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
platforms
– 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
Deliverables
1. SNP genotyping analysis result
2. QC result
Reference
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.
