How do I measure allele frequency in a population?

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Anuroop Venkateswaran Venkatasubramani

Hi.. If you have the genotyping results of all the individuals, you can use PLINK to calculate the allele frequency.. I hope I have answered your question!!

Yixin Zhao

Hi,

Thanks for answering! I don't have genotyping results of all the individuals. In fact, I want to get genotyping results in a fast way(less time-cosuming or labourious), so I would like to know if any convenient technique can be applied? The differences between the alleles are generated by TALEN(a way to knock out gene at specific site), so it is NOT SSR or markers. The difference between the alleles are usually 3 - 20 bp.

Hi Goumi,

Thanks for your suggestion. I think Sanger sequencing is one of the possible ways to solve this, but my concern is that the heterozygous individuals will give messy results(overlapping peaks, ect ). In addition, the cost of sequencing 1000 individual is approximately equal to that of HRM. Hence, I am still thinking which way is better or if any other high throughput ways.

Filippo Biscarini

I do not know which "material" you are analysing (plants, animals, humans, bacteria?). It seems that you are interested in a very specific region of the genome: in this case maybe you could use a custom SNP-array, or genotyping by sequencing. Both approaches should be relatively quick and inexpensive.

Ramesh Krishnan Ramasamy

There is some confusion in your question. Array is not a option here, considering the assay needs to be designed for only one locus. Sanger sequencing may be cheap and viable option.

Hi Filippo and Ramesh,

Thanks for your answers. I am studying Drosophila melanogaster, I am interested in a specific region of microRNA. I want to put the two different alleles into the population, and let them "compete with" each other. After several generations(~30-50 generations), I want to measure the alleles frequency in the population, hence, I am able to know which allele is "more fitting" in the experimental condition.

Hi.. I am also using TALENs but for a different reason.. However, I guess genotyping by sequencing is easier and faster and you could decide on whether to go for NGS or Sanger depending on the cost..