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Benchmarking of Oxford Nanopore whole genome sequencing for germline variant and CpG methylation detection across Canada’s national platform for genome sequencing and analysis
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DOI：10.3389/fgene.2026.1863034.png)
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Abstract
En 中文
Advances in sequencing technology have enabled population-level Whole Genome Sequencing (WGS) efforts to be undertaken in many countries. Often; this requires collaboration across a distributed network of sequencing centres to allow efficient use of existing resources. Previously we tested the robustness of short-read sequencing technology and analysis pipelines across three established sequencing centres located in Montreal; Toronto; and Vancouver; constituting CGEn; Canada’s national platform for genome sequencing and analysis (www.cgen.ca). In this work; we extend the study to cover Oxford Nanopore Technologies (ONT) long read-based WGS technology which is increasingly being used for large-scale genomics studies. Thus; we performed ONT WGS of the HG002 cell line; a well-characterized standard obtained directly from the Coriell Institute; aiming for a minimum of 30× coverage using one R10.4 PromethION flowcell at each centre. The sequencing datasets were analyzed using commonly developed pipelines for SNVs; Indels; SV; and CpG methylation detection and then compared to the relevant publicly available GIAB benchmark datasets. As a result; we tested the robustness of the laboratory protocols as well as the effectiveness of the analytical pipelines for simultaneous analysis of genomic variation and CpG methylation. Key findings include: SNV detection with higher F1-scores in RefSeq Coding regions for the ONT datasets (99.1%–99.5%) compared to Illumina NovaSeqX data (96.5%); additionally; there was high correlation of CpG methylation across all the sequencing centres (R = 0.97); as well as with publicly available WGBS (R = 0.88) and EM-Seq (R = 0.93) data from the EpiQC study.
Keywords:
nanopore
whole genome sequencing
methylation
benchmarking
long-reads sequencing
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