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PETER REDDIEN: Let's now try to apply these concepts
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to actual example pedigree and try to calculate a LOD score.
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I'm going to draw a pedigree.
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And I'm going to draw out where I stretch out
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the individuals in a way where I can show you data for SSRs
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below them.
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And this is our dominant trait that we're working
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with today, D over plus.
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OK.
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And now we're going to get some SSR data for SSR1.
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And I talked about last time how you
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can look for this by looking at the size of the SSR
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in individuals.
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So we could look at this with gel electrophoresis.
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All right.
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So I'll give you some data for these individuals where
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what I'm drawing here are the data below the individual that
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correspond to that individual.
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So this is the SSR1 genotype data for this individual.
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This is the data for that individual and so on.
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So that's our data.
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And now the next thing we're going to do
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is ascribe genotypes to these individuals.
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So this individual will be D over plus.
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And what is the SSR genotype?
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AA.
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What about this individual?
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BB.
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OK.
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So you've got the idea with that.
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Plus plus, BB.
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All right.
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So now let's go to the next generation.
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We have D over plus and A over B. By the way,
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do we know the phase of these alleles in this individual?
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These came together.
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So the phase is known.
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OK.
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Let's see.
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So we'll keep going.
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And I'll just now put the genotypes
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on the rest of these individuals.
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D over plus, A over A. Same exercise for each one.
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Plus over plus, B over B, plus over plus, A over B,
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D over plus, A over A, D over plus, B over B.
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This individual plus over plus, A over B.
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Now we need to look at this outcome
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and try to see if we can figure out
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whether we have non-recombinant gametes that were involved
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in the meiosis producing the gametes that
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made these individuals.
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So we have some individuals here.
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Now, there is a meiosis here that produced this individual.
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So we can consider that individual, this individual,
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this individual.
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Basically all of these are the results of some meiosis
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that we have some data about.
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And then we can ask if the meiosis was informative or not.
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So the meiosis that produced individual one--
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so this is individual one here--
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is that meiosis informative or not informative?
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So we're talking about the meiosis in this parent that
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produced this individual.
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You think it's informative?
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This is an uninformative meiosis because we have no information
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here about whether recombination could have happened
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between the D gene and this SSR1 because you
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were homozygous at this locus.
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So that's uninformative.
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Yeah, the phase doesn't tell you whether it's informative
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or not.
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Whether it's informative or not is
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whether you can tell if two different alleles of two
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options went together or not.
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The meiosis that produced this individual,
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it's uninformative because you had to get a big A
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allele from this SSR1.
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So do you have any hope of seeing whether there
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is any recombination between this allele and this D
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by looking at the genotype of the offspring?
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You're going to have A no matter whether it was
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recombinant or non-recombinant.
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When we're considering the phase,
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we're trying to determine what configuration the alleles would
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have been in the parent whose meiosis we're
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going to be evaluating.
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And whether it's this individual with phase known or unknown
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makes an informative meiosis is determined
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as we've gone through.
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OK.
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So when we're talking about phase,
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we're trying to figure out--
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so for this meiosis that this individual made,
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we need to think about if we have any phase information
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to evaluate their meiosis.
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For this individual and her offspring,
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we need to think about if we have any phase information.
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And then we can evaluate separately
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whether she had informative or uninformative meiosis.
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OK.
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So now let's think about the meiosis
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that produced individual two.
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We're looking at the meiosis from this individual
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that produced this individual.
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Is that informative or uninformative meiosis?
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Informative?
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Yes.
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We know you got the D allele going with the A allele.
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OK.
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Informative.
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What about this one?
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Informative.
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Individual number four?
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Uninformative.
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Individual five is informative, and individual six
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is informative.
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We have four informative meiosis.
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Now let's try to determine whether they're
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recombinant or non-recombinant.
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OK.
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So the meiosis that produced individual two, the gamete that
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came from this parent.
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Was it recombinant or non-recombinant?
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Non-recombinant.
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We're able to determine it's non-recombinant because we
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knew the phase in this person.
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OK.
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So the meiosis that produced the gamete that
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made individual three, also non-recombinant.
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We have plus and B coming together.
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Now individual five, we have D and A coming together,
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so non-recombinant.
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And what about individual six?
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Recombinant because D and B came together.
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And we know that would be recombinant because we
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knew the phase in the parent.
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We have four meiosis that are informative.
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And we can ascribe three as being non-recombinant and one
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as being recombinant.
9874
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