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, WGAS, genomic selection and many others. IGATech have optimized protocols for both hybridization-based and primer-based enrichment procedures. We also offer flexible optimization depending on whether you are looking for a tight target for genotyping (already known polymorphisms) or you need a full “discovery” approach.
IGATech, in collaboration with Nugen inc., have implemented a targeted genotyping system based on single primer extension technology (SPET, Nugen inc.) which provides a very efficient enrichment system coupled with the paradigm that every enriched reads will be useful to the genotype calling of one selected SNP site. Nonetheless the system maintains an “open” schema which allows to discover novel alleles by leveraging the sequencing information. Moreover, primer-extension methods are more robust when dealing with somewhat degraded material. The system provide the best reproducibility in sequencing-based genotyping methods and allows users to modify the panel of target loci over the time.
Utilization of hybridization-based enrichments have some advantages. They can be used also when a reference genome/transcriptome is available for closely related species (or even genera). The technique itself have some resilience to the rate of mutation one may expect in coding regions and therefore prevent allelic-specific enrichments. Hybridization-based enrichment is the most suited approach for discovery approaches, given the possibility to yield a wide target with uniform coverage. IGATech can provide up to 192-plex sample pooling system for large scale experiments. The target region can vary up to 50Mbp.