Hi Joanna,

well, in fact we'll need more details for a proper answer. what will you do with the SNP? how much SNP? how much samples to genotype? what sort of samples, I mean will you wait for wild type/heterogygous/homozygous genotypes or clonal genotypes (germane mutations or acquired mutations as in cancers)? will you consider the price and have you access to NGS facilities?

fred

The SNPs, which I would like to genotype are well known. I expect three genotypes: 2 oposite homozygotes and heterozygotes. It will be human genomic DNA. I would like to study three SNPs, but not necessary at once (in one reaction). I have Light Cycler 480, Roche, so I would like to use TaqMan probes or molecular becons methods for genotyping, but I don't have any experience with those methods, so I don't how to manage.

OK,

thermo fisher offers more than 10 million predesigned assays for 25 species. take some time in their website and see if your targets are waiting for you in their lists (http://www.thermofisher.com/fr/fr/home/life-science/pcr/real-time-pcr/real-time-pcr-assays.html?gclid=Cj0KCQjw9LPYBRDSARIsAHL7J5msnI54CPU9Jz71cou1ygsCuVi3V1wnpgk3k5p3XFxSn-m5JMmzdpwaAk4hEALw_wcB&s_kwcid=AL!3652!3!245695868609!b!!g!!taqman&ef_id=Wh@vxgAABFfpjRHK:20180530064023:s).

good luck

fred

Dear Joanna,

I support Federic's advice. My experience is the following: you should know at least:

- your SNP rs ID

- the alleles, genotypes and their frequency in the population.

You can verify this in Ensembl database to confirm.

Then, go to ThermoFisher website and type rs ID, adjusting and filtering the results if it is necessary.

If you will not find any relevant solution, you can contact them directly, there was a webpage form to explain your needs and they will contact you later. They support you with the explanation how to use their CAST tool to elaborate necessary solution, including primers and probes. Do not forget to mention you are going to work with LightCycler. I am not sure if it allows to follow passive dye, which is ROX in ABI reagents. I found this useful in case of manual pipetting.

Good luck!

Thank you all for help:-)