Illumina® Infinium HD Technology

Infinium HD Genotyping Technology (Illumina®)

  • Interrogate between 3,000 and >= 5M loci (SNP and indel) in parallel
  • Custom genotyping for studying targeted genomic regions of interest on any species
  • Commercial arrays with standard content


  • Genome-wide association studies (GWAS) for mapping genetic variation across populations to identify variants associated with a phenotype
  • SNP discovery validation
  • Copy number variation (CNV) analysis
  • Cytogenetic studies
  • Homozygosity mapping

The Infinium HD (High-Density) Assay is designed for genotyping (from customized studies on targeted regions to large-scale genome-wide association studies), for copy number variation (CNV) analysis and for cytogenetic studies. Depending on the BeadChip type used, the platform has the capacity to genotype from 96 to 576 samples daily and to produce from 288,000 to over 403,200,000 genotypes by enabling the parallel typing from 3,000 to more than 4,301,332 markers. Only bi-allelic SNPs (Single Nucleotide Polymorphisms) and indels (insertion/deletion polymorphisms) may be genotyped.

The reaction consists in an initial whole genome amplification step followed by a fragmentation. The product is then hybridized onto a planar silica slide of which micro-wells are filled with beads coated with specific address probes. Each probe type is represented multiple times for increased accuracy. Following that, the hybridized product is extended with labeled bases and the signal is detected with a scanner. The typical call rates are greater than 98 %. (For more details, see: Gunderson et al., 2005, Nat Genet 37: 549-554 or Steemers et al., 2006, Nat Methods 3: 31-33).

Illumina's website can be visited for more details.

Available Products

Either standard or custom content BeadChips (iSelect Custom Genotyping) may be ordered. The design of custom assays is realized solely by our personnel.

Several factors influence the conversion rate for Infinium custom BeadChips including the stringent QC criteria during manufacturing at Illumina, the sequence nature of the chosen SNPs and indels, and criteria used for the analysis. In order to maximize the chances of success, selecting validated loci and/or loci with high design scores is recommended. In general, a final design conversion rate averaging 80 % is expected.

Infinium High-Density (HD) BeadChips

For BeadChips with a customized content (iSelect-12, iSelect-24, HumanOmniExpress+, HumanOmni2.5S+ and HumanOmni5-Quad+), the minimum manufacturing scale is 1152 samples.

The HumanMethylation450 BeadChip offers a unique combination of comprehensive, expert-selected coverage of >450,000 methylation sites, high throughput, and low price, making it ideal for screening genome-wide association study (GWAS) populations.

Information and Service Request

The Client Management Office can be contacted for more information and for service request.