SNP Genotyping
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SNP Introduction

A single-nucleotide polymorphism (SNP) is a variation in a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population. SNPs are caused by conversion, transversion, insertion or deletion of nucleotide. Some SNPs affect gene function directly and lead to changes of biological character. SNPs are abundant in genome and widely used in study of population genetics and disease genes. Our service: Hi-SNP typing for high throughput screening by Nest Generation Sequencing and PCR-LDR SNP typing for middle and low scale screening.


PCR-LDR combines PCR and Ligase Detection Reaction (LDR) to detect SNP in genome. LDR can detect SNPs by the mechanism of thermostable ligase. Ligase-based assays are ideal for multiplexing, since several primer sets can ligate along a gene without the interference encountered in polymerase-based assays. The optimal multiplex detection scheme involves a primary PCR amplification, followed by LDR (two primers, same strand) detection. The thermostable ligase and engineered mutants exhibit high fidelity in discriminating all possible matched and mismatched base pairs. The discrimination is improved by using primers containing the discriminating base on the 3' side of the ligation junction.



Technical Flowchart





Technical Features


Technical Features


The method is suitable for all SNP typing. No induced restriction endonuclease site is need.

Typing is precise and guaranteed based on the method of hybridization and ligation reaction.

The method is high efficient and short cycle.

Multi-reaction makes the typing most economic and high efficient.

Multi-LDR can detect 20 SNPs in one reaction.

The mothed is recommended for middle scale typing, which SNP sites are smaller than 30.


PCR-LDR SNP typing is suitable for middle/low scale of SNP screening, such as QTL, candidate gene or loci association analysis, molecular breeding, etc. 




Hi-SNP Typing

Hi-SNP combines multiplex PCR and high throughput sequencing to screen SNPs in large scale of samples. Specific primes are designed for designated loci and samples are amplified through multiplex PCR and discriminated by different barcode primers. Amplicons are sequenced by Ion Proton, Illumina Hiseq or Illumina X10. The final SNP information are obtained by bioinformatics analysis of sequence data. Nest Generation Sequencingcan can analyze over millions of DNA molecules. Hi-SNP is much more accurate and sensitive than other SNP typing methods.



Technical Flowchart




Technical Features


Technical Feature


The mothed is high throughput and can screen SNPs from hundreds of loci in thousands of samples.

The data are homogeneous.  The sequencing depth  of 90% amplicons is controlled above 0.2X of the average sequencing depth.

The average sequencing depth is above 200× and the lowest sequencing depth is 20X. Quality control: Q30>90%.

High accuracy with molecular tags added in amplification. 

High specificity with PCR accurate capture in targeted region.

Sample DNA concentration can be as low as20-40ng/ul.


Hi-SNP is applicable for many genetic studies, such as genomics, tumor genomics, disease associated genetic study and clinical molecular diagnosis, et al.  Hi-SNP can also applied in QTL and molecular breeding in plant science, and is suitable for large scale of SNP typing. 


Selected Citations:

1. Li J, Huang S, Dai H R, et al. A promoter polymorphism rs2075824 within IMPA2 gene affecting the transcription activity: possible relationship with schizophrenia.[J]. Journal of Cellular & Molecular Medicine, 2016.

2. Chen K, Zhou Y X, Li K, et al. A novel three-round multiplex PCR for SNP genotyping with next generation sequencing[J]. Analytical and Bioanalytical Chemistry, 2016, 408(16):1-7.

3. Chen Z J, Zhao H, He L, et al. Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromosome 2p16.3, 2p21 and 9q33.3.[J]. Nature Genetics, 2011, 43(1):55-59.

4. Shi Y, Li Z, Xu Q, et al. Common variants on 8p12 and 1q24.2 confer risk of schizophrenia.[J]. Nature Genetics, 2011, 43(12):1224-7.