Genotyping

We Offer the Full Line of Illumina Genotyping Arrays

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Need assistance choosing the appropriate array for your project? Use the Contact Us button above to reach out.

REady to Order? Select the Illumina Genotyping Form.

• Global Screening Array (GSA)
  • This array combines multi-ethnic genome-wide content, curated clinical research variants, and quality control (QC) markers for precision medicine research. The  650,000 genome-wide markers were selected for high imputation accuracy at minor allele frequencies of >1% across all 26 1000 Genomes Project populations. The array provides a genomic tool for clinical research applications including disease risk profiling studies, pharmacogenomics research, wellness characterization, and complex disease discovery.
• Global Diversity Array (GDA)
  • The commercial version of the array chosen by the All of Us Research program, the GDA was designed to meet the needs of the program’s goals of genotyping the rich diversity of the United States. As such, the markers chosen for the array combine highly optimized multi-ethnic, genome-wide content with curated clinical research variants. The array is highly informative, with a backbone optimized for cross-population imputation coverage of the genome. It also enables polygenic risk score development and characterization of genetic architecture in diverse populations.
• Global Clinical Research Array (GCRA)
  • Containing approximately 1.2M carefully selected SNP markers for research and discovery applications, the genome-wide content of this array delivers high imputation accuracy at minor allele frequencies of >1% across all 1000 Genomes Project populations. The clinical research content includes variants with established disease associations and relevant pharmocogenomics (PGx) information. The array also provides imputation-based tag SNPs for HLA alleles, extended MHC region, the KIR gene, and exonic content from the gnomAD database.
• Cytogenetics (Cyto-850)
  • Featuring nearly 850,000 SNPs that have been chosen with input from the international cytogenetics community and peer-reviewed literature, this array has been optimized for use in constitutional and cancer studies. Coverage is enriched for dosage sensitive genes and designed to pick up challenging mosaics.
• Add-on Content
  • All of these arrays may be purchased with add-on content, including the neuro-booster, psych-booster, PGx-booster, PRS-booster, as well as custom content. Minimum sample numbers may apply to some products. Please inquire for details.
• Our Full Service Pricing Includes:
  • All reagents
  • Two HapMap controls per 96 well plate
  • 1 blind duplicate every other plate.
  • Repetition of any sample which has less than a 96.5% call rate for an Illumina array. We attempt the GWAS assay only twice.
  • Full data release: hapmap concordance, reproducibility of genotype calculations broken down by MAF bin for each sample pair, GenomeStudio project, SNP and samples tables, full SNP technical filter applied, samples reclustered on own data, final reports, PLINK file and README docs explaining the data in each directory

GWAS Array Pricing

Sample Requirements

50 ul of genomic DNA at a concentration of 30-50 ng/ul in 1xTE (10mM Tris, 1mM EDTA, pH8) or water.
* Uniform Volumes are required.
* Genomic DNA, even at low concentrations is generally preferred over Whole Genome Amplified (WGA) samples.  Please discuss your sample quality and quantity with your project manager before deciding which samples to send.
* Highly fragmented (FFPE or degraded) samples may be used with the restore process, which adds $100/sample to the cost.

Looking to do a linkage study or trying to sort out sample mix ups? We can help!

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We offer two affordable options. Have questions about them? Reach out using the Contact Us button above.

Ready To Order? Select the appropriate form in iLab.

• Fingerprinting or Human Linkage by Illumina QC Array
  • The Illumina QC array contains  15,949 markers which are useful for biobanking, fingerprinting, ethnic ancestry determination and QC. The array contains all of the SNPs which were on the former human linkage array, so it can also be used for linkage studies. It also includes ADME content.
• Fingerprinting by STR Analysis/Cell Line Authentication
  • The GRCF offers a short tandem repeat (STR) profiling service to customers who wish to confirm the identity of a line by comparison to a known profile or to establish an identity profile for a new cell line generated locally. For further information, including pricing, see our  Cell Line Authentication section.

We offer many options for every size of genotyping project

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Pick the size and assay type that best suits your project.

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• Hundreds to Thousands of Variants
  • The most economical option for customers wishing to look at large numbers of specific SNPs is to add custom content to one of Illumina’s GWAS arrays. Minimum number of SNPs varies by array, and there are usually a minimum number of arrays that must be ordered. Please contact Roxann Ashworth with the details of your project and she can work with you to find the best options.
• Dozens of Variants
  • Taqman Low Density Array cards are often the best option for this type of project. These can be ordered with discounted pricing through our ThermoFisher Dashboard, and then you can run them yourself on our self service instrument, or we can run them for you. Please inquire for more details.
• Individual Variants
  • For customers interested in individual variants, the GRCF offers custom genotyping to analyze short tandem repeats (STR), variable number tandem repeats (VNTR) and single nucleotide polymorphisms (SNP). SNP detection can be done using various methods:
    • TaqMan analysis with custom or predesigned kits on an Applied Biosystems 7900HT Real Time PCR System
    • Sanger sequencing of PCR products on an Applied Biosystems 3730XL DNA Analyzer
    • Pyrosequencing of PCR products on the Qiagen Pyromark Q24 using custom or predesigned kits
    • SNP assays via the QIAcuity digital PCR system. Custom and/or predesigned assays can be multiplexed and run in this system, which is ideal for looking at somatic or acquired mutations in addition to constitutive SNPs.
  • Frequently requested variants
    • We have well developed protocols in place for the following frequently requested assays
    • Pricing is sample number and project dependent for individual variant projects. Please contact our Nucleic Acid Technologies Group for consultation and a quote.

Frequently Requested Variants

• Self-Service Genotyping
  • If you wish to do your own Taqman genotyping, but don’t have the equipment to generate the results, you may rent time on our self-service equipment.
  • Pricing: $20/hour to thermocycle on the machine, $10 for an endpoint read.

Whether using an Illumina non-human array or looking at individual SNPs, we are happy to assist you.

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Minimum sample numbers vary by product. Use the contact us button above for inquires.

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• Illumina Panels
  • Murine
  • Bovine
  • Canine
  • Ovine
  • Porcine
  • Maize
• Mouse GigaMUGA Linkage Array
  • This product is part of Illumina’s GeneSeek GGP line. It is designed for SNP profiling, marker-assisted selection, disease research, and identity management. It includes 143,000 high MAF SNPs from 159 inbreed lines with an average marker spacing of 22.5kb.
• Mouse Genotyping
  • The GRCF offers mouse genotyping service from tail snips or ear punches to determine wild-type, heterozygous and homozygous alleles of genetically modified mice. Other tissues can be utilized, please inquire.
  • The GRCF will optimize PCR conditions with your primers for end-point PCR agarose gel electrophoresis and analysis. An internal control primer set can be included to exclude PCR failure or problems with DNA quality.
  • We use a KAPA Mouse Genotyping Kit for DNA isolation and PCR.