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CD Genomics is now offering Hi-SNPseq, which is an innovative and scalable method for high-throughput SNP genotyping by combining multiplex PCR and next generation sequencing technology, enabling quantitative multiplex data analysis and accurate SNP calling.

Advances in next generation technologies have spurred remarkable progress in the field of genomics and driven the costs of DNA sequencing down, and target enrichment has become a significant tool in focused genomic studies, making genotyping-by-sequencing feasible for large genome species, or large scale of samples. Multiplexing PCR is one of simple and proven ways to enrich genomic regions of interest for various genetic tests such as variant analysis or genotyping. By combining these two strategies, we could genotype interested regions in a fast and economic way.


Hi-SNPseq is a CD Genomics propriety high-throughput SNP genotyping multiplex system, which is a simple and robust platform to create target-enriched NGS libraries that excel over traditional PCR-based preparation methods. Hi-SNPseq utilizes the highly specific multiplex PCR reactions to capture a large number of targeted genomic fragments containing the SNPs of interest, which allows simultaneous genotyping of up to thousands of SNPs per sample in a single tube/sample. In a single PCR run, typically two functionally separated reaction steps are involved. In step 1, particularly interested region is captured by customized loop primer. In step 2, captured region is specifically amplified and labeled with customized common primer. The procedure of the multiplex PCR is illustrated in Figure 1, and Hi-SNPseq accomplishs all the required steps for accurate NGS testing (target selection, library preparation and molecular tagging) in a simple one-step workflow.

Two-step PCR with loop primer: target capture and library amplification Figure 1. Two-step PCR with loop primer: target capture and library amplification.

After PCR amplification using multiple specific primers that contain both library adaptors and sample indexes, all the PCR products are sequenced on NGS sequencer. All SNPs genotypes can be reported by bioinformatics analysis on NGS data.

Bioinformatics Analysis and Data Deliverable

  • Quality metrics, including mapping statistics, and base call quality distributions
  • Annotated SNP/indel list for targeted regions in VCF format
  • Genotyping-ready results delivered using VarSifter

Key Features and Advantages

  • High Throughput. Up to thousands of SNPs can be genotyped in one reaction, and thousands of samples can be genotyped together using multiplex sequencing with Illumina sequencer.
  • High Specificity. The primers require specific bindings of both 3’ arm and 5’ arm, resulting in a significant increase of specificity as compared to regular primers.
  • Cost Effective. Assay costs significantly less than most of other high throughput SNP genotyping platforms.
  • Simplified Hand-on Workflow. Just one amplification and one purification are needed before sample uploading on the NGS sequencer.
  • High Success Rate. SNP call rate routinely above 97%; Sample pass rate consistently above 98%.

With state-of-the-art sequencing platforms and deep collaboration within highly experienced technicians and scientists across departments in CD Genomics, we make this technique affordable and reliable to process large scale genotyping. Hi-SNPseq offers cost-effective, ultra-high resolution sequence analysis that enables accurate detection of SNPs. The flexibility and scalability of the technology means a custom assay can be tailored to fit a wide array of applications based on your specific needs. Based on rounds of development, the average target specificity and coverage uniformity are now consistently above 97%. Our full service package includes primers design & synthesis, DNA sample QC, PCR amplification, normalization and pooling, amplicon purification and pooling, Illumina Sequencing, de-multiplexing, alignment & mapping, and SNP calling.

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