P1027 Application of analysis tools from Affymetrix on Eureka Genotyping Solution to provide accurate and automated animal genotypes

Abstract

The BRLMM-P 2-dimensional clustering algorithm is used by mid- to high-plex microarrays from Affymetrix for genotyping single nucleotide polymorphisms (SNP) and insertion/deletions (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 allopolyploidy. BRLMMP 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 Genotyping Solution is an affordable, low- to mid-plex, high-throughput genotyping assay that uses common next-generation sequencing (NGS) platforms for signal readout. It enables the detection of tens to thousands of genetic markers, which are increasingly in demand for routine animal agrigenomics testing. Using 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 Axiom 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. The BRLMM-P algorithm has been shown to work on both microarray intensity and NGS reads. Various Eureka genotyping panels are tested, including a bovine panel, for which BRLMM-P generates an average sample call rate of 99.9% and an average sample concordance of 99.5%.