AmpliSeq for Illumina Custom and Community Panels FAQs

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  • Input


  • The assay uses between 1 and 100 ng of DNA per primer pool, with most designs using 10 ng per pool.

    We’ve seen success with low quality inputs using the protocol modifications indicated in the user guides.  Commercially available or laboratory validated DNA extraction methods typically yield DNA that is compatible with this assay. DNA purity should have an A260/A280 ratio of 1.8–2.0. PicoGreen is recommended for an accurate quantification. 

    Only use FFPE-derived DNA when using short amplicon lengths of 140 or 175 bp. Shorter amplicons provide better amplification than longer ones when the sample input is fragmented FFPE-derived DNA. 

    There is a limit of 12-6,144 primer pairs per pool. If generating target region greater than 5Mb, we recommend selecting an enrichment option.

  • Sequencing


  • A 2×150 bp paired-end read is recommended for 140-275 bp amplicon sizes. Up to 2x300 bp paired-end run on the MiSeq is recommended for 375 bp amplicon sizes.

    This kit has integrated sample barcodes that enable pooling of up to 96 samples per sequencing run. However, the actual number of samples that can be pooled together per sequencing run depends on the number of amplicons and the desired depth of sequencing coverage. An online calculator is provided in DesignStudio to help with these calculations.

  • Analysis


  • 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.

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

    DesignStudio returns high confidence amplicon designs that have delivered unprecedented amplicon multiplexing performance. Since each design is unique and sample input can vary, performance of the design will need to be tested empirically. 

  • AmpliSeq for Illumina On-Demand – IGV Viewer


  • The “observed coverage” track indicates the number of observed reads for each amplicon of each targeted gene during validation experiments on a NextSeq. Use this track as general guidance for the likely performance when running an experiment. While values can vary among assays, the general coverage trend should remain consistent.

    Gaps occur where there are no amplicons to provide coverage for the intended target. We have made every effort to minimize the occurrence of these regions in our On-Demand designs.

    The Y-axis represents the observed coverage normalized by the mean amplicon coverage for the gene.

    No. The IGV viewer can only focus on your gene of interest. In the Grid View, select a gene, and the IGV viewer updates automatically to center on that gene.

    All amplicons in the design contain reads that are visualized in the “observed coverage” track. If the number of reads covering an amplicon is relatively small in comparison to neighboring amplicons, the “observed coverage” track appears empty. However, if you change the scale to a lower value, you will then be able to visualize the lower number of reads. If the observed coverage track is not present, the designer notifies you why that track is not available.