| | Genotyping was performed with commercially available TaqManŽ Validated SNP Genotyping Assays from Applied Biosystems (Foster City, CA, USA), following the standard protocol suggested by the manufacturer utilizing 3ng of dried down DNA. A high-throughput |
| | assay design pipeline used in the TaqManŽ Custom SNP Genoptyping Assay design service (Applied Biosystems, Foster City, CA) was used to develop 5' nuclease allelic discrimination assays. After the design of primers and TaqManŽ probes, a computational qual |
| | ity-control step was performed to ensure uniqueness of the predicted amplicons in the genome assembly. This eliminated potentially problematic SNP targets that may arise from repeated genomic regions, pseudo-SNPs, and other possible assembly artifacts. Th |
| | e average genotyping error rate in our production lab was estimated at about 0.1% by routinely running duplicate control plates. |
