Infinium Arrays

Infinium arrays at GTAC@MGI support high throughput SNP genotyping and DNA methylation profiling using Illumina® BeadChip workflows, including current and legacy formats. Projects range from large cohort studies to focused disease studies where array based profiling is the right balance of scale, cost, and standardized outputs.

  • Support for SNP genotyping arrays and methylation arrays across multiple Infinium BeadChip formats.
  • Workflow execution designed for cohort scale processing with consistent handling and tracking.
  • Array QC review to protect downstream GWAS and epigenetic analyses.
  • Data delivery suitable for standard genotype calling and methylation analysis pipelines.
MGI scientist processing Illumina Infinium arrays in the lab

Infinium Arrays Platforms and Deliverables

Infinium arrays

Supported platforms

  • Infinium Global Screening Array and Global Diversity Array
  • Infinium MethylationEPIC v2.0
  • Array and Methylation Screening Array
  • Legacy SNP and methylation arrays
  • Non human arrays
Input material

Sample requirements

  • High quality genomic DNA
  • Typical input range 200 to 500 ng per sample
  • A260/280 approximately 1.8 to 2.0
  • Minimal degradation, contamination, or shearing
  • Consultation available for low input or challenging samples
Data outputs

Deliverables

  • Genotype calls and QC metrics for SNP arrays
  • Beta values, M values, and QC for methylation arrays

Infinium Arrays Services

Infinium Arrays Technology Comparison

SNP genotyping arrays

Use when large cohorts and comparability matter

  • Genome wide variant coverage optimized for association studies
  • Consistent marker sets across thousands of samples
  • Strong compatibility with existing GWAS datasets and consortia

DNA methylation arrays

Use when epigenetic profiling is the primary goal

  • Genome wide CpG coverage using standardized probe designs
  • Reproducible measurements across batches and time points
  • Alignment with established EWAS pipelines and reference datasets

Current array designs

Use for new studies and forward looking cohorts

  • Latest content and probe chemistry from Illumina
  • Improved genome coverage and updated annotations
  • Best option for new GWAS or epigenetic study launches

Legacy array designs

Use when continuity outweighs new content

  • Compatibility with historical datasets and prior study phases
  • Preservation of marker overlap for longitudinal analyses
  • Supported workflows for discontinued but widely used arrays

Final array selection depends on study design, cohort size, and the need for continuity with existing datasets. Consultation is recommended when mixing array generations or integrating array and sequencing data.

Infinium Arrays Instrumentation

Illumina iScan System instrument

Illumina iScan System

High-throughput imaging platform for Illumina Infinium SNP and DNA methylation arrays.

  • Processes Infinium SNP and methylation BeadChips on a single scanner
  • Compatible with both current and legacy Infinium array designs
  • Generates high-resolution IDAT files for downstream analysis
  • Supports large cohort and multi-batch array projects
  • Stable performance suited to long-term and multi-center studies