Best Practices for Genotyping Analysis of Plant and Animal Genomes with Affymetrix® Axiom® Arrays

Large scale multiplexed SNP genotyping has been made possible by the ongoing development of high density DNA oligonucleotide arrays coupled with new molecular biology assays. The data analysis processing of these arrays requires automated methods and workflows and thus Axiom genotyping best practices have been developed and applied to the human genome (http://www.affymetrix.com/support/downloads/manuals/axiom_best_practice_supplement_user_guide.pdf).  Plant and animal genomes however present additional challenges due to the complex organization of polyploid genomes; high levels of species-specific nucleotide and structural diversity; and the use of relatively novel sequencing-derived content that has not been validated with independent genotyping methods.

We describe the Axiom® workflow that combines the best practices for human genotyping with new steps and software that are specifically targeted to the complexities associated with plant and animal genotyping. Genotyping calls are produced for humans, plants, and animal genomes with AxiomGT1 which is an automated clustering algorithm used by the Axiom® Genotyping Console™ software and features adaptive, dynamic clustering. Following genotyping, “SNPolisher”, a newly developed R package for Axiom® genotyping arrays, uses AxiomGT1 output to (1) produce SNP Quality Control (QC) metrics; (2) divide markers into six classes that are relevant to the genomic complexities of plants and animals; (3) provide cluster visualization; and (4) execute “VINOtyping”. In summary, this workflow returns the maximum number of high quality genotype calls along with automatic division of polymorphic, high resolution markers from those markers that can benefit from further examination based on knowledge of the genetics of the sample under study.