How to use the Auxiliary File for Infinium BeadChips with Enhanced PGx Content

What is the Auxiliary File?

The Auxiliary file identifies markers that are used by the following DRAGEN Array Analysis types:

• DRAGEN Array - PGx - CNV calling

• DRAGEN Array - PGx - Star allele annotation

The tab-delimited text file can be imported into GenomeStudio and used to review and optimize PGx variant GenTrain cluster positions. The Auxiliary file is provided for each PGx Array product and is available to download from the DRAGEN Array Software Downloads page or the respective BeadChip Product Files page.

Instructions on how to import the Auxiliary file into GenomeStudio 2.0 genotyping project:

1. Create a GenomeStudio 2.0 genotyping project using the standard PGx product files provided by Illumina.

   1. Download the BPM manifest and EGT cluster file from the BeadChip Product Files page:

   2. Infinium Global Diversity Array + Enhanced PGx Product Files

   3. Infinium Global Screening Array v4.0 + Enhanced PGx Product Files

   4. Infinium Global Clinical Research Array + Enhanced PGx Product Files

   5. For more information on creating a GenomeStudio genotyping project, see the GenomeStudio 2.0 User Guide and GenomeStudio Genotyping Introduction webinar.

2. Download the Auxiliary file and extract the .txt file which contains information for several thousand probes.

• BeadChip	Number of probes
  Global Diversity Array v1.0 + ePGx (GDA + ePGx)	5811
  Global Screening Array v4.0 + ePGx (GSA v4 + ePGx)	7333
  Global Clinical Research Array v1.0 + ePGx (GCRA + ePGx)	7442

1. Import the Auxiliary file into the GenomeStudio Full Data Table or SNP Table.

   1. Select 'Import columns into the table' icon.
   2. The 'Import' window appears. Select 'Column Import' and browse to the location of the 'Import.txt' file.
2. Five new columns will appear in the table: rsId, combined_hgvs, combined_alleles, gene, and probe_in_map.
3. Repeat Steps 3-4 for the other table. For example, if columns were imported into Full Data Table first, repeat for SNP Table.

4. Select 'Filter rows' icon.
5. Filter by column 'probe_in_map' = 1 and click 'OK'.
6. The table will display a filtered list of several thousand rows which are used for PGx CNV calling and star allele annotation.

Column Headings Information

Column Name	Explanation
probe_in_map	A value of 1 means the probe is used for PGx CNV calling and star allele annotation. Filter by this column to display the probes used for PGx CNV calling and star allele annotation.
combined_alleles	Values Simple variant (begins with rs) Star allele haplotype Alleles are delimited by trailing semicolon. Always include trailing semicolon if using filter or using Find function in GenomeStudio. This will ensure search is specific to intended query (For example, if searching for *11 type *11; to ensure no unintended results for other star alleles)
gene	Provides associated Gene name. Use this column to filter for genes of interest. Review PGx Star Allele Coverage for more information.
combined_hgvs	Human Genome Variation Society (HGVS) nomenclature is used to denote variants. Every probe has a HGVS tag which includes the variant information. Refer to this resource on nomenclature: HGVS Simple Examples: Reference sequence for genomic (nucleotide): NC_ is a genomic reference sequence based on a chromosome Types of variants include substitution, deletion, duplication, insertion, deletion/insertion
rsId	The rsIDs are derived from public pharmacogenomics databases.

For additional information, refer to the DRAGEN Array User Guide.

For any feedback or questions regarding this article (Illumina Knowledge Article #8505), contact Illumina Technical Support [e-mail].