Multiplex Custom SNP Genotyping

We offer medium throughput SNP Genotyping using the Illumina BeadXpress Station and GoldenGate® assay with VeraCode® technology. Custom selected SNPs can be multiplex at the 48, 96, 144, 192 or 384 level and used to interrogate from a few dozen to a few thousand samples. Accuracy and reliability for the assays are above 95%. Basically, all the customer needs to do is to come up with a list of SNPs, order the appropriate assay from Illumina and provide the us with clean Genomic DNA. We'll do the rest and provide you with genotyping data! Download and read the technology note here!

Illumina BeadXpress Station

1- Choose the Assay

Illumina sells assay kits for 48, 96, 144, 192 or 384 SNPs. The kits are good for up to 480 samples.
From the table below, choose the SNP plex level and the number of samples that best fit your project. Keep in mind that we can always save the left over reagents for later use.

In addition to the price above, the Core lab charges a fee to process your samples and run the assays. The price is set per 96-well plate of samples:

Therefore, for example, if your have 690 samples (10X 96-well plates), no matter what plex level, your Core lab fee, aside from the cost of the assay kits, would be $3,000 if you are an UofU investigator.
You may choose not to use up all your assays at once and that's fine. We will only charge you for the plates we do process.

2- Build the SNP List

1. To build your SNP list use one of the templates below. You may use RS numbers, a list of Genes, Regions or simply the sequences around your SNPs of interest.
   -Download Zip file with templates.
   -View/Download PDF with instructions on how to build your list.
2. Submit your tentative list to Illumina at techSupport@illumina.com. Illumina will email back, usually in 24 hr, the scores of your SNPs.
   We suggest your submit more SNPs than you need and then later select the ones with the highest scores.
3. Review the scores, fine tune your list and repeat step 2 until you have a final list.
   

3- Order the Assay

Please order your assay directly from Illumina and have it shipped to our Core Lab (click here for the full address). Keep in mind that Illumina will take from 6 to 8 weeks to deliver the assay.
Illumina usually requires you to email your final list to orders@illumina.com, and to fax a copy of your Purchase Order to 858-202-4766. Contact them for more details at 800-809-4566.

The Core lab will bill you separately for processing and genotyping your samples after the project is finalized. Outside users must fax or email us a purchase order before work on the project begins.

4- Prepare DNA Samples

We prefer you bring or ship your samples to us close to the time we will be receiving your assay from Illumina.

1. The samples need to be organized in 96-well plate format. We prefer PCR type plates.
2. Submit at least 10 ul volume. DNA concentration needs to be, as close as possible, to 50 ng/ul.
   High quality DNA is necessary. A 260/280 OD ration above 1.8 is recommended. the DNA can be suspended in Tris buffer.
3. IF you are shipping the samples to us, please do it on ice and make sure the wells are tightly seal to avoid spilling or evaporation.

5- Receive Genotyping Data

The Core lab will provide you with Excel spreadsheets containing all the genotyping calls for your data. We use the BeadStudio software to analyze the raw data from the instruments and generate the calls.

Contact us if you are interested or have any more questions!

last update Jan '09