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Related Experiment Video

Updated: Jun 19, 2025

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical

Yang Pei¹, Melanie Tanguy², Adam Giess²

¹Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.

|July 27, 2024

Summary

Optical genome mapping (OGM) offers high precision for structural variant (SV) identification. Nanopore long-read sequencing with Sniffles2 surpasses Illumina short-read sequencing in SV detection sensitivity.

Keywords:

Bionano optical genome mapping Illumina sequencing Oxford Nanopore Technologies copy number variant long read short read structural variant

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Last Updated: Jun 19, 2025

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

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Published on: March 11, 2020

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Area of Science:

Genomics
Bioinformatics
Structural Variant Analysis

Background:

Accurate identification of structural variants (SVs) is crucial but challenging due to limitations in current genomic analysis methods.
Previous short-read whole-genome sequencing (Illumina) has shown variable sensitivity and specificity for SV detection.

Purpose of the Study:

To evaluate the precision of Bionano optical genome mapping (OGM) for structural variant identification.
To compare the sensitivity of Nanopore long-read sequencing (ONT) and Illumina short-read sequencing for detecting structural variants.

Main Methods:

High-quality DNA from 9 parent-child trios was analyzed using Bionano OGM and Nanopore long-read sequencing.
A "truth" dataset was established by verifying Bionano SV calls using Integrative Genomics Viewer with raw sequence data.
Structural variant callers were applied to Illumina and ONT datasets to assess detection sensitivity against the verified Bionano SVs.

Main Results:

Bionano OGM demonstrated high precision, with 95% of its calls verified as true positives.
Illumina sequencing showed high sensitivity for deletions (86%) but low sensitivity for insertions (22%).
Nanopore sequencing with the Sniffles2 caller achieved high sensitivity for both deletions (90%) and insertions (74%), outperforming Illumina.

Conclusions:

Bionano OGM is a highly precise method for structural variant identification.
Nanopore long-read sequencing, particularly with the Sniffles2 caller, offers superior sensitivity for detecting structural variants compared to Illumina short-read sequencing.