Can I use CleanPlex technology to detect SNV, CNV, and Fusions?
The CleanPlex system can detect SNV, CNV, and known Fusions. Unknown fusion detection on the other hand is not compatible with our chemistry.
What types of custom panels can you design?
We can design targeted panels for any target with a reference sequence. Some examples of target species include humans, animals, plants, insects, bacteria, and viruses. Our sample types include, but not limited to, cfDNA, FFPE samples, blood samples, and tissue samples. For bacterial panels, a minimum 7 amplicons is required. We can build 7 housekeeping …
How much DNA should I use to detect 0.1% somatic variant frequency?
With our CleanPlex UMI technoloy, one can detect variations down to 0.1% allele frequency. We recommend using 30-50 ng of genomic DNA input for somatic variant detection at 0.1%, or 20-30 ng for 0.25%. More input (50-80 ng input) may be necessary to improve variant calling when DNA quality is uncertain (such as DNA from …
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What is the recommended minimum read coverage for Cleanplex NGS panels?
For Genotyping applications, minimum read coverage per amplicon is 20X. However, we suggest starting with 1000 PE reads/amplicon/sample for the first sequencing run to account for any potential off target, non-mapping, or poor quality sequencing runs. For subsequent sequencing runs, the allocated PE reads/amplicons can be significantly reduced based on the panel’s performance and sequencing …
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How soon will I get my custom designs after submission?
It depends on the difficulty of the design. We have a robust assay design algorithm that handles most designs relatively quickly. One can expect between 3 days to 2 weeks turnaround time (TAT) starting from the moment our design team start working on the requests. The following are the most common reasons for potentially longer …
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Is there a minimum number of targets for a custom panel design?
Short answer is no. We have designed panels that contain as little as 2 amplicons and we can also offer single-amplicon options. However, it is recommended that a panel contains at least 10 amplicons per pool, to best utilize our multiplex capabilities, and to achieve the best sequencing results from our technology.
How do I submit a custom panel design request?
To submit a custom design request, you will need the following: 1. A Paragon Genomics customer account. Register here. 2. If you are targeting genomes other than human and mouse, be ready to provide the reference genome for design upon request; 3. If your targets are not human genes, please provide the target region in …
What are the differences between a ready-to-use panel and a custom panel?
Ready-to-use panels are initiated and designed by the Paragon Genomics R&D team that aim to provide the best solutions to specific research areas and/or clinical needs. The contents of these panels, as well as the performance, are internally validated to ensure that it passes our high standards. Custom panels are designed to satisfy the need …
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How much DNA should I use to detect 1% somatic variant frequency?
Lower DNA input will generally increase the possibility of inaccurate calling of variant frequencies. As shown in the following figure on the left, when less and less DNA was amplified with CleanPlex® OncoZoom Panel, increasingly larger variations were observed for calling alternative alleles at 50% frequency, even though the uniformity may not deteriorate significantly (figure below on …
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