Global Screening Array

The Infinium Global Screening Array (GSA) by Illumina has a very rich up to date content and is suitable for GWAS

including rare variants, while also containing clinically relevant content. We currently run the GSA MD version 3, the

GSA DTC version 3, and the GSA MD +GOALL version 3. These arrays fit 24 samples. The SNP lists of the Infinium Global

Screening Array are openly available. Please use the links below to download the csv file.

 

A new version of the GSA, the GSA version 4, is expected end of 2022. Contrary to earlier versions, this array fits 48

samples and does not have the additional MD or DTC content. It is a 850K SNP array, and can be run with or without

enhanced PGx.

 

GSA MD + GOALL version 3

Precision Medicine Arrays

Axiom Precision Medicine Diversity Array (PMDA) and Axiom Precision Medicine Research Array (PMRA) by Thermofisher are comprehensive imputation aware genotyping resources each offering >900K variants enabling insights into complex disease susceptibility, immune response, pharmacogenomics research among others. Arrays offer large GWAS grid (>800K markers) to boost disease association studies across diverse populations inclusive of EUR.

Global Clinical Research Array

By the end of 2022, Illumina is launching their new Excalibur workflow and arrays. The Global Clinical Research Array (GCRA ) is a 24 sample array, that covers 1.3M SNP’s. It is available with or without enhanced PGx.

 

GCRA version 1

MethylationEPIC array

The MethylationEPIC array by Illumina is a cost effective solution for epigenome wide association studies. The array gives single base methylation information for over 850.000 CpGs throughout the human genome. The EPIC array contains >90% of the original Methylation450 Beadchip content plus an additional 350.000 CpGs in enhancer regions.

The content of the Beadchip was selected by a global consortium of epigenomic experts The Methylation Epic v1.0, which we are currently running, will phase out in the first half op 2023, and will be replaced by the MethylationEPIC v2.0. Like version 1 this is a 8 sample chip with regular beads, and contains 900K CpGs. Expected release of version 2 is end of 2022.

The EPIC array has a comprehensive genome wide coverage of the methylome , featuring

• 95% of CpG islands

• sites outside of CpG islands

• Non CpG methylated sites identified in human stem cells

• Differentially methylated sites identified in tumor versus normal

• FANTOM5 enhancers

• ENCODE open chromatin and enhancers

• DNase hypersensitive sites

• miRNA promoter regions

 

 

 

For more information, please contact dr. Gaby van Dijk.