Hi, I'm looking for a method in order to discriminate few known SNPs (up to 10) in a large cohort (up to 1000 samples) simultaneoulsly. Until now I've found only techniques to study many SNPs in just one sample per reaction.
Do you know which could be the best technique for my purpose?
thank you in advance for your replies.
Molecular inversion probes are the method of choice for highly multiplexed analysis of large cohorts. However, I am not sure your number warrants such an approach. You might be best of with qPCR assays. If you have the option to outsource the analysis, Agena Bioscience MassArray may be the perfect match. That technology can multiplex up to 28 SNPs in one analysis and is offered at quite attractive pricing.
https://en.wikipedia.org/wiki/Molecular_Inversion_Probe
http://agenabio.com/products/massarray-system/
http://www.maf.ki.se/prices/MAF_prices_Agena_Genotyping_151101.pdf
You could have it analysed by LGC genomics also at attractive prices or do it your self with simple KASP or TaqMan assays. These kind of simple end-point PCR works very well and are easy and cheap. 1000 samples are 3x384 well plates and you can probably run 2-3 a day...
Firstly, thank you for your help!
The number of SNPs i have to genotype is 20, thus i was taking into consideration SNaPshot, SNPlex and MIP methods. Anyone of you have already tried one of these techniques? In your opinion is it possible to perform these techniques in a 384well plate?
Of course, but it depends on the settings of the Genetic Analyzer Instrument
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