AmpliSeq for Illumina SARS-CoV-2 Research Panel

The AmpliSeq for Illumina SARS-CoV-2 Community Panel, in combination with AmpliSeq for Illumina library prep, index, and accessories, is a targeted RNA/cDNA amplicon assay for epidemiological research of the SARS-CoV-2 virus (Research Use Only). The panel is a 2-pool design, containing 247 amplicons/primer pairs (242 unique amplicons (Pool 1: 125 amplicon, Pool 2: 122 amplicons): 237 viral specific SARS-CoV-2 targets and 5 human gene expression controls) ranging from 125-275 bps in length that covers >99% of the viral genome and all potential serotypes of the virus.

The panel is intended for research use only (RUO) applications, and not for use in diagnostic procedures. No claim or representation is intended to provide information to indicate the panel may be used in diagnosis, prevention, or management of an infection.

We recommend customers evaluate commercially available extraction kits capable of isolating viral RNA. The QIAGEN QIAmp Viral RNA Mini Kit (PN 52904) has been demonstrated to be compatible for use in next-generation sequencing library preparation and other testing methods internally. In the event of a back order, any commercially available extraction kit from other companies should be compatible as well.

See the following resources for additional information:

• https://www.fda.gov/media/134922/download
• https://www.illumina.com/documents/products/appnotes/ngs-coronavirus-app-note-1270-2020-001.pdf

Library preparation for the AmpliSeq for Illumina SARS-CoV-2 Community Panel follows the AmpliSeq for Illumina Custom and Community Panels Reference Guide: Chapter 3 Protocol for RNA Panels (https://support.illumina.com/downloads/ampliseq-for-illumina-custom-and-community-panels-reference-guide-1000000036408.html).

In “Amplify cDNA Targets”, proceed with the following:

• 2 primer pools for the AMP_RNA program
• Table 7: 97–192 primer pairs per pool at 18 cycles and 4 minutes
  • Pool 1: 125 amplicons/primer pairs, Pool 2: 122 amplicons/primer pairs
• Table 8: Adjustments can be made based on sample quality and sample input

Library preparation using the AmpliSeq Library PLUS for Illumina is compatible with all AmpliSeq CD or UD Index Sets for Illumina.

Read depth: 250,000 reads per sample.

Read length: 2 x 151 bp.

Platforms: AmpliSeq for Illumina libraries are compatible with iSeq 100, MiSeq, MiniSeq, and NextSeq systems.

After adding the panel to your MyIllumina cart and checking out, you will receive your panel order. The panel should state the solution ID: IAACY126664577_100.

Depending on sample throughput, the customer also needs to order the following:

Library Prep

• AmpliSeq Library PLUS (24 Reactions) for Illumina - 20019101
• AmpliSeq Library PLUS (96 Reactions) for Illumina - 20019102
• AmpliSeq Library PLUS (384 Reactions) for Illumina - 20019103

Index Adapters

• AmpliSeq UD Indexes for Illumina (24 Indexes, 24 Samples) - 20019104
• AmpliSeq CD Indexes Set A for Illumina - 20019105
• AmpliSeq CD Indexes Set B for Illumina - 20019106
• AmpliSeq CD Indexes Set C for Illumina - 20019107
• AmpliSeq CD Indexes Set D for Illumina - 20019167
• AmpliSeq CD Indexes Set A-D for Illumina® (384 Indexes, 384 Samples) - 20031676

Accessory Products

• Ampliseq cDNA Synthesis for Illumina® - 20022654
  • Sufficient for 100 reactions

1 order contains enough oligos to prepare 2250 samples.

1 order = $2223 USD is sufficient for preparing 2250 samples (~$9/amplicon). This does not include AmpliSeq Library PLUS for Illumina, Ampliseq cDNA Synthesis for Illumina, or AmpliSeq CD or UD Indexes for Illumina.

The BaseSpace Sequence Hub DNA Amplicon or DRAGEN Metagenomics Pipeline apps can be used for data analysis.