Enrichment probe design FAQ for Illumina Rapid RNA kits

For Illumina Rapid RNA Prep with Enrichment, what enrichment panels are compatible? Is there an option for custom panels?

Illumina Rapid RNA Prep with Enrichment chemistry supports the following panels, though several panels follow separate, dedicated Product Documentation:

As part of the main Illumina Rapid RNA Prep with Enrichment user guide:

• Illumina Custom Enrichment Panel v2 (design panels in Illumina DesignStudio)

Panels that follow separate, dedicated Product Documentation:

• Exome 2.5 panel,as part of Illumina Rapid RNA Prep with Exome 2.5 Enrichment

• Viral Surveillance Panel v2 panel, as part of Illumina Rapid Viral Surveillance Panel v2

• Respiratory Pathogen ID/AMR Enrichment Panel (RPIP),as part of Illumina Rapid Respiratory Pathogen ID/AMR Enrichment Panel Kit

• Respiratory Virus Oligo Panel v2, as part of Illumina Rapid Respiratory Virus Enrichment Kit

Can users use their existing Illumina Custom Enrichment Panels v2 with Illumina Rapid RNA Prep with Enrichment?

Users who have custom enrichment panels designed against DNA (primarily against CDS) may use these in the Illumina Rapid RNA Prep with Enrichment assay. A slight impact to mapping to RNA-transcripts vs intronic regions, and impact to coverage may be seen that may be more pronounced for smaller exons.

Users who have been using Concierge-designed RNA-specific custom enrichment panels in the Illumina RNA Prep with Enrichment assay can switch over to using them in the Illumina Rapid RNA Prep with Enrichment assay.

Custom panel testing with the Illumina RNA Prep with Enrichment assay in development was done with Custom Enrichment Panel v2, but legacy Illumina Custom Enrichment Panel ("ICEP") is expected to be compatible as well as the product uses the same format oligos used eg, in VSPv2 and CEX which were tested with Illumina Rapid RNA Prep with Enrichment assay.

Are RNA Custom Enrichment Panel v2 designs de novo or are the probes from a pre-designed database?

Probes are pulled from a pre-designed database for each gene in the Human genome. This means that RNA Custom panel designs can be generated and summarized within minutes for quick and easy custom designs.

Can RNA Custom Enrichment Panel v2 designs cross exon-exon boundaries?

The priority is to place the probe within an exon and flank a junction, but if that is not possible, it can span a junction to get the coverage needed. Note, UTR are not included in the design. Only Coding regions of Exons are included in the probe designs.

Can fusion genes or splice variants be incorporated into panel designs?

Illumina does not provide annotations for gene fusions in DesignStudio. All known and annotated transcripts for a given gene will be included in the design for coverage of all transcripts isoforms. This can be customized in DesignStudio by selecting the transcript isoform to design against instead of selecting the gene name.

What species of custom RNA panels are supported?

Human genomes: hg19, hg38. For non-human designs, contact the Illumina Concierge team.

Is there a way to tell if particular probes that are designed are isoform-specific or can target all isoforms of a given gene?

DesignStudio calculates the coverage of all transcript isoforms for a selected gene. The probe list does not specifically identify those probes that are unique for a single isoform. You can select a specific transcript as a target, instead of gene which has multiple transcripts, however that transcript may share exons with other transcripts of the same gene.

For any feedback or questions regarding this article (Illumina Knowledge Article #10211), contact Illumina Technical Support [e-mail].