Introduction
The Illumina Infinium Global Diversity Array with Enhanced PGx-8 provides streamlined sample preparation and high-level multiplexing. The assay uses improved pharmacogenomics (PGx) target preparation with core Infinium I and Infinium II probe designs and a dual-color channel approach to enable the DNA analysis of 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 target preparation process that combines whole genome amplification and targeted gene amplification with direct, array-based capture and enzymatic scoring of the SNP loci. PGx target preparation enables accurate calls for genes impacted by pseudogene interference. Locus discrimination or 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. With 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.
This resource provides instructions for performing the semi-automated assay workflow using the following systems:
| • | Infinium Automated Pipetting System (IAPS) with Illumina Lab Automation Software Solution (ILASS) |
| • | IAPS with Illumina Automation Control (IAC) |
The Infinium Global Diversity Array with Enhanced PGx-8 offers the following features:
| • | High-level multiplexing. |
| • | High call rate and accuracy. |
| • | Unlimited genomewide marker selection. |
| • | Minimal risk of carryover contamination. |
| • | Low DNA input of 200 ng per sample. |
| • | Compatibility with Infinium Automated Pipetting System (IAPS) for post amplification steps. |
| • | Compatibility with Illumina iScan System. |
| • | Multiple-sample BeadChip format. |
Best Practices
All Infinium Global Diversity Array with Enhanced PGx-8 documentation assumes that you have set up the laboratory space, are familiar with the standard procedures and safety precautions, and understand how to use the IAPS. For details, refer to the following resources:
| • | Infinium Lab Setup and Best Practices |
| • | Infinium Assay Consumables and Equipment List |
| • | Infinium RoMa (IAPS with ILASS) Product Documentation |
Modifying the protocol can result in assay failure, suboptimal results, or an increase in indeterminate calls.
Before hybridization, download the decode map (DMAP) files for the arrays. Refer to the Illumina Support Site to download the DMAP files from the Decode File Client.
System Maintenance and Usage
IAPS with ILASS
Before beginning an automated run, complete daily maintenance tasks and perform a system flush. Repeat the system flush if the instrument is idle for two hours or longer (on the same day). Perform a bleach wash at the beginning or the end of each day. For details, refer to the Infinium RoMa (IAPS with ILASS) Product Documentation.
IAPS with IAC
For maintenance and usage instructions, refer to Infinium Lab Setup and Best Practices and Infinium LiHa and Infinium RoMa Operating Manual (document # 1000000110155).
