I realize reduced-representation sequencing (e.g. RADseq, GBS) is much lower cost / bp, we are looking for inexpensive ways to genotype lots of individuals for 25-75 SNPs at a time. Thank you!
That's about as cheap as I've heard. I think KASP genotyping could be in that range. The all-inclusive service from the LGC calculator has 3,100 samples/40 SNPs for less than $6/sample ($16740 total, including DNA extraction). It looks like the non-all-inclusive service is more expensive, though, so not sure I am reading that correctly (http://www.lgcgroup.com/services/genotyping/cal ). Cost is higher with fewer samples.
Hi Andrew,
In my PhD project I'm also using Sequenom which is much more cost-effective (according to the calculation I made based on my own design of course) when dealing with >1000 individuals of several species (I need to genotype 160 SNPs for each one of my 18 species !)
Though if you are working on one specie and a lot of individuals, you might be interested in genotyping by amplicon re-sequencing, which is the principle of GT-Seq or Truseq Illumina kit. Someone in my lab will be trying this very soon, in his case this was the cheaper approach !
Also, have a look on the Access-Array, KASPar, or Wafergen Smartchip TE :) (and this is just a few !!)
Hope this helps :)
Hi Chrystelle,
Did you do any extra work in primer design since you were genotyping multiple species? How often does a primer set fail to work in all the species because of a SNP in the primer regions? Just curious!
Hi Eric !
Sorry for the delay ! It actually was a different set of 160 SNP for each species :) for a total of 2880 SNP ! This is why Sequenom was better for us : the price of 2880 primers pairs for GBS or KASP was huge. Sequenom uses standard 20-25 pb primers so this was way more preferable !
Each species will have its own Sequenom array. We developed SNP markers by using pool-seq.
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