Amp-Seq One - the new targeted genotyping by sequencing services

For a more detailed review of the quality, robustness and performance of the Amp‑Seq One targeted genotyping by sequencing method please see the application notes in the "Resources" section or contact us.

Design compatibility and high-quality sequencing data

Across both plant and livestock panels, design compatibility is clearly demonstrated with panels developed for original Amp-Seq performing comparably when utilised with Amp-Seq One technology. Figure 1 illustrates an example of this comparable performance between methods for a 1920 marker panel for maize. Table 1 summarises high quality sequencing data from four panels, illustrating typical genotyping call rates of greater than 90% and typical genotyping efficiencies of greater than 95% (on target genotyping rate).

Figure 1. Dataset for 1,920 marker panel for maize, illustrating comparable performance between Amp-Seq One and original Amp-Seq technology. For both protocols, percentage of reads mapped to the reference genome was greater than 98.5% and the percentage of reads mapped to the target SNP location was greater than 95%. Genotyping call rates and uniformity (read depth consistency across markers) were also comparable between both methods

Table 1. Summary of high-quality sequencing data obtained for four Amp-Seq One panels.

Compatible with diverse sample materials

Results obtained with the 1,100-marker soy panel demonstrate almost identical performance between Amp-Seq One and original Amp-Seq technology when using biologically diverse soy leaf samples (figure 2).

Figure 2. Dataset for 1,100 marker panel for soy, illustrating almost identical performance between Amp-Seq One and original Amp-Seq technology. DNA was purified from 384 individual soy leaf punch samples using sbeadex™ plant DNA purification chemistry.

Marker density

Amp-Seq One is suitable for genotyping large numbers of SNPs (>5000) per reaction. Figure 3 illustrates high-quality sequencing data obtained for a high-density maize 5,200 marker panel.

Figure 3. Dataset for 5,200 marker panel for maize illustrating high-quality sequencing results obtained with Amp-Seq One technology and a high-density panel. Overall genotyping call rate for this panel was >99% and 97% of reads were mapped to the reference genome.