Flexible and Scalable Polymorphism Surveys in the Dog to Decipher Functional Variants Using Dynamic Array™ IFCs and the BioMark™ HD System

The domestic dog is an important mammalian model organism. Unbiased genome-wide mapping in the dog efficiently links causative pathways to phenotypic effects. Strong linkage disequilibrium (LD) in breed isolates confers power for association studies. A dense, fixed SNP array ensures coverage for mapping. A strong LD that drives mapping with modest case-control cohorts (100:100) yields large ancestral haplotypes (3Mb), segregating intact within the population. However, detecting the single causal mutation from within large genomic intervals remains a challenge.

Whole genome sequencing (35X) can now generate a large list of variants (SNPs, Indels, and CNVs) corresponding to a mapped interval. In silico methods help prioritize variants, but the computational approach still yields 12-24 variants per locus, with only one of these expected to be causal. Tiered genotyping screens, ultimately encompassing thousands of purebred dogs, are a powerful means of refining variant lists. A single flexible and scalable platform for screening variants is needed to accommodate the trend during a project toward larger sample sizes and fewer variants. Here, we demonstrate that Dynamic Array™ integrated fluidic circuits (IFCs) enable custom genotyping that fulfills these aims. Using different configurations of IFCs, it is possible in a single experiment to test as many as 96 different samples against 96 different loci or as few as 12 samples against 12 different loci. This flexibility enables a cost-effective solution for scalable genotyping without up front development of set multiplexes.