israel

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bioRxiv. 2024 Jun 13:2024.03.31.587463. doi: 10.1101/2024.03.31.587463. PubMed

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Optical genome and epigenome mapping of clear cell renal cell carcinoma