All language subtitles for 27031x_PR_DNA_Markers_04_Frequencies_SNPs_v3-en

PETER REDDIEN: Now, to think about our expectation.

I'm going to draw out another chromosome.

So I just drew on this board one chromosome,

chromosome 1, the chromosome that gene X happens to be on.

So let's just think about what would happen with chromosome 2

in this cross, for thinking about our expected outcome.

So I'm going do the same cross now, but now

with just chromosome 2.

So I'm just going to start with the F1, where our F1 we

had polymorphisms that differ.

Now I'm going to draw the two homologues of chromosome 2.

So we have one with white SNPs from this original individual,

and one chromosome with the blue type SNPs.

So that's a different chromosome.

But these chromosomes have polymorphisms as well.

So let me just give you an example.

Let's say this polymorphism is SNP2,

we have a white type SNP2, and a blue type SNP2.

So we crossed to one of these individuals

with these white type SNPs for chromosome 1 and chromosome 2.

So that's the same cross we did before,

but I'm just adding on this other chromosome.

And now we select individuals that are

gene X minus over gene X minus.

We know we're going to get one of these chromosomes 2

from this parent.

So we'll have one chromosome that has SNP2, the white type.

And what will we get from this parent?

Any predictions?

What will the genotype of these individuals

be, this next generation for SNP2?

50% of the time, you'll get this white SNP2.

And 50% of the time you'll get this blue SNP2.

That's just equal segregation.

So nothing really too fancy here.

It's just equal segregation.

But instead of just alleles of like big A and little a,

it's just a white allele and a blue allele of a polymorphism.

Other questions?

Yeah?

But yes.

So crossing over is only happening

between the same chromosome.

So you're only having this crossing over possibility

between the two homologues of chromosome one.

Let's now think about our data.

So let's make a graph.

Let me give myself some space.

So we're going think about our sequencing data.

And we want to look at the frequency of the reads,

our frequency of sequence reads.

We're going look at the frequency of sequencing reads

in our data that are blue type.

So we're going to look at the frequency of the reads that

have this blue polymorphism, as opposed

to the white polymorphism.

So that'll be our y-axis here.

And then our x-axis is going to be--

I'm going to depict it.

It's going to be positioned along a chromosome.

So this is going to be chromosome 2 position.

So you can imagine lining out the sequence of the chromosome

here on our x-axis from one nucleotide to the other.

We've got a long chromosome here.

And we know where all the polymorphisms

are on here, from our reference sequence and our information.

And we can now look, and these individuals

and our data that we have for the frequency of the sequence

reads that are blue type.

Any predictions?

So I have one prediction.

It's 50-50.

Let's see, raise your hand if you think it's 50-50.

Raise your hand if you think of something else.

No one votes for anything else.

Oh, wait.

Maybe one vote in the back.

OK, I'll come back to you.

Raise your hand if you're unsure.

So let's think about it.

These we just talked about, are our expected outcomes,

and the ratio of these individuals

is going to be 1 to 1.

So 50% will be this way, and 50% will be this way.

Why is that?

Well, again, if we just think about this

as a big A and a little A, or something like that,

half the time you get this allele, half the time you

get that allele.

We'd expect 50% of the time you get this,

50% of the time you get that.

So now we have to do sequencing.

So let's say these bottom SNP2s came from this parent.

They are going to be included in our sequencing data.

Half of the reads are going to come from this chromosome.

We're going to be sequencing all these individuals pooled.

So half of the reads are going to come from these chromosomes.

So 50% are going to be from here.

The other 50% are going to be the ones that

came from this parent.

And half of the time they'll be white,

and half the time they'll be blue.

All right, so now given that, what

is your expected frequency of blue type

SNPs in our sequencing data?

STUDENT: 25%?

PETER REDDIEN: 25%.

So we've got some value here, 0.25.

And if we look--

now we look SNP by SNP across the chromosome.

We just talked it through for SNP2.

We say it'd be 0.25 for SNP2.

What would it be for some other SNP right next to SNP2?

The same or different?

Same.

So what would this graph look like?

STUDENT: Some points scattered throughout?

PETER REDDIEN: Yeah, basically a straight line.

Might have some variance.

But that's what you'd expect for any SNP that's

unlinked to our gene X. We could have

the same graph for chromosome 3.

We get the same thing.

Chromosome 4, we get the same thing.