AmpliSeq for Illumina Comprehensive Panel v3 FAQs

The adapters used in this assay are optimized for the AmpliSeq workflow. Nextera or TruSeq Adapters are not compatible with this assay.

See Contents & Storage.

It is possible to run 3 different AmpliSeq for Illumina designs each with barcodes on the same sequencing run. However, your target amplicon size and required coverage must be achieved in a single run.

A 2×151 bp paired-end read is recommended.  

See Product Compatibility.

You can manipulate coverage by increasing sequencing throughput (eg, a larger flow cell output or sequencing platform) or reducing the number of samples pooled per run.

Yes, there are example data sets in BaseSpace Public Data.

On-target bases shows the percentage of total sequenced bases that map to target regions in the reference genome. This metric reflects the percentage of bases from amplicons that a) were designed, synthesized, and pooled and b) generated sequence data mapping to the target regions.

No. Manifest files for any RNA panel containing fusions are unavailable in a non-encrypted format. Only the encrypted manifest file is available. 

Information about exact breakpoints contained in all RNA fusion panel designs is not provided. The result files produced by Illumina software analysis tools provide details of any RNA fusion events identified by the software. For information on which gene pairs are evaluated for your panel, see the panel's data sheet. 

Local Run Manager and BaseSpace Sequence Hub have apps available for analysis. The DNA Amplicon Analysis App and RNA Amplicon Analysis App are available on BaseSpace Sequence Hub. Further analysis can be performed on any variant calls using BaseSpace Variant Interpreter. Local Run Manager has a similar DNA Amplicon Analysis Module and RNA Amplicon Analysis Module which utilizes the same workflow and algorithm as the BaseSpace Sequence Hub Apps. 

The DNA Amplicon analysis workflow can be used to perform alignment and variant calling and the RNA Amplicon analysis workflow for fusion calling.  Additionally, OncoCNV caller, a BaseSpace Lab Apps is available for CNV analysis.

Illumina software packages, including BaseSpace Sequence Hub Apps, do not provide alignment files as output from the analysis. At this time, only the final reporting of the results from the analysis are provided. For more details, consult the software's documentation. 

No. The software only reports detected fusion events. For information on which gene pairs are evaluated for your panel, see the panel's data sheet.