Long-Read Sequencing, Complemented.

EGM: The Ideal Partner for Long-Read Sequencing (LRS)

The complexity of SVs makes detection challenging, often leading to false positives and ambiguous calls. Repetitive genomic regions and rearrangements can sometimes produce uncertain results, impacting analysis. Electronic genome mapping (EGM) provides orthogonal validation to improve accuracy and clarify uncertainties. By combining EGM with LRS, researchers gain greater confidence in SV detection and interpretation. This pairing also aligns with industry standards like American College of Medical Genetics¹ guidelines and regulatory mandates that recommend orthogonal validation for variant calls related to pathogenicity. Finally, EGM can help identify large or complex SVs that LRS may miss, ensuring comprehensive genomic insights.

Complement Your Long Reads with EGM

Quickly and easily verify and confirm your long-read SV calls on the spot. The Nabsys OhmX™ Platform uses EGM to provide a turnkey approach to orthogonal verification and confirmation. Highly accurate with low consumable costs and minimal upfront investment, EGM allows you to verify findings, clarify results, and gain more confidence in your research.

1. Accurate Detection with High Concordance with Long-Read Data

Leverage advanced precision technology specifically designed to accurately verify and identify all SVs, including those found in complex and challenging genomic regions. This innovative approach ensures high concordance with long-read data, providing reliable and comprehensive genomic insights for research and clinical research applications.

In the case study, Electronic Genome Mapping for Confirmation of Long Structural Variants, we compare genome-wide SV calls exceeding 5 kilobase pairs (kbp) from EGM and PacBio HiFi in HG002. EGM data demonstrates a strong correlation to insertion and deletion calls made by PacBio HiFi. The data demonstrate EGM's precision in confirming PacBio's SV calls with nearly identical size estimates, underscoring its capability as an orthogonal validation method.

2. Clarification of ambiguous SV calls

Some SV calls may be ambiguous due to the complexity of genomic rearrangements, sequencing errors, or challenges in mapping repetitive and GC-rich regions. In these cases, EGM may provide clarity or additional context.

In two examples below, EGM identified larger insertions, 33,287 base pairs (bp) and 31,932 bp, in two instances where only smaller or no SVs were called across PacBio replicates runs of HG002.  In both cases, EGM confirmed one of the PacBio calls but added additional information about the repetitive nature of the SVs.

3. Low-Cost Validation Without Compromising Accuracy

Achieve robust results at a fraction of the cost compared to other orthogonal validation approaches, enabling scalable research and diagnostics.

To learn more about affordable acquisition options for the OhmX platform, click here.

Two cloud-based software pipelines are available on Google Cloud to confirm or clarify structural variants (SVs) that require orthogonal validation. To evaluate a candidate SV, users can conduct EGM analysis on the OhmX platform, then upload the resulting data to one or both pipelines for further analysis.

The first pipeline, Human Chromosome Explorer (HCE), performs de novo genome assembly and genome-wide SV calling, delivering a comprehensive set of SV calls. Users can manually compare their candidate SV with HCE's output to confirm the SV or gain additional insights into the structure of the SV.

The second option is the SV Verify pipeline, which employs read-based mapping within a user-defined targeted region. This pipeline specifically confirms or refutes the presence of the SV in the designated area.

Accurate, reliable, and cost-efficient validation is just a step away. Discover how our cutting-edge technology can transform the way you approach SV analysis.

Contact us to learn more about the OhmX Platform.