January_28_2013_NKW_NEW

38 6561 genotypes calculaon of haplotype frequencies

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Unformatted text preview: A1B1 A1B1 A1B1A1B2 A1B1 A2B2 A1B2A2B1 A1B2A2B2 A2B2A2B1 A1B2A1B2 A2B2A2B2 A2B1A2B1 How many genotypes for 8 loci each with 2 alleles? = 38 = 6561 genotypes (!) Calcula:on of haplotype frequencies at Linkage Equilibrium ALLELE FREQUENCIES: f(A1)=p f(A2)=1 ­p f(B1)=r f(B2)=1 ­r HAPLOTYPE FREQUENCIES at Linkage Equilibrium (random associa+on) f(A1B1) = pr f(A1B2) = p(1 ­r) f(A2B1) = (1 ­p)r f(A2B2) =(1 ­p)(1 ­r) What is Linkage Disequilibrium (LD or D)? The associa+on of alleles at different loci more frequently or less frequently than expected based on their frequencies. **Coefficient of Linkage Disequilibrium for 2 alleles at each of 2 loci: D = f(A1B1) x f(A2B2) – f(A2B1) x f(A1B2) This equals zero when alleles are randomly associated and is non ­ zero when alleles are LINKED (can be nega+ve). D = [pr x (1 ­p)(1 ­r)]  ­ [p(1 ­r) x (1 ­p)r] = 0 at linkage equilibrium 3 DIPLOID GENOTYPES A1 B1 A1 A2 B1 B2 A2 B2 A1 A1 A2 B2 A2 B2 A2 B2 A1 B1 B1 heterozygotes at both loci—the only genotype that can generate the new, recombinant gamete types 4...
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