All language subtitles for 77031x_PR_LOD_Scores_06_Q&A_v1-en

PETER REDDIEN: OK question.

STUDENT: Where does the theta come from?

PETER REDDIEN: I'm giving it in this example.

There might have been, let's say,

other individuals in the pedigree, something like that.

But we're testing all LOD scores at a theta 0.1.

Yeah.

STUDENT: Where does the 0.45 come from?

PETER REDDIEN: Yeah, because I was giving a theta of 0.1,

then the nonrecombinant fraction is 0.9, so for a given gamete

0.9 over 2.

Like we had said earlier, you could have made this bottom 0.5

to the cubed and then you wouldn't

have divided these by 2.

Other questions about this.

Say it again.

STUDENT: If we have a pedigrees from known and unknown phases,

can you determine theta for known phase

and apply to unknown phase?

PETER REDDIEN: You could.

You could.

But it might be a little hard then

to know what the theta hat is going to be, the optimal theta.

Because then you'd have to figure out

what would be a theta that would allow these to contribute

and give a maximum.

So you could test over a series of theta

and figure out theta hat.

You're not going to be doing that by hand and paper.

So in a scenario like that, let's say it was a problem,

you would often be given the theta

to test rather than having to determine it yourself

because of that complexity.

Yeah.

Yeah.

So I'll say that again.

So if you have parents where there's

an informative meiosis one informative meiosis,

but their phase was not known, then

if you do this calculation, your LOD score

will be 0 for that meiosis.

It's either going to be positive or negative,

you don't know but it will deviate from zero.

Actually let me just-- sorry come back to that.

But I'll just finish off just to try to make that intuitive.

Let's imagine we only had one meiosis here.

So we take away this cubed and this cubed, right?

It'd be 0.45 plus 0.05, which is 0.5 divided by 2,

which is 0.25.

So 0.25 divided by 0.25 is 1, log base 10 of 1 is going to be

0 .

OK, but let me come to your question.

You were asking about why didn't we know the phase here?

STUDENT: Yes.

PETER REDDIEN: We have to use the averaging when

we don't know the phase for whatever

meiosis we're considering.

And in this example, we're considering the meiosis

that comes from this female.

It was this meiosis that was informative.

So we're looking at whether we know the phase in this female

and we did not.

This male has no informative meioses,

so we're going to-- we don't need

to consider the male at all.

The male has no informative meioses

because he's homozygous wild type for the disease gene.

Yeah.

Yeah.

So the question was if you don't know the mother's parents

genotypes then the phase will always be an unknown

and that's correct.

And often that is the case in real pedigrees.

You have some individuals, I mean

you're always going to start somewhere in the pedigree

with getting genotypes.

So there's always going to be some individuals where

you don't know the parents' genotypes.