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DRAGEN Array PGx Star Allele Annotation

Quality Control Recommendations

For PGx CNV calling, it is recommended that 96 or more samples passing LogRDev <= 0.2 are included in the analysis. For PGx star allele calling, it is recommended to QC the samples and review the samples that have Log R Dev > 0.2, call rate < 0.99, or TGA Control probe < 1.0 to assess the reliability of the analysis. These metrics are provided in the genotyping sample summary file (gt_sample_summary.csv). For more details, see the explanation for the local analysis.

Custom Configuration Options

When using DRAGEN Array – PGx – Star allele annotation cloud analysis type, you have the following configuration option:

  • Metabolizer Status Database: Option to change the default metabolizer status database

    • Default: CPIC (Clinical Pharmacogenetics Implementation Consortium)

    • Alternative: DPWG (Dutch Pharmacogenetics Working Group)

Semi-Custom PGx Products

Running Semi-Custom PGx Analysis on Cloud

Detailed notes on running this analysis for local can be found here. But for cloud, a workaround is necessary because semi-custom product samples are filtered from the BeadChip table in BaseSpace. Follow these steps:

  1. Select an existing commercial product configuration (e.g., GDA_PGx-8v1-0_G4 - GRCh38)

  2. Kick off an analysis using the Import Sample Sheet option for the semi-custom product samples

Alternatively, to upload IDATs directly for a semi-custom product (rather than using Import Sample Sheet with a commercial configuration):

  1. If a custom configuration does not already exist, create one using the Add Custom Configuration option and upload the product files for the semi-custom product.

  2. Select the custom configuration for the semi-custom product.

  3. Proceed to sample selection, choose Import IDAT Files, and upload the IDATs.

For step-by-step details on these options, see Running Analysis / Launch Analysis.

Important Notes for Semi-Custom Arrays

  • PGx CNV and star allele calls are limited to content included on the commercial Infinium PGx arrays. Additional semi-custom content will not be included in the pharmacogenomic results.

  • When designing a semi-custom array based on a commercial Infinium PGx array (such as the Global Diversity Array with enhanced PGx), it is important to retain all commercial content (i.e., keep all content from the commercial product, such as GDA-ePGx) in the design, as removing content could decrease the quality of results.

For detailed information on running complete semi-custom PGx analysis (including steps with semi-custom product files and commercial product files), see the Pharmacogenomic Analysis for semi-custom arrays section in the DRAGEN Array Local Analysis documentation.

Applicable Arrays

For specific product compatibility, see the Product & Analysis Compatibility table.

Additional Resources

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