Genotyping – Fluidigm EP1, Genotyping by Sequencing, Illumina Infinium Arrays (discontinued)

A number of options exist for high-throughput genotyping in our Core: sequence-based genotyping protocols, and PCR-based genotyping assays using the Fluidigm EP1 instrument (please note, we discontinued Illumina Infinium genotyping as of October 2023). The best approach for your project depends mostly on the number of SNPs to be interrogated and the number of samples to be assayed over the course of the project. There is also flexibility in the number of samples processed, although economies of scale dictate the lowest optimum sample size. Here are some rough guidelines matching assay type to desired SNP multiplex level:

  • 24, 48, 96, 192 SNPs/sample: PCR-based genotyping Fluidigm EP1.
  • 192 SNPs to thousands of SNPs and 192 or more samples: Tecan Allegro genotyping-by-sequencing
  • Skim-Seq: Low coverage whole genome sequencing
  • Reduced Representation Sequencing: GBS, RAD-Seq, semi-random-PCR based protocols

We suggest discussing the options on a Zoom call (

Illumina Infinium genotyping was discontinued in the DNA Technologies Core as of October 2023 — please contact the VGL (530) 752-2211.