All language subtitles for 37031x_PR_LOD_Scores_02_LOD_from_Pedigree_v2-en

PETER REDDIEN: And now we can calculate the LOD score.

OK.

All right.

OK, so this is just straight from last time, the equation

for the LOD score--

the log base 10 of the probability of the data,

given linkage at some distance theta,

divided by the probability of getting the data

if the loci were unlinked.

OK, now, the theta can't equal 0--

this is the distance--

if there are any recombinants.

So, if recombinants are present, theta can't be equal to 0.

You can estimate theta some hypothetical distance

from the data.

OK, in our case, our theta that we would estimate

would be 0.25 because one out of four gametes was recombinant.

That would be the best we could hope for that, if this SSR was

from our gene at 0.25, that would sort of give us

the highest possible LOD score.

And theta hat is the distance that

gives you the max LOD score.

OK.

Now, what I want to do is to actually calculate a LOD score,

just go through an example of calculating the LOD score.

And I'll go through this example that we had in class last time

where we had this pedigree, and we inferred the genotypes

of these alleles of SSR1.

And then we talked about calculating a LOD score,

figuring out the distance.

So let's just go ahead and go through that process

of calculating a LOD score for this pedigree.

So, last time, we had four-- we found that we

had four informative meiosis.

That was individuals 2, 3, 5, and 6 here.

And we had one recombinant gamete and three

non-recombinant gametes.

So, if we wanted to calculate a map

distance with this data, recombinant frequency,

what would it be?

We've got four gametes.

One is recombinant, three non-recombinant.

STUDENT: 0.25.

PETER REDDIEN: 0.25.

Recombinant frequency is just the number

of recombinant gametes over the total number of gametes.

So you could see then that this would

give a recombinant frequency of 0.25.

We're going to, for calculating a LOD score,

pick some distance to test.

You could be given the distance in some scenario,

or you could estimate the distance yourself.

For example, from the recombinant frequency,

we estimated the theta, which is our distance we're

going to use, from the data.

We estimated it to be 0.25.

So we're going to use theta is 0.25.

Now, what fraction of our gametes should be recombinant?

That's theta, right?

Recombinant fraction.

And our non-recombinant gametes if we

wanted to express this in terms of theta?

Yeah?

STUDENT: 1 minus theta.

PETER REDDIEN: 1 minus theta.

Now, we have two types of gametes.

We can have two types of recombinant gametes.

So each type then will be theta over 2 in frequency.

So we went through this right at the beginning

when we were talking about recombinant frequencies,

but, if you go back and think about this example,

you could have two types of recombinant gametes.

The recombinant gametes, as a pool, are theta.

You could have a big A with little b

or a little a with big B.

So there's two types of recombinant gametes

for each gamete class.

Then the frequency would be theta over 2, OK?

Same thing here, 1 minus theta over 2,

for each type of recombinant-- possible recombinant gamete.