Application of Affymetrix Analysis Tools on Eureka NGS Technology to Provide Accurate and Automated Animal and Crop Genotypes

The BRLMM-P two-dimensional clustering algorithm is utilized by mid- to high- plex, Affymetrix microarrays for genotyping SNPs and Indels.  The algorithm has successfully been implemented across arrays designed to study many dozens of organisms.  Its Bayesian step gives it the flexibility to automatically adapt to cluster patterns exhibited by diploid and various levels of allo-polyploidy.  BRLMM-P also incorporates methods for accurately genotyping samples originating from normal and inbred populations.

SNPolisher is a tool developed by Affymetrix to calculate SNP quality control metrics, such as call rate, cluster separation, cluster variation, and deviation from expected cluster position.  These metrics are used to classify the SNPs into performance categories for downstream applications.

Eureka Genomics is a developer of cost-effective, low- to mid-plex, high throughput genotyping assays that uses common next-generation sequencing (NGS) platforms for signal readout. It enables the detection of hundreds to thousands of genetic markers which are increasingly in demand for routine crop and animal agrigenomics testing.

Utilizing the tools developed by Affymetrix for genotyping high density SNP microarrays to analyze the low density Eureka genotyping panels will automate the genotyping process, produce highly accurate results, and allow researchers to migrate between the Affymetrix and Eureka platforms seamlessly.

The Eureka NGS read counts are appropriately scaled, normalized, and transformed to process genotyping in the BRLMM-P and SNPolisher framework. Various Eureka NGS panels are tested, including a Bovine panel, for which BRLMM-P generates an average sample call rate of 99.6% and an average sample concordance of 99.6%.