Optimizing SNP microarray probe design for high accuracy microbial genotyping.

  title={Optimizing SNP microarray probe design for high accuracy microbial genotyping.},
  author={Shea N. Gardner and James B. Thissen and Kevin McLoughlin and Tom Slezak and Crystal J. Jaing},
  journal={Journal of microbiological methods},
  volume={94 3},
Microarrays to characterize single nucleotide polymorphisms (SNPs) provide a cost-effective and rapid method (under 24h) to genotype microbes as an alternative to sequencing. We developed a pipeline for SNP discovery and microarray design that scales to 100's of microbial genomes. Here we tested various SNP probe design strategies against 8 sequenced isolates of Bacillus anthracis to compare sequence and microarray data. The best strategy allowed probe length to vary within 32-40 bp to equalize… CONTINUE READING


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