What read length should I use on MGI sequencers for CleanPlex for MGI libraries?
MGI sequencers support 2 x 100 bp and 2 x 150 bp read lengths. CleanPlex® for MGI Ready-to-Use Panels are designed for 2 x 150 bp read length. However, 2 x 100 bp can also be used. CleanPlex® for MGI Custom Panels can be designed to accommodate either 2 x 100 bp or 2 x 150 …
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What is the recommended minimum read coverage for Cleanplex UMI NGS panels?
The suggested minimum read coverage is 7,500 paired-end reads/ amplicon/ nanogram of DNA input for detection of 0.1% allele frequency, when the minimum DNA input amount is also met. 7,500 paired-end reads equates to 3,750 clusters or single-end reads on the sequencing chip. Please see FAQ for DNA input requirement for detecting 0.1% somatic variant …
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Does Paragon offer bioinformatics and data analysis support for ready-to-use panels and custom panels?
We’re actively developing a cloud-based data analysis package and customer facing software using our analysis algorithms. In the near term, our bioinformatics team can provide plug-ins specific to Cleanplex libraries for common data analysis pipelines. The team can also offer support, assistance, and guidance to customers who may need additional help in data analysis for our …
What is the uniformity of a typical CleanPlex target enrichment library?
The uniformity ( ≥ 0.2X mean depth) of most CleanPlex libraries are greater than 95%. For example, the observed uniformity (at ≥ 0.2X mean depth) of the CleanPlex OncoZoom Panel is greater than 99% for both NA12878 (a genomic DNA standard) and Horizon Discovery’s HD780 (a cfDNA standard) (see plots below).
What are the AT and GC biases of CleanPlex target enrichment libraries?
The observed AT and GC dropouts are below 3% in CleanPlex® ready-to-use libraries. Below is a typical plot of Coverage Depth vs. GC Content of a library made with CleanPlex® OncoZoom Panel.
What read length should I use on Illumina sequencers for CleanPlex and Cleanplex UMI libraries?
All ready-to-use libraries are designed for 2 x 150 bp read length, meaning final library molecules with sequencer-specific sequences are < 300 bp. Custom panels are typically also designed for 2 x 150 bp read length. However we can also design amplicons of 500 bp for 2 x 250bp reads. Please specify your preference when submitting the design.
What is peak around 150 -190 bp in addition to the main library peak on the fragment analyzer trace?
Peaks from 150 – 190 bp are residues of digested non-specific amplification products (see examples below). They come from incomplete removal of small-molecular-weight materials during magnetic bead purification after digestion. The digestion reagent cuts non-specific amplification products into small pieces, which are then removed during magnetic bead purification. Peaks from 150 – 190 bp are …