High-Plex Off-Target Confirmation.
No Optimization Required.
LockSeq captures each target independently — no primer competition, no per-panel redesign. Run 1 to 1,000+ sites in a single standardized reaction. Send us your coordinates and DNA; we return a UMI-corrected variant report in 15 business days.
0.1% Variant Allele Frequency (1:1,000)
1,000+ sites per reaction in a single assay
Near-zero target loci dropouts
15 days turnaround time from DNA-in to report-out
Validated across various gene editors, such as Cas9, Base editors, Prime editors and Transposon systems.
FDA Now Requires Orthogonal Off-Target Assessment
The FDA's April 2026 Draft Guidance on genome editing safety explicitly calls for orthogonal confirmation methods — independent of the nomination assay — for IND-enabling submissions.
Multiplex PCR suffer from target dropout. Missing sites isn't a data gap. It's a development and regulatory risk.
LockSeq is purpose-built for this requirement.
DNA-In. Report-Out. No Infrastructure Required.
Countagen runs LockSeq as a complete service. You provide genomic coordinates and DNA samples. We handle probe design, library prep, sequencing, and bioinformatic analysis — and return a UMI-corrected variant report in 15 business days.
No sequencer. No bioinformatics team. No optimization burden.
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Why LockSeq Outperforms Multiplex PCR
Sequence-Level Truth & Resolution
LockSeq uses gap-fill ligation to lock onto each target molecule before amplification. UMI-tagged reads are collapsed into consensus calls that suppress sequencing noise. Result: 0.1% VAF sensitivity with minimal false positives — even across 1,000-plex panels.
Fewer Dropouts. Better Coverage.
One probe per target — no cross-reactive primer interactions, no amplification bias. Across all panels run to date, LockSeq has delivered 0-10% dropout and recovers on average 70% of rhAmpSeq dropouts. Dropouts that do occur tend to fall in different locations, making LockSeq complementary.
1 to 1,000+ Sites. Same Workflow.
Add, remove, or reconfigure target coordinates without redesigning the entire assay. LockSeq panels scale from single-site on-target confirmation to above 1,000-plex off-target characterization in one reaction. Sequencer-agnostic — Illumina and ONT confirmed.
Trusted by Leading Gene Editing Research Programs
