Illumina Genotyping Service
For whole genome SNP genotyping, focused panel genotyping, or copy number variation analysis
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.
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.
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.
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.
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:
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:
For LOH/copy number variation analysis projects, the following reports are available:
Contact a Technical Support representative to order or to discuss your specific need at firstname.lastname@example.org.
The Illumina Genotyping Service is highly suited to applications requiring whole genome SNP genotyping, focused panel genotyping, or copy number variation analysis.