How we help you design the best custom target enrichment panels
Target enrichment panels are an extremely useful tool in a scientist's arsenal, enabling the collection of highly focused and sensitive NGS data.
Instead of sequencing all of the genetic material in a sample, target enrichment helps researchers enrich for specific regions of interest by hybridizing sample libraries with biotinylated oligonucleotide probes. After pulldown, the captured targets can then be sequenced.
There are now many off-the-shelf target enrichment panels available to researchers, including the wide variety of panels offered by Twist, such as the Comprehensive Exome Panel and the Mitochondrial Panel which provide coverage of the whole human exome and the mitochondrial genome, respectively.
While these off-the-shelf panels are useful, some researchers require higher resolution and depth of coverage for their specific application. This is where custom panels are a valuable tool. Custom target enrichment panels designed for a researcher’s specific needs can lead to more efficient and sensitive data collection as they are designed to be focused on the precise research question at hand.
Designing an effective custom panel, however, is far from trivial. Probes must be carefully selected to ensure that each one carries minimal complementarity with repetitive elements of the genome to avoid off-target capture. Also, probes must be designed with relevant genomic events—such as insertions/deletions, fusions, and microsatellite instability—in mind.
So, how can such a panel be designed effectively? We believe the answer is with a little help from Twist.
When buying a custom panel from Twist, we don't just print the targets you want. The Twist Custom Panel Design Team is on hand to consult with you throughout the design and build process to ensure every Twist Custom Panel is optimized for your needs, while providing uniform capture of your desired targets regardless of GC content.
In the sections below, we’ll describe how you can bring custom panels to your experiments through the Twist Custom Panel design process.
1. If you know what you want, we will build it.
The first step in the process is to identify your targets, be it a list of genes, genomic coordinates, or even a FASTA file with specific target sequences. Any of these will do. The goal is to have a clear understanding of what you need from the custom panel and to give our Custom Panel Design Team a solid starting point.
Once you have your targets, reach out to set up an intro call with your account manager.
2. The meeting of minds
Once you’ve contacted us, we’ll set up a meeting to get to know you and your project needs. At the meeting will be a Twist Bioinformatics Application Scientist, Twist Field Application Scientist, and an Account Manager who will be working with you throughout the design process.
Before the meeting, we’ll send over a form to help you gather and organize relevant information that may inform panel design, such as the material you’ll be targeting (DNA vs RNA) and if you’re interested in capturing splice variants, gene fusions, or indels.
In the meeting, you will discuss your goals with the Twist team, so we can clarify exactly what you need from your custom panel. If your target list includes known problematic sequences, such as HLA genes, we’ll also discuss strategies for overcoming these challenges to produce the best design possible.
3. Two to Three days to design your target enrichment panel
After the predesign meeting, Twist’s team of bioinformaticians will dive into the design process, producing a draft version of the custom target enrichment panel. Typically your custom design takes two to three days to complete.
4. Draft review and project quote
At this stage, the Twist team will send you a folder containing a design summary report, an outline of the targets encompassed by the panel, and an overview of target coverage. This will give you a chance to ensure the panel provides sufficient coverage and probe depth for each of your targets. If refinements are needed, the Twist team will return to the drawing board and iterate on the panel’s design.
Once you’re happy with the draft panel design, your account manager will provide a price quote. Then we’ll move forward with synthesizing—or writing—the oligos that make up the panel.
5. Silicon-based panel writing
Twist is a leading synthetic biology company, in part, because of its silicon-based oligonucleotide synthesis platform that allows for rapid, highly accurate oligonucleotide synthesis on a large scale.
Custom panels benefit from this platform. Each probe is precisely printed which ensures that the panel is both accurately synthesized and uniform in probe representation. If you are curious about the importance of uniformity, we dove into the topic in this white paper.
The process of manufacturing your custom panel includes balancing the number of individual probes for better uniformity, as well as the generation of double-stranded DNA probes that enable higher complexity hybridization. Typically, it takes about three weeks to complete this process.
6. Pilot testing your target capture
Once we’ve printed the panel, you’ll be able to test it. To make sure the custom panel fits your needs, we provide a small, discounted sample with which you can run pilot studies to confirm the panel’s performance.
Together, we can then review your results and, if necessary, identify strategies to improve the panel—such as increasing probe density for specific targets or altering the tiling strategy.
When the panel meets your standards, we’ll deliver a larger aliquot of your custom target enrichment panel.
7. Run a sensitive, custom panel
At this point in the process, you have a custom panel that’s been precisely printed to meet your needs and help you perform sensitive sequence analyses.
Should you need to refine the panel at a later time, we will be here to help!
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