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How to use the Infinium Global Diversity Array with Enhanced PGx Auxiliary File

What is the Auxiliary File?

The Infinium Global Diversity Array with Enhanced PGx Auxiliary File identifies markers that are used by the following DRAGEN Array v1.0.0 Analysis types:
  • DRAGEN Array - PGx - CNV calling
  • DRAGEN Array - PGx - Star allele annotation

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

  1. 1.
    Create a GenomeStudio genotyping project using the standard GDA + enhanced PGx product files (either Build 37 or Build 38) provided by Illumina.
    1. 1.
      Download the BPM manifest and EGT cluster file from Infinium Global Diversity Array with Enhanced PGx Product Files page.
    2. 2.
      For more information on creating a GenomeStudio genotyping project, see the GenomeStudio 2.0 User Guide and [GenomeStudio Genotyping Introduction webinar](
      ).
  2. 2.
    Download the Auxiliary File from the Infinium Global Diversity Array with Enhanced PGx Product Files page. Extract the .txt file. This file contains information for 5811 probes.
  3. 3.
    Import the auxiliary file into the GenomeStudio Full Data Table or SNP Table.
    1. 1.
      Select 'Import columns into the table' icon.
    2. 2.
      The 'Import' window appears. Select 'Column Import' and browse to the location of the 'GDA_ePGx_E1_E2_GS_Import.txt' file.
  4. 4.
    Five new columns will appear in the table: rsId, combined_hgvs, combined_alleles, gene, and probe_in_map.
  5. 5.
    Repeat Steps 3-4 for the other table. For example, if columns were imported into Full Data Table first, repeat for SNP Table.
  6. 6.
    Select 'Filter rows' icon.
  7. 7.
    Filter by column 'probe_in_map' = 1 and click 'OK'.
  8. 8.
    The table will display 5811 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 [email protected].
Last modified 25d ago
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