# 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](/dragen-array-v1.3/product-guides/dragen-array-local-analysis.md#run-dragen-array-local).

## 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](https://cpicpgx.org/) (Clinical Pharmacogenetics Implementation Consortium)
  * Alternative: [DPWG](https://www.pharmgkb.org/page/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](https://github.com/illumina-swi/dragen-array-docs/blob/DAv1.3/docs/product-guides/dragen-array-cloud-analysis/dragen-array-local-analysis/README.md#pharmacogenomic-analysis-for-semi-custom-arrays). 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

### 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 using a commercial Infinium PGx array backbone (such as the Global Diversity Array with enhanced PGx), it is important to retain all backbone content 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](/dragen-array-v1.3/product-guides/dragen-array-local-analysis.md#toc150786131) section in the DRAGEN Array Local Analysis documentation.

## Applicable Arrays

For specific product compatibility, see the [Product & Analysis Compatibility](/dragen-array-v1.3/overview/our-features.md#_product_compatability) table.

## Additional Resources

* [PGx Allele Definitions and PGx Guidelines](/dragen-array-v1.3/reference/pgx-allele-definitions-and-pgx-guidelines.md)
* [PGx Star Allele Coverage](/dragen-array-v1.3/reference/pgx-star-allele-coverage.md)
* [PGx CNV Coverage](/dragen-array-v1.3/reference/pgx-cnv-coverage.md)


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