Long‑Read NGS Service
Understand impurities early. See what standard assays miss. De-risk you vector design.
Traditional assays only detect what you ask them to measure.
Early‑stage gene therapy programs often move forward without a full understanding of what’s actually inside the vector. Truncations, backbone carryover, Rep/Cap fragments, host‑cell DNA, or other unexpected species can remain invisible until much later.
By that point, fixing the problem is expensive, time‑consuming, and can jeopardize regulatory submissions or even clinical safety.
Discovery teams need a way to uncover these hidden impurities early, during vector optimization and candidate selection, when design decisions are still flexible and inexpensive to change.
Ascend’s solution – Oxford Nanopore long-read sequencing customized for viral vectors
Our long‑read nanopore NGS service provides a complete, unbiased view of your vector—capturing every DNA species present, including unexpected impurities that targeted assays miss.
With extremely low material requirements (e.g. as little as ~5E9 vg for AAV), it’s ideally suited for groups who want deep characterization without needing to manufacture high‑titer batches.
Whether you’re selecting between multiple candidates, validating a novel production platform, or de‑risking your plasmid system, our analysis gives you confidence that your vector is structurally sound and ready for the next stage.
NGS Insights into Vector Quality and Composition
Vector Genome Integrity and Sequence Length Distribution
Sequence length distribution reveals the proportion of full-length vector genomes relative to shorter fragments, enabling detection of truncations and structural heterogeneity. The dominant peak corresponding to the expected genome size indicates intact packaging, while absence of secondary peaks supports minimal truncated species. Optionally, read size profiles can be corrected for Oxford Nanopore sequencing size bias with co-sequenced lambda phage DNA digest.
Read Mapping Across Vector, Process, and Host Components
NGS reads are mapped against reference sequences to quantify contributions from the vector genome, plasmid backbone components, helper elements, and host cell DNA. This analysis provides a comprehensive view of sample composition and enables detection of residual process-related impurities not captured by targeted assays.
Coverage Analysis Across the Vector Genome
Coverage plots show sequencing read distribution across the ITR-to-ITR region, including promoter, transgene, and regulatory elements, as well as nucleotide polymorphisms. Uniform coverage supports intact genome representation, while localized drops or discontinuities may indicate structural abnormalities detectable through NGS.
Identification of Truncations
Base-level analysis enables identification of truncation events across the vector genome, allowing early identification of potential quality or design risks.
NGS Service Overview
Typical material requirements for AAV:
- Standard: ~1E11 vg
- Minimum: 5E9 vg (case‑dependent)
Modality support:
- All single‑ and double‑stranded DNA viruses
- Exploratory support available for RNA viruses under an R&D model
- Analysis‑only option for raw data generated by 3rd party sequencing services
What we deliver:
- Long‑read, AAV‑focused NGS using Oxford Nanopore technology
- Complete impurity and integrity profiling across all DNA species
- Customizable analysis for any plasmid system (1‑, 2‑, 3‑plasmid, or proprietary)
- Multiplexing of up to six samples per run, with a minimum of 500,000 reads per sample
- Short data focussed or extended, submission-ready report formats available
- Turnaround time of 20–25 business days
Ready to speak to a member of the team about your analytical requirements?
Please contact us using the form below.
NGS Service Form
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Related Resources
Publication
Recombinant AAV batch profiling by nanopore sequencing elucidates product-related DNA impurities and vector genome length distribution
Poster
Advancements in nanopore sequencing allow in-depth characterization of rAAV vector batches comparable to SMRT™ sequencing
Poster
The Good, the Bad, & the Chimeric: Using Nanopore Sequencing to De-Risk rAAV Genome Packaging
Publication
Recombinant AAV batch profiling by nanopore sequencing elucidates product-related DNA impurities and vector genome length distribution
Poster
Advancements in nanopore sequencing allow in-depth characterization of rAAV vector batches comparable to SMRT™ sequencing
Poster
The Good, the Bad, & the Chimeric: Using Nanopore Sequencing to De-Risk rAAV Genome Packaging
