SNP Genotyping of Markers with Nearby Secondary Polymorphisms using the Affymetrix® Axiom® Genotyping Solution

Axiom^® SNP microarrays utilize oligonucleotide probes complementary to the genomic sequence adjacent to the candidate SNP. Following hybridization of amplified target DNA and on-array enzymatic ligation with hapten-labeled solution probes, a multi-color signal complex is detected and processed as a genotyping cluster.

Highly polymorphic organisms pose unique challenges in microarray-based genotyping.  Eucalyptus and potato genomes contain SNPs up to frequency of one per every 16 bp or 29-40 bp, respectively. In principle, the presence of a secondary polymorphism in the target DNA in close proximity from the candidate SNP location introduces a destabilizing base-pair mismatch that can interfere with the hybridization and ligation properties of the probe and hence change the genotyping intensity cluster properties for a given primary SNP.

Exploiting the shorter length of probes on Axiom^® arrays, we report on the (i) characterization of Axiom^® SNP genotype clusters with respect to the presence, location and alternate allele frequency of nearby secondary polymorphisms and (ii) Axiom GT-1 genotyping calling algorithm robustness to cluster changes induced by secondary polymorphisms.

The Axiom^® Genotyping Solution capability to accommodate nearby secondary polymorphisms, coupled with high-throughput sample processing and advanced polyploid genotyping algorithms, addresses the un-met needs of genotype-trait association studies and marker assisted selection in both plants and animals.