PGx Star Allele Coverage
Theoretical Coverage
The PGx genes and star/variant alleles listed below can be detected by DRAGEN Array v1.1 if available on the microarray. Known and novel star alleles not in the below list will not be reported. Star allele definitions are sourced from PharmVar and PharmGKB.
Among the PGx genes, HLA-A, HLA-B, and IFNL3/IFNL4 alleles are covered through tagging variants, specifically HLA-A,*31:01 (rs1061235.A>T); HLA-B,*15:02 (rs144012689.T>A); HLA-B,*57:01 (rs2395029.T>G); HLA-B,*58:01 (rs9263726.G>A); IFNL3/4, rs12979860 variant (T). Reliability of the tagging SNPs varies depending on the population. Additional information on PGx gene types, variant type versus star allele type, can be found here: Introducing-dragen-array-1-0-for-infinium-array-based-pharmacogenomics-analysis
PGx Star Allele Coverage for Specific PGx Products
PGx star alleles can only be called when the related variants in the star allele definition are present in a PGx product. An auxiliary file ([Product]_GS_import.txt) is provided for each product with the PGx variants and associated star alleles. The product files pages that contain the auxiliary files are listed in the table below.
Instructions on how to use the auxiliary file can be found here: How to use the auxiliary file.
Known Limitations of GDA-ePGx, GSAv4-ePGx, and GCRA-ePGx.
APOE: GSAv4-ePGx and GCRA-ePGx do not support calling E2 and E4 due to the lack of functional probes for rs7412 and rs429358.
CYP2A6: GDA-ePGx does not support *5 due to lack of coverage for *5 core variants.
CYP4F2: for all three products
*1 and *2 are not distinguishable due to the lack of probes for rs30193105. Samples with *2 will be called as *1.
*3 and *4 are not distinguishable due to the lack of probes for rs30193105, while *3 core variant rs2108622 is covered by all three products. Samples with *4 will be called as *3.
UGT1A1: *28 (rs8175347 [TA]8) and *37 (rs8175347 [TA]9) are not covered in all three PGx products due to the lack of functional probes.
UGT2B15: GSAv4-ePGx and GCRA-ePGx do not support *4 or *5 due to the lack of probes for rs4148269 and rs1902023.
PGx Variants Masked in DRAGEN Array
During DRAGEN Array star allele calling, poorly performing PGx variants are masked and treated as "No Calls". Star alleles that are solely defined by the masked variants will NOT be called by DRAGEN Array. The tables below provide the variants that are masked per product with each row represents a single variant. The Variant_ID matches the ID field of the corresponding SNV VCF entry of the PGx product.
GDA-ePGx
GSAv4-ePGx
GCRA-ePGx
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