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SNP Genotyping
TraitGenetics supports a variety of platforms for SNP genotyping. The question which platform to use will depend on the type and scale of the study at hand.


Pyrosequencing is a high quality quantitative genotyping system based on the detection of pyrophosphate residues released during nucleotide incorporation. In addition to SNP genotyping, the quantitative nature of the Pyrosequencing reaction allows a precise determination of allele frequencies within DNA pools and in polyploid species.

Pyrogram for a G/T polymorphism


Determination of allele frequencies using Pyrosequencing



The allelic discrimination of SNPs on the basis of the TaqMan technology is a single-plex high throughput system allowing the analysis of thousands of samples a day at a reasonable cost. Fluorescence is released while the target fragment is amplified by the sequence detection primers. PCR is performed in standard PCR machines and the actual analysis as an endpoint analysis in a real time PCR machine. This platform is particularly well suited for the analysis of a large number of samples with a moderate number of SNPs.
Allelic discrimination using TaqMan assay 


The SNPlex genotyping system is a robust platform that allows simultaneous genotyping of up to 48 SNPs (single nucleotide polymorphisms) in a single biological sample. This can happen either in a 96 well or in 384 well format. The system is ideal for fine mapping, candidate gene and population structure analysis using moderate to high marker numbers. SNP genotypes are detected in a multiplex oligo ligation assay. Reaction products are purified, amplified by universal PCR and hybridized with a mix of universal zip chute probes carrying fluorescent dyes plus size modifiers. Eluted zip chutes representing individual SNP alleles are separated by capillary electrophoresis on a 96 well DNA sequencer and analyzed using GeneMapper software.



SNPlex samples plot data for 4 SNPs 

The SNPlex system generates 4608 data points from a single 96 well plate. This throughput, along with built-in quality control features, data analysis tools and automated assay design, now allows large scale studies to be carried out at high accuracy within a very short period of time and at reasonable cost. Pre-validated SNPlex multiplexes are available at TraitGenetics for most major crop plants like maize, sugar beet, tomato, rapeseed and the vegetable Brassicas.

Illumina GoldenGate Assay

Illumina’s GoldenGate Assay has rapidly become the industry standard for quality high-throughput SNP genotyping. It is a pre-optimized oligo extension and ligation assay capable of analyzing between 96 and 1536 SNPs simultaneously in a 96 well format. Allele discrimination is followed by PCR using universal primers carrying fluorescent dyes. Products are then hybridized to an optical array and detected by a laser scanner.

Using the TraitGenetics SNP database we have designed and validated a variety of GoldenGate multiplex arrays for most major crop plants. These multiplexes deliver proven performance and are available for analysis at TraitGenetics. In addition to that, we can design custom GoldenGate multiplexes based on customer specifications using our TraitGenetics GoldenGate assay design pipeline. Illumina’s GoldenGate Standard Panels for SNP analysis in human and mouse are available for analysis as well.


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The Illumina GoldenGate assay


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Illumina BeadStation 500G


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SNP data analysis using the BeadStudio software


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