Population Genetics

Genotype and Allele Frequency Estimation is the first step in studying a polymorphism. Used for family data and independent individuals in a population. We can use a subset of individuals who are independent and count alleles, or use the maximum likelihood methods to take all genotypes into account for pedigree data.

Consider the following example of allele frequency estimation:

We can take the frequency of each allele by the observed proportions:
    p_M = (2*298 + 489)/(2*1000)
    p_N = 1 - pM

Hardy-Weinberg Law

Describes how we expect allele frequencies and phenotype frequencies to be related in a population.

1. For a large, random-mating population, in the absence of forces that change allele frequencies, the allele and genotype frequencies remain constant from one generation to the next
2. After one generation of random mating, for an autosomal locus with alleles 1 and 2 (frequencies p and q = 1 - p), the relative frequencies of the genotypes 11, 12, and 22 are:
        p², 2pqm q²

Assumptions

• Random mating with respect to genotype
  • No assortative mating
  • No population structure
• No selection, mutation, or migration
• Discrete generations
• Infinite population size
• Autosomal locus