Yes it is possible to use allel-specific primers in qPCR. Another option is to use common probes (for both alleles) and use allele-specific hybridization probes or beacons, but this requires that the allelic ratio is somwhere within 1:10 to 10:1.

Hi Nesrin

it looks like the old technique called ARMS-PCR.

you'll need to design your primers with one of the containing the variation at 3', and you need to buy the common primer and the WT and mutated primer, and run you PCR separately. take a look at this paper:

https://www.cd-genomics.com/diseasepanel/arms-pcr-in-disease-research.html

all the best

fred

The best way to address this question is with ddPCR:

http://cshprotocols.cshlp.org/content/2016/8/pdb.prot086801.full

RNA sequencing. You’ll get abundances of transcripts of interest, and a bunch of more data that may also be relevant.

Frederic Lepretre As far as I understood, this method will be only helpful if there is a single base substitution which is not the case. Kindly correct me if I am missing something.

Thank you

ARMS is useful to distinct variants at heterozygous or homozygous state.

you just need to design a PCR with 3 primers, a common primer (let's say the reverse) and two forwards, one containing the variant at 3', and run both PCR separately with an internal positive PCR to be sure when there is no amplification that you didn't miss something.

fred