We perform customized genotyping, using Illumina's GoldenGate technology. This allows for flexibility to decide on the SNPs, and SNP combinations to be analyzed. You decide on the SNP content of the assay (together with GPCF and with advice of Illumina's experts) and we take care about the technical feasibility and quality of the data. You may customize in panels of 96 and 384-3072 SNPs (minimum spanning of multiple of 96).
For users new to genotyping technology, we offer project consultancy to design the best experimental set-up in order to answer your scientific question. Before commencing the project, detailed information will be provided, including guidelines for project set-up, QC parameters for DNA isolation, purification and preparation and a precise description of the service workflow. Just prepare and your DNA samples and have a rough estimation of its concentration (must be above 100 ng/µl).
Sample requirements and exact project workflow depend on the experimental approach chosen. We provide a one-stop solution for SNP genotyping projects, meaning you provide us with samples and we’ll process them and provide you with high-quality, robust results. Our standard service does require your personal support in processing your samples in the lab. We deliver the raw experimental data, including scanned images (if applicable), the results of all quality measures and the final data extracted from these images following image analysis. The raw data can be analysed using external software at your convenience.
Up to now we processed more than 14.000 samples using this plattform.
The whole project of customized genotyping is run interactively with your close participation.
In the early design phase you will need to provide a list of your targets in form of either:
- RS numbers
- Sequences
- Regions
- Gene Identifiers
You will receive the full annotation as part of standard results, which include design score, design rank, minor allele frequency (MAF), and validation status, based on recent versions of both Genome Build and dbSNP, as calculated by Illumina. In some minor cases, we will need to substitute markers, to achieve compatible marker sets to run the assays. The priciple set-up of the GoldenGate technology is described below.
Please checkout our pricelist and contact Matthias Schick (-4703) for more details.
Principle steps
Step1: Hybridization of locus specific oligonucleotides. For each locus interrogated, 3 oligos are used: 2 Allele Specific Oligos (ASOs), and 1 Locus Specific Oligo (LSO).
Step2: Allele specific primer extension and ligation reaction. The ASO that matches a SNP is incorporated into a structure perfect for universal amplification.
Step3: Assay amplification. Amplification is completed with the addition of only 3 primers: one labeled with Cy3 hybridising to PCR sequence 1 (P1), one with Cy5 hybridising to PCR sequence 2 (P2) and a third unlabeled primer hybridising to PCR sequence 3 (P3).
Step4: Hybridisation to Universal IllumiCodeTM Array: After amplification the products are hybridised to the Sentrix® Universal Array for detection. The internal IllumiCode that is specific for each locus binds preferentially to its complementary bead. Then, the genotype is automatically called.
