LockSeq Technical FAQ

We simply require the genomic coordinates of your intended edit and/or nominated off-target sites. Providing the gRNA sequence allows us to utilize in silico prediction algorithms if you require support in Nomination or don't have the on- and off-target coordinates.

LockSeq is engineered to enable scalable gene-editing validation with minimal target dropout. Virtually, our chemistry supports panels of 1000+ sites in a single tube. Get in touch with us for the depth required in case much larger panels are in scope for your project.

Yes. One of our core advantages is Panel Flexibility. Because our ligation probes capture targets independently, you can "Mix and Match" coordinates. You can simply add new probes to your existing LockSeq panel without compromising data integrity.

LockSeq is a confirmation technology. It sequences nominated sites at high 
sensitivity.

You'll need to provide off-target site coordinates from one of the following 
nomination methods:

• Empirical: GUIDE-seq, INDUCE-seq, CHANGE-seq, DISCOVER-seq CIRCLE-seq, or equivalent

• In silico: Cas-OFFinder, CRISPOR, or equivalent

If you have gRNA sequences but haven't run a nomination assay yet, we can 
perform in silico prediction as a starting point. Contact us to discuss what's 
appropriate for your regulatory context.

LockSeq has demonstrated Limit of Detection of 0.1% variant frequencies (1:1,000).

This is achieved under the following conditions:

• At least 3,000 consensus reads per target site

• At least 3 consensus reads supporting a variant.

• Libraries prepared and analyzed using the standard LockSeq service workflow.

At this sensitivity level, LockSeq reliably resolves and differentiates low-frequency edits from stochastic errors, such as DNA polymerase or sequencing errors.

By integrating Unique Molecular Identifiers (UMIs) into the LockSeq probe design, our automated pipeline generates consensus reads and filters sequencing artifacts. This suppresses the noise floor to an extremely low FPR, ensuring that rare variants are biological truth backed by high-confidence reads, not stochastic noise.

LockSeq provides high uniformity across high-plex panels. Typically, 70-90% of targeted loci remain within a range of 80% of the mean read depth. This high uniformity significantly optimizes sequencing depth and minimizes drop-outs.

LockSeq captures each target with a single probe before amplification, reducing assay complexity, non-specific interactions, and target dropout. UMI-based consensus sequencing further suppresses technical noise, enabling high-confidence detection of low-frequency edits down to 0.1%.

Unlike multiplex PCR or hybrid capture, where increasing panel size adds primer/probe complexity and raises the risk of bias and coverage gaps, LockSeq is designed for scalable, quantitative gene-edit characterization.

In some cases, a genomic target may fall in a repetitive genomic region or have sequence characteristics that prevent a specific probe design. When this happens, we flag the site during in silico probe validation — before library preparation begins.

For any site that cannot be captured, we will tell you upfront during the study design and not charge for it.

From receipt of DNA material in our Solna laboratory to the delivery of the final Variant Report, the standard TAT is 15 business days.

Yes! Analysis is included in the service price. There are no separate software fees, analysis credits, or per-run charges for bioinformatics.

You pay for the full LockSeq service — we return data and a complete overview report.

Every LockSeq report delivers:

• Observed Allele Frequency per site: the fraction of reads showing a variant at each targeted site.

• Sequence Alignments: Allele alignments for site in the panel.

• Coverage summary: consensus and read depth per site.

• Raw data: Aligned BAM files for all sequenced sites and samples

Overview reports are delivered as self-contained HTML summaries with accompanying data tables and figures. 

For standard off-target confirmation at 0.1% Limit of quantification, LockSeq targets 
a minimum of 15,000 (Illumina) to 30,000 (Oxford Nanopore) raw reads per target site. This delivers approximately 3,000 consensus reads per site.

We handle sequencing depth planning as part of the project scoping process — 
you don't need to specify run parameters. It's included in the service, and can be adjusted to your needs.

LockSeq is a library prep workflow that is compatible with any sequencing platform. We have comparisons with Illumina and Oxford Nanopore Technologies with a high correlation (0.99).  For your project, we scope this at the start of the project.