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Illumina Genotyping and Copy Number Variation Analysis

 
Genotyping
 
SABiosciences Service Core offers whole genome, focused panel genotyping or copy number variation analysis service based on Illumina's Infinium chemistry-based whole genome DNA analysis beadchips and iSelect beadchips. The Illumina genotyping service supports whole-genome association studies, 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. SABiosciences supports any chips currently available from Illumina, including the following as examples.


Human Omni1-Quad beadchip analyzes greater than 1.1 million SNPs and probes for the most comprehensive genome-wide coverage (covering additional high-value regions including new content from the 1000 Genome Project).
Human 660W-Quad beadchip analyzes greater than 657,000 genetic markers per sample for whole-genome genotyping and CNV analysis.
Human 1M Duo beadchip analyzes 1.2 million genetic markers per sample for whole-genome genotyping and CNV analysis.
Human Cyto12 beadchip analyzes approximately 300,000 genetic markers per sample for whole-genome genotyping and cytogenetic analysis.
Focused Panel beadchips analyze samples with more specific marker sets such as such as cardiovascular disease or from other species such as canine, bovine, equine, ovine or porcine.

SABiosciences Illumina genotyping services:

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

 

 

Recommended Samples & Protocol Data Delivery Pricing
 

Recommended samples

Purified genomic DNA. Genomic DNA isolated using standard genomic DNA isolation kit, such as Qiagen's DNeasy Blood & Tissue kit or similar kits is compatible with Illumina genotyping. SABiosciences recommends 1.5 micrograms of DNA per sample at a concentration higher than 100 nanograms per microliter (DNA concentration measured using picogreen assay; if a NanoDrop is used, please indicate in sample submission form). A 260:280 ratio of 1.7 or greater is required. Customers should check sample integrity by agarose gel electrophoresis before sending samples to SABiosciences. Sample gel pictures, if available, should accompany the submitted samples. For the Infinium assay, the recommend fragments should be greater than 2 kb. For samples of lower quality (OD ratio, degradation etc.) or amount, consult a SABiosciences technical support representative. When sample number is above 48, customers are encouraged to submit samples in 96 deep well plate (sealed) format. One blank position should be left on each 96 well plate for SABiosciences to include a positive control sample. Customers also have the option of including one duplicate sample (for duplication error analysis) on every or every other 96 well plate. The blank/positive control well position should be indicated on the sample manifest sheets (Excel format preferred, containing the following information: sample ID, concentration, OD260/280, OD260/230, total volume, total DNA amount).

Saliva/Buccal cells. SABiosciences recommends the Oragene DNA sample collection kit (DNAgenotek) and the manufacturer's DNA isolation procedure. Purified DNA should be resuspended in TE (10 mM Tris, 1 mM EDTA). Alternatively, saliva containing buccal cells can be collected in an Oragene DNA sample collection kit. Saliva mixed with the stabilization fluid should be shipped to the Service Core 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.

Blood. A sample of at least 0.5 milliliters of whole blood treated with citrate, heparin or EDTA can be submitted on dry ice. Buffy coat sample (a minimum of 200 microliters per sample) and lymphocytes (a minimum of 5x10^6 per sample) can also be submitted on dry ice.

Other Samples. Please contact Technical Services at (301) 682-9200 or your local distributor for International Customers.
Samples should be shipped with overnight delivery to our Service Core on dry ice. Currently for GWAS studies, only purified genomic DNA samples can be received at the service core.

Illumina Genotyping Sample Protocol
Genomic DNA samples are then processed by SABiosciences for Illumina analysis using the following outline:
Amplification, Fragmentation, Precipitation and Resuspension, Hybridization, X-stain, Imaging and Data Analysis.

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Recommended Samples & Protocol Data Delivery Pricing
  The results can be accessed on a secure FTP site.

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 will be made available to the customer:

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

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Recommended Samples & Protocol Data Delivery Pricing
 
Customers are strongly encouraged to purchase Infinium genotyping kits (including chips and reagents) directly from Illumina to minimize material cost. Customers who would like SABiosciences to provide the Infinium chips should contact a technical support representative at 301-682-9200 to inquire about the chip and reagent costs.

For Human 660W-Quad, Human 1M-Duo, Human Omni1-Quad or semi-custom Infinium BeadChips, SABiosciences charges a per sample processing fee based on the number of samples. For HumanCytoSNP-12, HumanCVD whole genome, iSelect custom or other organism chips, SABiosciences charges a per sample processing fee based on the number of samples.

Related Services:
DNA Isolation and Quality Assessment Fee based on the number of samples
Initial Set Up and Consultation Fee

Contact a Technical Sales Representative to obtain pricing or to discuss your specific need at support@sabiosciences.com or 301-682-9200.

* Service prices are volume-dependent; therefore please contact a Technical Sales Representative for detailed pricing. Progressive discounts for fees and services are available. All prices are in US Dollars. Prices are subject to change at any time without notice.

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