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Illumina Genotyping Service

For whole genome SNP genotyping, focused panel genotyping, or copy number variation analysis

  • Illumina trained and certified technical staff
  • Standard and custom content beadchips supported
  • Sample capacity from tens to thousands
  • All organisms supported

The Illumina Genotyping Service provides a complete service for genomic analysis that delivers robust and reproducible results. The service accepts and processes a variety of biological samples and then leverages cutting-edge tools for either pathway-focused or genomewide analysis yielding superior results for scientists in academic, government, and industrial settings. QIAGEN is an Illumina-certified service provider.

Cat No./ID: 338908 CS30##
Illumina Genotyping Service
The Illumina Genotyping Service is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

The Illumina Genotyping Service offers whole genome genotyping, focused panel genotyping, or copy number variation analysis based on Illumina's Infinium-based whole genome DNA analysis beadchips and iSelect beadchips. The Illumina Genotyping Service supports genomewide association studies (GWAS), DNA copy number/cytogenetic studies, linkage analysis, and fine mapping studies. The Infinium assay allows whole genome genotyping at different levels of coverage using a variety of fixed content chips (see Table). QIAGEN is an Illumina-certified service provider.

Table 1. Fixed-content chips.
BeadChip  Arary formatNumber of markers per sample



~4.3 million



~2.5 million



~2.5 million



~1.25 million



~1.1 million









Recommended sample types are detailed below.

Purified genomic DNA

Genomic DNA isolated using a standard genomic DNA isolation kit, such as the DNeasy Blood & Tissue Kit, which is compatible with Illumina genotyping. We recommend 1.5 µg DNA per sample at a concentration higher than 100 ng/µl (DNA concentration measured using picogreen assay; if a spectrophotometer is used, please indicate this in the sample submission form). A260/A280 ratio of ≥1.7 is required. Customers should check sample integrity by agarose gel electrophoresis before sending samples to QIAGEN. Sample gel pictures, if available, should accompany the submitted samples. For the Infinium assay, the fragments should be ≥2 kb. For samples of lower quality (OD ratio, degradation etc.) or amount, consult QIAGEN Technical Services.

A minimum order of 48 samples is required. Customers are encouraged to submit samples in sealed 96-well, deep-well plates. One blank position should be left on each 96 well-plate for QIAGEN to include a positive control sample. Customers also have the option of including one duplicate sample (for duplication error analysis) on each or alternate 96-well plates. The blank/positive control well position should be indicated on the sample submission sheets. Excel format is preferred for sample submission, and the spreadsheet should contain the following information: sample ID, concentration, A260/A280, A260/A230, total volume, total DNA amount.

Saliva/buccal cells

QIAGEN recommends the Gentra Puregene Buccal Cell Kit for purification of archive-quality DNA from buccal cells and mouthwash. Purified DNA should be resuspended in TE (10 mM Tris, 1 mM EDTA). Saliva mixed with the stabilization fluid should be shipped to the Illumina Genotyping Service in the sample collection tube closed with the small cap (No refrigeration or freezing is required). Customers can ship buccal cell pellets on dry ice via overnight mail.


A sample of ≥0.5 ml of whole blood treated with citrate, heparin, or EDTA may be submitted on dry ice. Buffy coat sample (a minimum of 200 µl per sample) and lymphocytes (a minimum of 5 x 106 per sample) may also be submitted on dry ice.

Other samples

Please contact QIAGEN Technical Services for more information regarding other samples. Samples should be shipped using overnight delivery on dry ice. Currently for genomewide association studies, only purified genomic DNA samples can be received by the Illumina Genotyping Service.

Illumina Genotyping Service sample protocol

Genomic DNA samples are processed by QIAGEN for Illumina analysis in the following steps: 

Precipitation and resuspension 
Imaging and data analysis  
Data analysis

Results can be accessed on a secure FTP site and all original image data files (.idat) can be provided to the customer, upon request.

For genotyping projects, standard data analysis performed in Illumina GenomeStudio will deliver the following report types as Excel workbooks, as appropriate:

Final report containing genotype data 
DNA report 
Locus summary report 
Locus x DNA report 
Reproducibility and heritability report (genotype concordance data will be provided for duplicate samples)

For LOH/copy number variation analysis projects, the following reports are available: 

Final report containing B allele frequency (BAF) and Log R ratio (LRR) values, CNV region (start, end) and value summary table 
CNV region display
Genomewide BAF and LRR plots are available as a custom data analysis option for CNV projects

Contact a Technical Support representative to order or to discuss your specific need at support@sabiosciences.com.


The Illumina Genotyping Service is highly suited to applications requiring whole genome SNP genotyping, focused panel genotyping, or copy number variation analysis.