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 …

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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 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 …

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