How do I calculate allele frequency?

Sourav PanOctober 25, 2024

Answered

General Formula:
Allele Frequency = (Number of copies of the allele) / (Total number of copies of all alleles at that locus in the population)

Methods to Calculate Allele Frequency:

1. Direct Counting (Discrete Data)

• Step 1: Count the number of individuals with each genotype.
• Step 2: Determine the total number of alleles in the population (2 times the total number of individuals, since each individual has 2 alleles).
• Step 3: For each allele, count the number of its copies:
  • For homozygous genotypes, count 2 copies per individual (e.g., MM contributes 2 M alleles).
  • For heterozygous genotypes, count 1 copy per individual (e.g., MN contributes 1 M allele and 1 N allele).
• Step 4: Calculate the allele frequency for each allele using the general formula.

Example from the Text:

• Total Alleles: 12,258 (2 * 6129)
• Allele M Frequency (p): f(M) = [(2*1787) + 3039] / 12,258 = 0.5395
• Allele N Frequency (q): f(N) = [(2*1303) + 3039] / 12,258 = 0.4605

2. Using Genotypic Frequencies (when genotypes are known)

• Given: Frequencies of genotypes (e.g., MM, MN, NN)
• Step 1: Assign p as the frequency of one allele (e.g., M) and q as the frequency of the other allele (e.g., N), knowing that p + q = 1.
• Step 2: Calculate p and q using the genotype frequencies:
  • p = f(MM) + ½ f(MN)
  • q = f(NN) + ½ f(MN)

Example from the Text (Greenland):

• p (M allele): 0.835 + ½(0.156) = 0.913
• q (N allele): 0.009 + ½(0.156) = 0.087

3. From Molecular Data (e.g., fragment sizes)

• Step 1: Count the number of individuals with each fragment size.
• Step 2: Assuming each individual has two alleles, calculate the total number of alleles.
• Step 3: Calculate the frequency of each allele as in the direct counting method.

Example from the Text (Molecular Data):

• Total Alleles: 200 (2 * 100)
• Allele 6.5 kb Frequency (p): [(2*30) + 50] / 200 = 0.55
• Allele 3.0 kb Frequency (q): [(2*20) + 50] / 200 = 0.45