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PETER REDDIEN: So let's turn now to informative meiosis
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and phase in order to be able to calculate our LOD scores.
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OK, I'll start with informative meiosis.
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I have it defined on the screen, and I'll
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come to that in a moment.
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So let's think about what we're trying to do.
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We're trying to do some mapping, essentially, here.
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And, when we've gone through this before,
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one way we've looked at it is, for example,
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in a test cross where we have some scenario like this where
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an individual is heterozygous for two alleles
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of the A gene and the B gene.
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We crossed with some tester strain.
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So this is a test cross.
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This test cross was nice and handy.
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We set this up in a way where we can determine
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the genotype of every gamete produced
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by this individual and their offspring.
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So the gametes that we could infer, if you recall,
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would have been big A big B, little a little B, big A little
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b, little a big B. And we can see in all of the offspring
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what the identity of the gametes where
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that came from this individual just by the phenotype
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of the offspring.
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And we figured out that these were non-recombinant
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and these were recombinant.
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And then we used that information
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to get a map distance by the frequency--
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the fraction of the gametes that were
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recombinant over the total.
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OK, so that's what we've done in the past.
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Now, we want to try to do something similar here
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with data in the pedigree, but the challenge
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is, as I've been talking about, we
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can't design the ideal cross.
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We have to live with what we've got.
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So we just have to look at the meiosis we have
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and figure out if we can infer this kind of information
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from the data we have.
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So that's the extra challenge that we
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have to go through here.
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So, just to put it in context, let's
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imagine a different kind of cross like this.
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Could we get any information out of this cross about the map
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distance between A and B?
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What do you think?
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I've got a thumbs down in the back.
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Why not?
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So what kind of gametes could we get here?
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So the gametes from this individual
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would be big A big B, little a big B.
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Can we tell whether recombination happened
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between the A gene and the B gene?
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We can't tell.
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So are we going to get any information here
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that allows us to tell recombinant fraction?
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No.
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And the problem is, we may have many meiosis like this
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in a pedigree where you might want to get information,
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but you can't.
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I've described informative meiosis on the screen here.
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They're meiosis where we have two alleles of some marker
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and two alleles for some trait gene,
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and we can determine which we're transmitted together.
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And we're going to need that kind of information
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in order to identify recombinant and non-recombinant gametes.
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So, to do that, we must have an informative meiosis.
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