--- title: LockSeq FAQ | Off-Target Sequencing Questions Answered | Countagen description: "Answers to common questions about LockSeq: sample requirements, panel size, sensitivity limits, turnaround time, sequencing platforms, and pricing. Ask anything not covered here." --- [![Logo\_horizontal\_colored logo with black text](https://www.countagen.com/hubfs/Logo_horizontal_colored%20logo%20with%20black%20text.png)](https://www.countagen.com/?hsLang=en) - [Technology](https://www.countagen.com/technology?hsLang=en) - [Bioinformatics](https://www.countagen.com/bioinformatics?hsLang=en) - [Sample Report](https://www.countagen.com/lockseq-sample-report?hsLang=en) - [Resources](https://www.countagen.com/resources?hsLang=en) - [FAQ](https://www.countagen.com/faq) - [About Us](https://www.countagen.com/about-us?hsLang=en) [Request a quote](https://www.countagen.com/contact?hsLang=en) LockSeq FAQ # What teams ask before they send samples Inputs, panel design, sensitivity and what comes back at the end. If your question isn't here, ask us directly. [Starting a project](https://www.countagen.com/faq#start)[Panel design](https://www.countagen.com/faq#panel)[Sensitivity & data quality](https://www.countagen.com/faq#data)[Turnaround & results](https://www.countagen.com/faq#delivery) 18 questions [Starting a project](https://www.countagen.com/faq#start)[Panel design](https://www.countagen.com/faq#panel)[Sensitivity & data quality](https://www.countagen.com/faq#data)[Turnaround & results](https://www.countagen.com/faq#delivery) Still have a question? Our scientists answer these themselves. [info@countagen.com](mailto:info@countagen.com) ## Starting a project What do I need to send you to start?+ Three things: - **Your sites** — the on-target site plus the off-target candidates you've nominated. A BED file, spreadsheet or plain list of coordinates is fine. - **Your gRNA sequence(s)** — we use them to check the coordinates and, if needed, add in silico candidates. - **Genomic DNA** — edited samples and controls. We confirm amounts during scoping. We take it from there: probe design, library prep, sequencing and analysis. How much DNA do you need?+ Typically 100–500 ng of high-quality genomic DNA per sample, at more than 20 ng/µL in 1× TE or nuclease-free water. If your material is limited, tell us at scoping and we'll work out what's possible. Do you nominate off-target sites, or do I need to bring them?+ LockSeq is a confirmation method: it sequences sites that have already been nominated, at high sensitivity. Most teams bring sites from an empirical assay (GUIDE-seq, CHANGE-seq, CIRCLE-seq, DISCOVER-seq, INDUCE-seq or similar) and/or in silico tools such as Cas-OFFinder or CRISPOR. If you only have a gRNA so far, we can run in silico prediction as a starting point. Which organisms can you work with?+ Any organism with a reference genome, since probes are designed from the coordinates you provide. We've run human and mouse panels so far. For other species or custom cell lines, get in touch and we'll check panel design first. What does a project cost, and how do we order?+ Projects start from €1,000. The quote depends on the number of sites and samples and the sensitivity you need, and it covers panel design, library prep, sequencing and analysis. You can order directly, or through **Scientist.com** if your procurement team already uses it. ## Panel design How many sites can one panel cover?+ From a single site up to panels designed for 1,000+ sites in one tube. Each target gets its own probe, so adding sites doesn't add primer interactions the way multiplex PCR does. For very large panels, talk to us about the sequencing depth you'll need. Can I add sites to an existing panel later?+ Yes. Probes capture their targets independently, so new sites can be added to a panel you've already run, for example when a new nomination assay turns up more candidates. You can also mix and match panels without losing performance. Are there sites LockSeq can't capture?+ Some. Sites in highly repetitive regions, or with sequence features that rule out a specific probe, can't always be designed. We check every site in silico before any lab work starts, flag the ones we can't cover, and don't charge for them. You know exactly what's in the panel before samples are run. What kinds of edits does LockSeq detect?+ Substitutions and indels inside the target window each probe reads, which can be up to 200 bp long. Each report includes an indel profile per site. ## Sensitivity & data quality What's the limit of detection?+ 0.1% variant frequency (1 in 1,000) in the standard workflow, with at least 3,000 consensus reads per site and at least 3 consensus reads supporting a variant. The limit at each site is set by its own consensus coverage, so it's reported per site. How do you keep false positives down?+ Every probe carries a unique molecular identifier (UMI). Reads from the same original DNA molecule are collapsed into one consensus read, so random PCR and sequencing errors that show up in only some reads drop out. Each sample is also compared with your untreated control, which catches systematic background. That's what lets us separate real low-frequency variants from noise. How even is coverage across a panel?+ Typically around 80% of sites fall within 80% of the mean read depth, so you don't need to over-sequence the whole panel to reach the weakest sites. How much sequencing depth does a site need?+ For confirmation at 0.1%, we aim for at least 15,000 raw reads per site on Illumina, or 30,000 on Oxford Nanopore, which gives about 3,000 consensus reads. We plan depth for you during scoping and can adjust it to your needs. Which sequencing platforms do you use?+ LockSeq is a library prep workflow, so it isn't tied to one sequencer. We've validated it on Illumina, MGI and Oxford Nanopore, and choose the platform with you at the start of the project. ## Turnaround & results How long does a project take?+ 15 business days from the day your DNA arrives in our lab in Solna, Stockholm to the delivered report. What do I get back?+ Every project includes: - UMI-corrected variant frequency per site, compared with your control - Indel profiles and allele alignments per site - Coverage per site (raw and consensus) - Raw data: FASTQ and aligned BAM files The report is a self-contained HTML file with tables and figures. [See a sample report →](https://www.countagen.com/lockseq-sample-report?hsLang=en) Is analysis included in the price?+ Yes. There are no separate software, analysis or per-run fees. How does LockSeq fit the FDA's draft guidance?+ The April 2026 draft guidance treats confirmation of nominated off-target sites as its own step, done with a sensitive sequencing method. That's the step LockSeq is built for. [Read our summary of the guidance →](https://www.countagen.com/countagen-insights/fda-april-2026-guidance-off-target-confirmation?hsLang=en) ## Ready to scope your panel? Send us your nominated sites and sample count, and we'll come back with a quote. [Request a quote](https://www.countagen.com/contact?hsLang=en)[See a sample report](https://www.countagen.com/lockseq-sample-report?hsLang=en) [![Countagen\_Logo\_White](https://www.countagen.com/hubfs/Logo_horizontal_colored%20logo%20with%20white%20text.png)](https://www.countagen.com?hsLang=en) | Countagen AB Nobels väg 16 171 65 Solna Sweden | Registered supplier on [Scientist.com](https://app.scientist.com/providers/countagen-ab) [![Scientist.com](https://www.countagen.com/hs-fs/hubfs/Scientist-com.png?width=1244&height=259&name=Scientist-com.png)](https://app.scientist.com/providers/countagen-ab) | | --- | --- | ### LockSeq - [Overview](https://www.countagen.com?hsLang=en) - [Technology](https://www.countagen.com/technology?hsLang=en) - [Bioinformatics](https://www.countagen.com/bioinformatics?hsLang=en) - [Sample report](https://www.countagen.com/lockseq-sample-report?hsLang=en) ### Resources - [Resources](https://www.countagen.com/resources?hsLang=en) - [FAQ](https://www.countagen.com/faq) ### Company - [About us](https://www.countagen.com/about-us?hsLang=en) - [Contact](https://www.countagen.com/contact?hsLang=en) © 2026 Countagen AB All rights reserved [Terms of Use](https://www.countagen.com/terms-of-use?hsLang=en) [Privacy Policy](https://www.countagen.com/privacy-policy?hsLang=en) [Cookie Policy](https://www.countagen.com/cookie-policy?hsLang=en) [Service Terms & DPA](https://www.countagen.com/legal?hsLang=en) [Powered by Atlas - a B2B SaaS HubSpot theme](https://www.kalungi.com/atlas-hubspot-theme-for-b2b-saas-software) ```json { "@context" : "https://schema.org", "@type" : "FAQPage", "mainEntity" : [ { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Three things: your sites (the on-target site plus the off-target candidates you've nominated, as a BED file, spreadsheet or plain list of coordinates), your gRNA sequence(s), and genomic DNA from edited samples and controls. We take it from there: probe design, library prep, sequencing and analysis." }, "name" : "What do I need to send you to start?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Typically 100–500 ng of high-quality genomic DNA per sample, at more than 20 ng/µL in 1× TE or nuclease-free water. If your material is limited, tell us at scoping and we'll work out what's possible." }, "name" : "How much DNA do you need?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "LockSeq is a confirmation method: it sequences sites that have already been nominated, at high sensitivity. Most teams bring sites from an empirical assay (GUIDE-seq, CHANGE-seq, CIRCLE-seq, DISCOVER-seq, INDUCE-seq or similar) and/or in silico tools such as Cas-OFFinder or CRISPOR. If you only have a gRNA so far, we can run in silico prediction as a starting point." }, "name" : "Do you nominate off-target sites, or do I need to bring them?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Any organism with a reference genome, since probes are designed from the coordinates you provide. We've run human and mouse panels so far. For other species or custom cell lines, get in touch and we'll check panel design first." }, "name" : "Which organisms can you work with?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Projects start from €1,000. The quote depends on the number of sites and samples and the sensitivity you need, and it covers panel design, library prep, sequencing and analysis. You can order directly, or through Scientist.com if your procurement team already uses it." }, "name" : "What does a project cost, and how do we order?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "From a single site up to panels designed for 1,000+ sites in one tube. Each target gets its own probe, so adding sites doesn't add primer interactions the way multiplex PCR does. For very large panels, talk to us about the sequencing depth you'll need." }, "name" : "How many sites can one panel cover?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Yes. Probes capture their targets independently, so new sites can be added to a panel you've already run, for example when a new nomination assay turns up more candidates. You can also mix and match panels without losing performance." }, "name" : "Can I add sites to an existing panel later?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Some. Sites in highly repetitive regions, or with sequence features that rule out a specific probe, can't always be designed. We check every site in silico before any lab work starts, flag the ones we can't cover, and don't charge for them. You know exactly what's in the panel before samples are run." }, "name" : "Are there sites LockSeq can't capture?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Substitutions and indels inside the target window each probe reads, which can be up to 200 bp long. Each report includes an indel profile per site." }, "name" : "What kinds of edits does LockSeq detect?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "0.1% variant frequency (1 in 1,000) in the standard workflow, with at least 3,000 consensus reads per site and at least 3 consensus reads supporting a variant. The limit at each site is set by its own consensus coverage, so it's reported per site." }, "name" : "What's the limit of detection?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Every probe carries a unique molecular identifier (UMI). Reads from the same original DNA molecule are collapsed into one consensus read, so random PCR and sequencing errors that show up in only some reads drop out. Each sample is also compared with your untreated control, which catches systematic background. That's what lets us separate real low-frequency variants from noise." }, "name" : "How do you keep false positives down?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Typically around 80% of sites fall within 80% of the mean read depth, so you don't need to over-sequence the whole panel to reach the weakest sites." }, "name" : "How even is coverage across a panel?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "For confirmation at 0.1%, we aim for at least 15,000 raw reads per site on Illumina, or 30,000 on Oxford Nanopore, which gives about 3,000 consensus reads. We plan depth for you during scoping and can adjust it to your needs." }, "name" : "How much sequencing depth does a site need?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "LockSeq is a library prep workflow, so it isn't tied to one sequencer. We've validated it on Illumina, MGI and Oxford Nanopore, and choose the platform with you at the start of the project." }, "name" : "Which sequencing platforms do you use?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "15 business days from the day your DNA arrives in our lab in Solna, Stockholm to the delivered report." }, "name" : "How long does a project take?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Every project includes UMI-corrected variant frequency per site compared with your control, indel profiles and allele alignments per site, coverage per site (raw and consensus), and raw data as FASTQ and aligned BAM files. The report is a self-contained HTML file with tables and figures." }, "name" : "What do I get back?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "Yes. There are no separate software, analysis or per-run fees." }, "name" : "Is analysis included in the price?" }, { "@type" : "Question", "acceptedAnswer" : { "@type" : "Answer", "text" : "The April 2026 draft guidance treats confirmation of nominated off-target sites as its own step, done with a sensitive sequencing method. That's the step LockSeq is built for." }, "name" : "How does LockSeq fit the FDA's draft guidance?" } ] } ```