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    SNPscan is propriety multiplex SNP genotyping system developed by Genesky; it allows simultaneous genotyping of 48/96/144/192 SNPs per sample in a single tube/sample. SNPscan uses the highly specific ligation reaction to discriminate alleles. Three probes are used in the ligation reaction: two allele-specific probes with one end stops at the SNP and another locus-specific probe with one end starts at the base next to the SNP. When the allele-specific probe and the locus-specific probe anneal to the target strand, the DNA ligase forms a phosphodiester bond between the two adjacent probes. 2 or 3 additional bases are added to either of the two allele-specific probes in order to discriminate alleles. For multiplexing, short oligonucleotides with different length are added to the locus-specific probes to separate each individual SNP in a single assay. Then, PCR is done by using fluorescence-labelled universal primers which are complementary to the a short oligonucleotide attached at both ends of the ligation product. PCR products with different length representing different SNPs are separated using capillary electrophoresis. Fluorescence signals are read out and genotypes are determined using the software, GeneMapper.

    Technique Highlights

    High Accuracy  Accuracy of SNP calling > 99.9%

    High Throughput  With one ABI3730XL, over 110,000 genotyping data can be generated within one day

    Cost-Effective  Assay costs significantly less than most of other medium to high throughput SNP genotyping


    High Success Rate  SNP call rate routinely above 95%; Sample pass rate consistently above 98%

    High efficiency and Fast Turnaround  Take the 96 loci, 2000 samples genotyping project for example, it only takes 

       8 weeks to complete assay system preparation, optimization and testing, and one extra week to analyse and 

       interpret the result

    Sample Requirement

    Sample Type: Genomic DNA
    Sample Quantity: DNA >= 5 ug; concentration >= 100 ng/ul
    Sample Purity: OD260/280 = 1.7~2.0
    Sample without severe degradation

    Service Workflow

    1. Cusomtized experimental design
    2. Sample receiving
    3. DNA extraction and QC
    4. SNPscan multiplex genotyping
    5. Project final report


    1. SNP genotyping analysis result
    2. QC result


    Du, W., et al., A rapid method for simultaneous multi-gene mutation screening in children with nonsyndromic hearing loss. Genomics, 2014. 104(4): p. 264-70.

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