Genotyping

BeadXpress

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BeadXpress Applications

The BeadXpress reader (available at GGF) and the GoldenGate assays from Illumina (see below) create a cost-effective high-throughput SNP genotyping platform. Custom SNP assays are ordered from Illumina in 96-plex, 144-plex or 384-plex format and samples are processed in a 96-well plate format (http://www.illumina.com/pages.ilmn?ID=36).

Other assays available on the BeadXpress platform include:

For an overview or video of the VeraCode technology which is the foundation of the assays that run on the BeadXpress system please visit: http://www.illumina.com/pages.ilmn?ID=6. For specific information to determine if the BeadXpress system is suitable for your project or to get started please contact us.

Sample preparation for the BeadXpress using the GoldenGate Genotyping Assay for VeraCode

The GoldenGate assay is a very efficient tool for high-throughput genotyping. No amplification of Genomic DNA is required. A file containing the desired SNPs to be used for genotyping should be prepared by the customer following the guidelines provided by Illumina (http://www.illumina.com). The bioinformaticians at Illumina will analyze the SNP to be used in the genotyping and provide the final oligonucleotides sequences to be used in the GoldenGate assay. That service is included in the cost of the oligo pool ordered form the company. Once the final oligonucleotide file is ready, the customer should place the order by submitting the file to Illumina. Then, GGF will order the reagents necessary for the assay. Please note that the custom Illumina GoldenGate genotyping reagent is also referred to as oligonucleotide pool assay (OPAs).

Input genomic DNA should be reasonably free of contaminating RNA and protein, typically determined using the absorbance ratios from UV readings. Methods for DNA extraction that we have used successfully for vertebrate tissue include Qiagen, Gentra, and MUD protocols although other protocols might be suitable. Please contact us if you need to determine whether your extraction protocol or processed sample is compatible with the assay. A total of eight samples might then be used to determine if the extraction protocol is compatible with the assay.

Generally the BeadXpress workflow processes 96 samples in a single run. The recommended sample submission volume and concentration for genomic DNA in a 96-well plate is 15 ul of a 50 ng/ul solution in water, TE or Qiagen EB. The assay utilizes 5 ul and is tolerant of differences in concentration so it is not absolutely necessary to normalize concentration across the plate but the tightest clusters and the best data will be generated when the samples do not vary considerably in concentration. While the assay is tolerant of poor quality DNA (i.e. partially degraded, http://www.illumina.com/downloads/WGA_TechNote_29Sep05.pdf ) it is not suitable to to use with poor quality DNA preparations containing large amounts of protein or RNA or anything else that will interfere with the initial biotinylation of the gDNA or subsequent steps. Please electronically submit a spreadsheet (Excel or CSV format) with sample name and well position information. Genotype calls will be generated using Illumina’s GenomeStudio Genotyping Module and the data and other supporting files required for further analysis will be available via a secure FTP. Remaining DNA samples should be promptly picked up by the customer after project completion. GGF can only store the samples for a maximum of one month after the project is completed.

Prices for BeadXpress from purified samples to data

Number of OPA kits* purchased UGA users Non-UGA users Profit users
1-2 $550/plate $570/plate $595/plate
3-4 $500/plate $525/plate $550/plate
*One OPA kit contains 5 96-well plates. Therefore, one kit provides enough OPA to assay 480 samples (5 X 96 well plates).