ATOM-Seq
Discover the Unknown
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Identify integration sites, making it an ideal companion for gene therapy technologies
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Identify known and unknown gene fusions
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Ideal for cell-free DNA and all other short, fragmented material
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Identifies all viral integration sites
Home > ATOM-Seq Capture Chemistry > Custom Assay Development Overview
ATOM-Seq Chemistry
​​ATOM-Seq offers a truly game-changing approach for NGS-based sample testing, with broad application across both clinical and research life science environments.
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As an alternative to ligation-based capture, combined with amplicon based enrichment, it provides the best of both worlds.
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​​For a detailed explanation of the ATOM-Seq capture chemistry please read our technological overview
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In a novel approach, sample molecules are captured by treating them as if they were primers. Their 3' ends are first annealed to a synthetic template, known as an Adaptor Template Oligo (ATO). A polymerase then extends the original molecule, incorporating Unique Molecular Identifiers (UMIs) and a universal primer site directly onto available 3' ends of every original sample molecule.
​A key element to ATOM-Seq's flexibility is that it requires only a
single targeting primer to enrich for regions of interest.
Target enrichment workflows can enrich any sequence between the location of your targeting primer(s) and the end of the (c)DNA molecule it binds to.
Customising ATOM-Seq workflows
Customising off-the-shelf kits
Our off-the-shelf targeted enrichment workflows are all available for customisation.
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For more information on our cfDNA, RNA and FFPE workflows please click the relevant link below
Custom assays for cell-free DNA from liquid biopsies include:
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Monitoring treatment response
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Minimal residual disease (MRD)
Custom assays for FFPE or high-quality RNA include:
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Detection of known and unknown fusions
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Therapy guidance - fusions and exon skipping
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Detecting therapy based resistance via novel fusions.
Custom assays for FFPE or high-quality DNA include:
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Therapy guidance - mutations/CNV/MSI
Supporting Gene Editing
ATOM-Seq is an essential companion tool for the development of gene editing systems and treatments, as it is ideal for the monitoring and detection of off target gene editing.
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ATOM-Seq can amplify any CRISPR-induced genetic changes, including both intended target site(s) or unintended off-target sites. Targeting primers are designed on one or both sides of a CRISPR target site, or designed similarly for a predicted off-target site. In a multiplexed PCR reaction, each of these target-specific primers pairs with a universal primer that targets the captured 3' end of the target molecule. Error-resistant PCR between these primers allows library generation and identification of both expected and unexpected CRISPR-induced genetic changes.
Eliminate all ligation-based false positives
because ATOM-Seq is 100% free of ligation steps
Virus Integration Mapping
Viral integration is a partially random process, but the specific sites can have an effect on the oncogenicity of a virus. The same is also true of viral vectors carrying genetic payloads, so it is important to know if and where the virus/plasmid integrates.
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Targeting primers do not have to target human DNA, they can target viral sequences. When enrichment primers are designed at the ends of viral genomes they will enrich any human DNA between the primer site and the ends of the captured DNA molecule. This allows you to use the inherent sensitives of ATOM-Seq to detect and count rare integration events.
Accurate counting of integration events by using UMI for reliable deduplication of PCR duplicates ensuring each integration is counted
Organ Rejection
Organ rejection results in cell death and the release of DNA from the donated organ into the recipient's blood stream. By targeting genetic signatures only present in the organ it is possible to monitor and track rejection.
Identify donor organ DNA sooner using ATOM-Seq's high level of cell-free DNA capture from plasma or urine samples
Let us know how we can support you
As an ISO:13485 certified manufacturer, everything we do is oriented around ensuring the highest levels of quality.
If you have a clinical or research question where ATOM-Seq's power could support you, please let us know how we can help you.
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Below is a quick series of questions so we can understand your objectives.