The sequencing read

Gencove - May 12, 2022

Introducing InfiniSEEK - Low-pass Genotyping Plus Target Capture in One Assay

Whether it is genotyping a whole herd or building support for new species and breeds, at Gencove, we’re continually looking for ways to empower companies and scientists to discover more using sequencing. That’s why we’re excited to share the latest milestone in this pursuit with the launch of InfiniSEEK™– available now through NEOGEN.

Future-Proof Your Investment in Genomics

Despite sequencing costs declining over the past decade, it’s still prohibitively expensive to deeply sequence an entire population’s genomes. Alternative methods to reduce cost, such as arrays, miss context for the variation across the whole genome. With InfiniSEEK, you don’t have to sacrifice the depth needed to see variation in high resolution for whole genome context. This is because in a single InfiniSEEK assay, you get low-pass sequencing across the whole genome for high-quality genotype calls and high-coverage targeted sequencing at specific loci to better identify genetic variants.

Illustration of InfiniSEEK data.

A Simple and Reliable Process

Available now for bovine projects, InfiniSEEK delivers 2.2 million variants for each sample (1.4 million from a superset of all NEOGEN array deliverables plus 786,000 functional variants) imputed to a reference panel generated from 1,800 high-coverage genomes from a globally diverse set of breeds. The easy to interpret final report is formatted for existing NEOGEN and Illumina catalog arrays for seamless transition to sequencing based genotyping.

InfiniSEEK process

Accurate and Concordant Results

InfiniSEEK has been rigorously validated and delivers highly accurate low-pass whole genome and high-coverage targeted sequencing information to help you understand the key traits that drive your breeding program. In a comparison between low-pass sequencing and microarray data, researchers at USDA MARC demonstrated >99% genome wide concordance in beef steers. The authors note, “Imputation from low coverage sequence offers a viable, low-cost approach to obtain functional variant genotypes that could improve genomic prediction.”

Genome Wide Concordance
AngusHerefordSimmental
99.3%99.1%99.2%

Table data from Snelling, W.M. et al. (2020). Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers. Genes (Basel). 2020 Nov; 11(11): 1312.

In addition to the low-pass information across the whole genome, hybrid capture probes designed for 774 sites to look at the important traits the cattle industry has been using for years, such as those associated with diagnostics and parentage, are the standard inclusion with InfiniSEEK. Tested and validated in 340 animals, the results show 100% genotype match to microarrays.

LocusGenotype Match
Polled100%
MCR1100%
A2100%
Calpain100%

Validation data in 340 animals shows 100% genotype match to microarrays for various key loci

InfiniSEEK is a revolutionary, high-throughput, cost-effective solution for whole genome sequencing and targeted high-coverage information from two trusted leaders in genomics. If you’d like to learn more about the InfiniSEEK offering or low-pass sequencing and the Gencove analysis platform, please contact us.