Assume that you have DNA from a bunch of patients, say 1000 (i.e. the DNA molecules from each patient are not specifically tagged or identifiable).
I would like to find out whether SNP alleles are present in that mixture of DNA, and ideally determine their frequency.
To give a practical example, I might be interested in 100 different SNP alleles in a particular bunch of 1000 patients, and it is likely that I would repeat this procedure for a different bunch of patients and a different set of alleles.
Can you give some advice on suitable genotyping technologies and how much they would cost?
Designing a SNP chip seems to be too much effort given that the set of SNPs would be likely to change with every bunch.
Targeted sequencing is an alternative but would probably not have very high sensitivity, and here too I would have to design a specific target panel for each new set of SNPs.
Digital PCR / qPCR sound interesting, but I how much would that approximately cost and how complicated is it to target a new set of SNP alleles?
