Linkage Disequilibrium

Linkage Disequilibrium - NETICS IN MEDICINE qIigTP:gL!E u...

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Unformatted text preview: NETICS IN MEDICINE qIigTP:gL!E u 11. "r]J ft\ il\ t_J \ f(A)= 50% Figure-''! 0-9. r Diagramof linkageequilibriumanddisequilibriumbetweenallelesatlocusl andallelesarlocus2.A,Loci 1' and2 are located very close to one another. Allele frequencies of A and a ar locus 1 are both 50%. Allele frequencies of D and d at locus 2 are 10"/" and 90'k . B, Haplotype frequencies under linkage equilibrium. Haplotypes containing the D allele, D-A and D-a, each have a frequercy o{ )% and together constitute 107", equal to the allele freq,r.,r.y f(D) oFthe D allele. Similarly, haplotl'pes c_ontaining the A.allele, D-A and d-A,have frequencies tf SZ and 45%, respectively, and rogether con- stitute 507", equal to frequency f(A) of the A alleie._similarly, the frequency f(a) of the a allele is S% + +56t" = 50%, and f(d) of the d allele = 90"/". C,.Haplotype frequencies under linkage disequilibrium. The haplotype containing the disease allele D is enriched for allele a at locus 1; haplotype D-A is not present-in the population. The frequencies of the rlmaining haplotvpes are such that there is no change.in the allele frequencies f(A), f(a), f(D), and f(d), only in ihe frequencies of the unlrioor 1rnplo types. D, Partial linkage disequilibrium, with the haplotype D-A rare but nor absent from the popularion. Complete linkage disequilibrium tical task. There is, however, another characteristic of the genetic landscape, a phenomenon known as linkage disequilibrium, that permits a higher resolution map based on inferring recombinations that occurred during millions of meioses over thousands of generations, back to the origins of modern humans. To understand linkage disequilibrium, we need first to explain its opposite: linkage equilibrium. Consider two loci: a polymorphic marker locus 1 with two alleles, A and a, and a nearby disease locus 2, with disease allele D and normal alleIe d. Suppose aliele A is present on 50% of the chromosomes in a population and allele a e- Locus 1 f(A) = 567. f(a; = 567" d<- Locus 2 Linkage equilibrium = 10% f(a) = 567. f(A) = 597. f(a) = 567. Partial linkage disequilibrium d on the other 50% of chromosomes. At locus 2, disease allele D is present in 10% of chromosomes and d in 90% (Fig. 10-9A). Knowing the allele frequencies for these two loci does not mean that we know how these alleles are distributed into the four possible haplotypes, A-D, A-d, a-D, and a-d. Shown in Figure 10-9B is the situation in which the population frequency of both haplotypes containing the A allele (A-D plus A-d) is 50%, the same as the allele frequency for A in the population. Similarly, the frequency of the two haplo- types containing the D aiieie (A-D plus a-D) is I0o/", the same as the frequency of the D al1eie in the popula- 107o D C 90% = 10"/" y multiPle generations ry ffi x ffilifilEl{---ffiffir @ ffi N ffi I I v ffi Mutation located within region of linkage disequilibrium tion. !(/hen the frequency of each tion....
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This note was uploaded on 09/14/2011 for the course PHARM HB taught by Professor Staff during the Spring '11 term at UCSD.

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Linkage Disequilibrium - NETICS IN MEDICINE qIigTP:gL!E u...

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