SNP Genotyping using Affymetrix' AxiomŽ Genotyping Solution

The use of DNA microarrays for easy, cost-effective genotyping of single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels) continues to play an important role in genotype-trait association studies and marker-assisted selection in both plant and animal breeding programs.

Axiom^® Genotyping Solution enables complete automation of DNA target preparation, DNA amplification, and enzymatic fragmentation of post-amplification products on the Biomek^® FX^P Target Prep Express platform. Following target preparation, arrays are processed using GeneTitan^® Multi-Channel (MC) Instrument. Here we describe a new Axiom^® product in which 384 individual arrays, contained in the footprint of a standard microtiter plate, offer the capability to genotype approximately 50,000 variants in combination with a processing throughput of greater than 3,000 samples per week. The 384-array layout is ideal for high-throughput screening in molecular breeding programs where ease of use, accuracy and turnaround time are all essential. The Axiom 384-array layout retains full compatibility with the currently existing Axiom instrumentation platform and downstream data analysis stream. Genotyping performance metrics obtained with Axiom 384-array layout will be presented.

In summary, new Axiom advances to DNA sample type compatibility, high-throughput sample processing enabled with laboratory automation, and the 384-array layout further extend the platform’s capabilities to genotype thousands of samples per week with minimal manual intervention that is consistent with the needs of both animal and plant agrigenomics solutions.