Recommendations for 200 SNP markers genotyping

Question

[PolenP]

I have 200 SNP markers that I would like to use for genotyping. We wanted to do the genotyping in house, and we have funds available to buy the equipment. We will do the genotyping routinely. Can you please suggest some options for the equipment and methods (etc. microarray reader) or other options such as targeted genotyping by sequencing that can be done in house?

For the number of samples, we were only looking at 300 samples per year, so just something small and not industrial scale.

I am also open to explore any options. Thank you.

[Michael]

Which organism are you talking about, and are these markers fixed? You can search for existing genotyping options using this information. For example, there is a large difference between human SNPs and bacterial antibiotic resistance markers. Search for targeted genotyping vs. genome-wide genotyping. It will possibly turn out to be Illumina or Oxford Nanopore. A MinION sequencer with duplex/HQ base-calling could possibly do the trick, provided you have good DNA concentration, giving you all the rest of the structural variation as well. A small Illumina machine will be good or better for the SNPs. Compare the cost estimates for flow-cells, kits and reagents. Check if you can do the library in-house.

Answer 1

[Aleksandra]

For a 200-SNP panel at your sample throughput, I would recommend an amplicon-based targeted sequencing approach. The workflow involves designing a custom multiplex PCR panel, often with a vendor like IDT or Illumina, to amplify all 200 targets simultaneously. Following a straightforward PCR and barcoding protocol, you would then pool the samples for sequencing. An Illumina iSeq 100 or a similar benchtop sequencer is the ideal instrument for this scale. It combines a manageable capital cost with low per-run expenses, providing the most cost-effective and flexible in-house solution for your specific needs.