Lecture 11

Learning outcomes

  1. Describe how meiotic recombination can be used to map the relative positions of linked genes

    • The map distance between two loci is a theoretical concept that is based on actual data — the extent of observed recombination, θ, between the loci.

    • Map distance is measured in centimorgans (cM).

    • A recombination fraction of 1% (θ=0.01) translates approximately into a map distance of 1 cM.

    • The recombination frequency between two loci increases proportionately with the distance between two loci only up to a point, because once markers are far enough apart that at least one recombination event will always occur, the observed recombination frequency will equal 50%.

  2. Understand the correlation between genetic and physical maps

    • To accurately measure true genetic map distance between two widely spaced loci, one has to use markers spaced at short genetic distances (< 1 cM) in the interval between these two loci, and add up the values of θ between the intervening markers.

    • The values of θ between pairs of closely neighboring markers will be good approximations of the genetic distances between them.

    • 1 cM per Mb

    • This is just an average though, and begins to break down when looking at a higher resolution.

      • There are recombination hotspots that account for ~60% of all the meiotic recombination in the human genome, but only occupy ~6% of sequence in the genome.

      • This can lead to linkage disequilibrium

  3. Understand how the frequency of genotypes in a population can be used to determine if alleles are in linkage equilibrium

    • Linkage equilibrium is when the frequency of haplotypes = the product of frequencies of alleles in the population.

      • If we want to tell if recombination is happening freely, the frequency will average out to the product of alleles.

    • Linkage disequilibrium is when the frequency of haplotypes does not = the product of frequencies of alleles in the population.

      • As we examine haplotypes involving loci that are very close together, we find that knowing the allele frequencies for these loci individually does not allow us to predict the four haplotype frequencies.

    • Deviation (D’) is the quantitative measure of LD

      • D’=0 means that the alleles are in linkage equilibrium

      • D=+1 indicates very strong LD.

      • LD is a result, not only of genetic distance, but of the amount of time during which recombination had a change to occur and the possible effects of selection for or against particular haplotypes.

      • Different populations living in different environments with different histories can have very different values of D’ between the same two alleles at the same locus.

  4. Describe how linkage disequilibrium can lead to the generation of a disease haplotype

    • When a pathogenic allele first enters the population (by mutation or immigration of a founder who carries the altered allele), the particular set of alleles at polymorphic loci linked to the disease locus constitutes a disease-associated haplotype.

    • The degree to which this original disease-associated haplotype will persist over time depends in part on the probability that recombination removes the disease associated allele from the original haplotype and onto chromosomes with different sets of alleles at these linked loci.

      • The smaller the value of θ, the greater the chance that the disease-associated haplotype will persist intact.

      • Over many generations, the only alleles that remain in coupling phase with the variant are those so close to the disease associated locus that recombination between loci is very rare.

      • These alleles are in linkage disequilibrium with the pathogenic variant.

  5. Explain how to calculate the linkage of a disease gene to a marker allele using linkage analysis

    • Linkage analysis is a method of mapping genes that uses studies of recombination in families to determine whether two genes show linkage when passed from one generation to the next.

    • Information from the known or suspected mendelian inheritance pattern is used to determine which family members have inherited a recombinant or nonrecombinant chromosome.

    • To decide whether two loci are linked, and how close or far apart they are, we rely on two pieces of information:

      • Using family data, we estimate the recombination frequency (θ) between the two loci.

      • Next, we ascertain whether θ is statistically significantly different from 0.5, which is the fraction expected for unlinked loci.

      • Estimating θ and determining the statistical significance of any deviation from 0.5 relies on the likelihood ratio.

  6. Calculate the LOD score and recombination frequency for a disease gene and marker allele based on one or more family pedigrees and information about the genotypes of family members

    • LOD stands for logarithm of the odds.

      • The use of logarithms allows likelihood ratios calculated from different families to be combined by simple addition rather than multiplying them together.

      • It provides the best estimate of distance (θ) between genes and assesses strength of evidence.

      • Basically finding (what is the ratio of observed data)/(what you would get if you had no recombination)

      • A LOD score of > 3 is considered strong evidence of linkage. In other words, there is enough evidence that θ is statistically significantly different from 0.5.

    • LOD score = log10θR(1-θ)NR/0.5(R+NR)

      • R: number of recombinant chromosomes

      • NR: number of non recombinant chromosomes

      • θ: fraction recombinant

      • 1-θ: fraction non recombinant

Key terms

Independent assortment

  • After recombination and chromosomal segregation are complete, there will be four possible combinations of alleles in a gamete: AB, ab, Ab, and aB.

  • Each combination is as likely to occur as any other. This is independent assortment.

    • In unlinked genes, the ratio is 1:1:1:1 —> 50% parental and 50% recombinant.

Meiotic recombination

Linkage

  • Linkage is the term used to describe a departure from the independent assortment of two loci.

  • In other words, the tendency for alleles at loci that are close together on the same chromosome to be transmitted together, as an intact unit, through meiosis.

  • Analysis of linkage depends on determining the frequency of recombination to measure how close two loci are to each other on a chromosome.

  • If two loci are so close together that θ=0, they are said to be completely linked.

  • If they are so far apart that θ=0.5, they are assorting independently and are unlinked.

Phase

  • Refers to which allele at the first locus is on the same chromosome with which allele at the second locus.

  • Basically the orientation of alleles on homologous chromosomes.

Coupling (cis)

  • When the set of alleles on the same homologue (A and B, or a and b) are in cis

  • Form a haplotype

Repulsion (trans)

  • Alleles on the different homologues (A and b, or a and B) are in trans

Informative

  • Individual is heterozygous at both loci

Recombination frequency

  • The closer together two loci are, the smaller the recombination frequency and the fewer recombinant genes in the offspring.

Centimorgan

  • The genetic length over which, on average, one crossover occurs in 1% of meiosis.

Recombination hotspot

Linkage equilibrium

Linkage disequilibrium (LD)

  • Because of LD blocks, in reality there are way less haplotypes than what is possible.

Deviation

LD blocks

  • Clusters of loci with alleles in high LD across segments of only a few kilobase pairs to a few dozen kilobase pairs.

  • These blocks have the potential to generate a huge number of haplotypes, but because there is really high LD, only a few haplotypes constitute most of all haplotypes seen.

Disease haplotype

Marker allele

Logarithm of the odds (LOD) score