A custom genotyping collaboration for low- and high-throughput screening

PACE (PCR Allele Competitive Extension) SNP genotyping is a fluorescent, competitive allele-specific PCR genotyping technology. It is designed for projects that require a reliable, cost-effective approach for bi-allelic discrimination of single nucleotide polymorphisms (SNPs) and insertions and deletions (indels) at specific loci. PACE is especially suitable for high volume screening projects, such as plant breeding research. IDT and 3CR Bioscience (3CR) have partnered to provide optimally designed genotyping assays with a high-performance master mix, all provided in a short delivery time and at the lowest overall cost in the industry. Learn more about our partnership and how PACE technology works.

• Screen larger sample libraries affordably
• Get cleaner data from an improved reduction in non-specific amplification
• Change reaction volumes without losing performance or ordering a different master mix

Simplified genotyping—a universal master mix and common reverse primer

The PACE genotyping system, developed by 3CR, uses a universal PCR master mix (PACE Genotyping Master Mix) containing a fluorescent reporting reagent, with allele-specific forward primers and a common reverse primer. The master mix is optimized to reduce non-specific amplification compared to other competitive allele-specific PCR master mixes. Unlike KASP^® master mix (LGC Biosearch), only one PACE master mix formulation is required for all reaction volumes, regardless of platform used, and without any compromise in performance. KASP, on the other hand, requires one mix version for normal reaction volumes, another for low volumes (1536 mix variant), and a third for the Array Tape^® Platform (Douglas Scientific).

Learn more about the versatile PACE Genotyping Master Mix.

3CR also provides a special master mix (PACE-IR) formulation for samples containing PCR inhibitors.

Competitive with industry leader—both on data and cost

The PACE and KASP systems are both easy to use, and the 2 methods produce very similar quality data (Figure 1). However, PACE Master Mix is a better use of research funds, especially when using larger pack sizes.

Figure 1. The PACE genotyping system provides improved, cost-effective genotyping compared to the KASP system. Genotyping was performed on purified corn DNA samples. Distinct genotyping assays (4) were selected to assess sequence variability that can affect genotyping outcome. (A) Normal GC/AT content (48% GC). (B) Slightly GC-rich content (68%), (C) AT-rich content (28% GC), and (D) Slightly AT-rich content (40% GC). Master mixes for the PACE and KASP methods were used for genotyping each of the 4 assays (identical primers and samples), in 4 µL reactions, following each manufacturer's protocol. Assay results were analyzed as cluster plots. Genotyping clusters from the PACE reactions were as well or better defined than those from the KASP reactions. In addition, the clusters of the PACE reactions were optimal at a fixed number of PCR cycles, whereas with KASP reactions, different cycle numbers were needed.

Partnership provides faster, more cost-effective genotyping

The PACE genotyping system was developed by 3CR to widen access to quality custom solutions for genotyping screening. The partnership between IDT’s industry-leading oligo synthesis and high-quality primers, and 3CR’s PACE Genotyping Master Mix and expertise in designing assays, enables researchers to quickly and economically conduct genotyping experiments. This collaboration speeds up results and reduces cost for high-volume genotyping, particularly useful for those working in the agricultural biotech sector.

The new PACE SNP assays join the innovative rhAmp™ SNP and rhAmpSeq™ IDT technologies, providing a complete selection of genotyping solutions for any requirement. IDT rhAmp PCR technology is popular for its accuracy and sensitivity, which is great for identifying, validating, and performing small screens on genetic markers. Now, PACE technology provides a cost-effective, high performance solution for scaling projects from low- to high-throughput screens, ideal for PCR-based SNP or indel genotyping.

For each PACE SNP assay, a technical service team of experts from both IDT and 3CR work together to design the sequences for industry-leading, individually synthesized, IDT oligos. This collaboration ensures the best possible assay design and manufacture customized to your experiments. In addition to improving reliability, this service lowers the cost-per-sample compared to existing market alternatives.