Couple of options to think about: in terms of moderate throughput genotyping, our lab uses the Fluidigm fluidic circuits with TaqMan assays. We can genotype 96 samples at 96 loci at a time. Each 96 sample run requires a ~$500 chip plus cost of assay development, but it is a pretty standard technique. Not sure how well it works with lower quality samples (e.g. saliva samples from predation): we have had issues with carcass samples and lower genotyping success rate.

If you really want to push the limits, you could try amplicon sequencing, in which you can potentially genotype hundreds of loci for thousands of samples. You probably don't need that high of throughput, but you could run a couple of 96 well plates full of samples on a MiSeq for about $1000-1500 per flow cell. Gives you lots of flexibility in terms of which primer panels you can use. Check out Campbell et al. 2015 (Article Genotyping-in-Thousands by sequencing (GT-seq): A cost effec...

Hi Andrew,

Genotyping could also be done with MALDI-TOF mass spectrometry. As Justin said, you can do through amplicons sequencing (here we use Ion platform) but we are thinking to change this. Have a look at Agenaa Bioscience: http://agenabio.com/products/massarray-system/.

Best,

Michele

Hi Andrew.

I had elaborated and worked on QuantStudio 6 equipment with 384 well block configuration for TaqMan Genotyping. My experience comprised testing of 440 samples by 20 SNPs. I developed the methodology working in 5 mcl reaction volume, which ensured samples and reagents savings, and decreased per sample costs. I used to divide the 384 well plate in 3 or 4 blocks of the same samples, corresponding to 3 or 4 SNPs tested per plate. I have not calculated final costs but (except of the equipment, which you can replace with any thermocycler and a fluorescence reader for VIC and FAM /+ROX/) roughly the costs are not higher then 0.4-0.5 Euro per sample. I performed manual pipetting, so turn-around time was 6 plates per week.

Still the methods lacks the possibility to identify exactly which polymorphism is present, TaqMan shows you only the alleles you are checking, while, as Justin and Michele mentioned, sequencing would give you exact answer.

Good luck!!!

We've had success with MassArray/iPlex chemistry (Agena, formerly Sequenom), and this continues to be our go to platform for pilot studies (fee hundred samples) as well as few thousand when samples are limited (saliva), and when the number of polymorphisms is small to medium. Our designs cover in average 29 SNPs at a time and the PCRs and extensions are done in 384 plates, using small volumes (cost saving). Another advantage is that depe ding on the surrounding sequence one can also test small indels. If you have a set of target polymorphisms, this is great, otherwise sequencing or pyrosequencing, as you get to take a peek at the surrounding nucleotides.

The Fluidigm system as Justin has discussed has worked very well for similar studies I've been involved with. To add to that discussion, we have had a fair amount of success using degraded, or low content DNA samples.