Introduction

The Illumina Infinium Global Diversity Array with Enhanced PGx-8 provides streamlined sample preparation and high multiplexing. Using improved pharmacogenomics (PGx) library preparation with core Infinium I and Infinium II probe designs and a dual-color channel approach, the Infinium Global Diversity Array with Enhanced PGx-8 enables the DNA analysis of up to several million SNPs and copy number variation (CNV) markers per sample.

The Infinium Global Diversity Array with Enhanced PGx-8 accomplishes multiplexing by using a new PGx library preparation process that combines whole genome amplification and targeted gene amplification with direct, array-based capture and enzymatic scoring of the SNP loci. PGx library preparation enables accurate calls for genes impacted by pseudogene interference. Locus discrimination or copy number variation (CNV) determination comes from a combination of high bead type representation per feature, sequence-specific hybridization capture, and array-based, single-base primer extension. With the Infinium I probe design, the 3' end of the primer overlaps with the SNP site. If there is a perfect match, extension occurs and a signal is generated. If there is a mismatch, extension does not occur and no signal is generated. In the case of the Infinium II probe design, the 3' end of the primer is positioned directly adjacent to the SNP site, or if a nonpolymorphic probe, directly adjacent to the nonpolymorphic site.

Allele-specific, single-base extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labeled nucleotide. C and G nucleotides are biotin labeled. A and T nucleotides are dinitrophenyl labeled. Signal amplification of the incorporated label further improves the overall signal-to-noise ratio of the assay.

The Infinium Global Diversity Array with Enhanced PGx-8 offers:

• High multiplexing
• High call rate and accuracy
• Unlimited genomewide marker selection
• Minimal risk of carryover contamination
• Low DNA input—200 ng per sample
• Compatibility with LCG automated X-stain
• Compatibility with Illumina iScan System
• Multiple sample BeadChip format

Before using the procedures in this guide, read Infinium Lab Setup and Best Practices. All Infinium Global Diversity Array with Enhanced PGx-8 documentation assumes that you have already set up the laboratory space and that you are familiar with the standard procedures and safety precautions.

• If you are using Infinium Global Diversity Array with Enhanced PGx-8 with Illumina Connected Analytics (ICA), see the ICA page on the Illumina support site for setup information, including managing workgroups.
• Before run setup, download the DMAP files for the arrays, and prepare a sample sheet. Use the Decode File Client to download the DMAP files.
• Accession BeadChips using the instructions in the product documentation for your analysis product.
• Samples that were prepared together must be analyzed together. Do not combine samples prepared in different sample preparation batches into a single analysis. A batch size of 96 samples or more is recommended to remove batch effect. A minimum of 48 samples is required to run analysis.