TY - JOUR
T1 - Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping
AU - Margalit, Sapir
AU - Tulpová, Zuzana
AU - Zur, Tahir Detinis
AU - Michaeli, Yael
AU - Deek, Jasline
AU - Nifker, Gil
AU - Haldar, Rita
AU - Gnatek, Yehudit
AU - Omer, Dorit
AU - Dekel, Benjamin
AU - Feldman, Hagit Baris
AU - Grunwald, Assaf
AU - Ebenstein, Yuval
N1 - Publisher Copyright:
© The Author(s) 2025.
PY - 2025/3/1
Y1 - 2025/3/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85214501287&partnerID=8YFLogxK
U2 - 10.1093/nargab/lqae190
DO - 10.1093/nargab/lqae190
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C2 - 39781516
AN - SCOPUS:85214501287
SN - 2631-9268
VL - 7
JO - NAR Genomics and Bioinformatics
JF - NAR Genomics and Bioinformatics
IS - 1
M1 - lqae190
ER -