All language subtitles for 77031x_PR_DNA_Markers_01_Assembly_v1-en

PETER REDDIEN: I'd say it's just an amazing era we're

operating in now with the power of DNA sequencing.

You may think of DNA sequencing as something you do just

to get the sequence of a genome or sequence of an individual,

but there is a bewildering array of methods

that you can do with DNA sequencing to explore biology,

lots of different types of contexts in which you

can use sequencing to get information

about cells or an organism.

So for example, you can get information

about epigenetic states, which we'll talk about,

gene expression levels, variance, regions

that regulate genes, and so on.

So lots of information can come using

the method of DNA sequencing.

You'll get some exposure to some of these methods

throughout the course.

OK.

Right now we're really focused on just sequencing

to get the sequence of a genome and today, a little bit

of the uses of sequencing with respect to that.

So the first part of the lecture here is about mapping

reads to an assembly, like an assembled genome sequence,

then I'll talk about genetic mapping with DNA sequencing.

And finally, time permitting, a little bit of commentary

on genome annotation.

OK, so let's start with this first part,

mapping reads to an assembly.

All right.

So after performing some kind of DNA sequencing,

you have a set of individual reads,

so we have these sequencing reads.

And we may have some huge number of them,

millions of them depending upon the method used,

where each of these reads have some sequence reading

from 5 prime to 3 prime.

And then we want to do something with these reads.

OK?

Taking these reads, which are all individual pieces of data--

so this is your data.

Taking these reads and then trying

to see where they align to stitch them all together

into some kind of assembly.

So that was one application.

For example, to assemble the sequence

of a genome, a genome assembly.

OK.

OK, so what else could you do with these reads?

Well, a second application could be

not to take these and from scratch,

try to assemble them into a genome,

but simply to map them to an existing

genome sequence or some existing reference assembly.

So we could map them to a reference sequence.

OK?

And this reference sequence, for example,

could be an already existing assembled genome.

OK, so let's take a look at that.

So let's say we have some assembly here,

like some genome reference.

This will most likely exist in multiple different pieces

of sequence.

In a perfect assembly there'd be one piece of sequence

for each chromosome.

Most assemblies are very imperfect

and are fragmented into lots of different pieces.

You have this assembly and then you can take your reads

and go on a search, computationally intensive,

to look for where in the genome--

because the genome is large--

these things align.

So you can get these reads and align them.

So you might take this read, some read one,

and you might notice that this aligns here to this reference.

And by align I mean it has a sequence match.

It's the same sequence.

So it's a sequence matched to that location

in the genome assembly.

OK?

And so then you can do this with all of your reads,

line them up, and they'll all line up,

stacking up to some locations in the genome.

So you'll know those reads came from wherever

your sample came from, from that part of the genome.

Now, so one of the things you could do from this-- so these

reads, for example, your data, could be from some individual.

Let's say someone has presented with some kind of disease

in a clinic.

You could do some DNA sequencing from that individual,

take the reads you get, align them

to a reference sequence, the human reference sequence,

and then look at your alignment for any relevant information.

For instance, you might notice that at this position,

you have, in the reference sequence, a nucleotide A.

And then when you look at the sequence

reads from the individual at that position,

you might notice it's a G. And that way you

would have identified a DNA sequence variant that

existed in your individual with respect

to some reference sequence, your genome assembly.

So you'd have a sequence variant here,

and you might have learned something

that might be relevant for your purposes from this.

OK, so lots of other applications

of aligning sequencing reads to a genome assembly.

This is just one, and we'll come back to some others.