Targeted Genotyping

Our expertise in targeted sequencing solutions and tailored consultancy are the perfect mix that have made IGATech the company of choice for many customers and projects.

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Nucleic acids extraction
Hybridization-based enrichment
Primer-extension enrichment


Features and benefits

  1. Tailored consultancy and project optimization
  2. Reproducibility and transferability
  3. Genotyping and discovery in one experiment
  4. Maximized flexibility and panel customization
  5. Scale from thousand to hundred thousand loci

Pricing examples

Experiment Price starting from
Allegro 10k SNPs 39 euro/sample (384 samples)
Allegro 50k SNPs 69 euro/sample (384 samples)
Hybridization-capture 1Mbp 98 euro/sample (240 samples)
Hybridization-capture 5Mbp 127 euro/sample (240 samples)


Full control of your experiment


Either choosing hybridization-based systems or primer extension, the sequencing information will always provide additonal and off-target data, eliminating errors in diversity estimation caused by closed genotyping experiments as in arrays. 

Several scenarios and specific analyses require moving from random markers (for which ddRAD is our system of choice) to targeted regions when performing genotyping experiments. Focusing on a specific set of SNPs, genes or genomic locations is a crucial factor to cope with tasks such as genomic selection, local adaptation studies, TILLING, eco-TILLING, fine mapping, GWAS, genomic selection and many others. IGATech have optimized protocols for both hybridization-based and primer-based enrichment procedures.


Single primer enrichment technology - Allegro

IGATech, in collaboration with Nugen inc., have implemented a targeted genotyping system based on single primer enrichment technology (Allegro, Tecan Genomics), which provides a very efficient approach to specifically target SNPs of interest. Every enriched read will be useful to the genotype calling of one selected SNP site. Nonetheless the technology allows to discover novel alleles by leveraging the sequencing information ensuring no restriction of transferability of each panel to other populations or even species. Sequencing read length can be scaled depending on the need of unknown (rare) variants versus the cost-effectiveness of focused genotyping.

Allegro provides highest reproducibility in the sequencing-based genotyping panorama while maintaining flexibility of continuous customization.



          Pre-designed panels                   Request a new panel




Learn on SPET Technology:

Tecan Genomics 

See our webinar on SPET-based genotyping

See out NEWER webinar on GWAS application on maize

Read our seminal paper (Annals of Botany)



Eggplant and Tomato genotyping (Frontiers in Plant Science)

Oil Palm genetic map (Scientific Reports)




Utilization of hybridization-based enrichments have several advantages. They can be used also when a reference genome/transcriptome is only available for closely related species (or even genera) or when no information on polymorpisms and rate of occurrence is available. The technique is resilient to mutation rates and therefore prevent allelic-specific enrichments. Hybridization-based enrichment is the best suited approach for discovery approaches on gene panels/families or large genomic loci, given the possibility to yield a wide target with uniform coverage. IGATech has developed in-house 384-plex UDI (unique dual index) to cope with large scale experiments on NovaSeq6000 platform. The target region can vary from few Mbp up to 200Mbp.




For small amounts of loci (tens up to hundred) in very large scale experiments (thousands of samples) IGATech can deploy a customized multiplex PCR panel to run massive genotyping based on simple amplicon sequencing, providing a high-throughput and cost-effective platform. The panel can be easily modified and increased in markers over the time without an impact on costs.


Documents & Reports

Human samples clearance

Terms and Conditions v04.pdf


Privacy Information

Samples Spreadsheet v7.xlsx

Shipping and Packaging Guidelines.pdf

Allegro Data delivery specifications.pdf

Genotyping Sample requirements guidelines v02.pdf

Target Resequencing Data delivery specifications.pdf

Target Resequencing Sample preparation guidelines v03.pdf