Original subtitles

PETER REDDIEN: It's expensive to sequence

the genome of an individual, but it's

getting cheaper and cheaper.

So we could sequence the genome.

It's about $1,000 to $2,000 per person.

Which you could do this for the individuals in a pedigree.

You could also sequence what's called the exome.

So the exome are just the exons of the genome, which is

about 1% to 2% of the genome.

So genes exist in these exons separated by introns,

and there's lots of repeats and other stuff.

And you could say, well, let's just

guess that the mutation is going to be in an exon that's

causing the trait.

It doesn't have to be.

It could be somewhere else.

And we'll talk about that later.

But let's just for now say, well,

let's guess it's in an exon.

And wouldn't it be nice if we could just

sequence those things, and that cuts

by a couple of orders of magnitude

the size of what you're sequencing.

And this is a bit cheaper.

So it's about $500 per person.

And the way you do it is by taking

genomic DNA from an individual and making lots

of little fragments for it.

So you chop it up into fragments.

And let's say these dark blue fragments are sequences

that happen to come from exons.

Well, you can hybridize those to synthesized

pieces of DNA, that's these orange ones, that

correspond to the exons throughout the genome.

So these would be synthesized.

And then you can hybridize by base pair complementarity

the regions of DNA of interest, and then you can sort of

pull these out, washing away that sequences you don't want,

and then sequence the library from it.

These exons will be known from prior efforts

in annotating the genome.

So there's lots of ways to annotate a genome.

You can look for open reading frames present in exons.

You can look for expressed genes.

There's experimental ways to find

the sequence of expressed genes and then map that information

onto a genome.

So work in annotating the genome leads to this information.

All right, so one place in which this is applied,

either genome or exome sequencing,

is for rare diseases.

There are a lot of rare diseases where

someone has something wrong and it's really hard

to explain what it is.

It's not matching some known disease.

Someone comes into the clinic with this.

And what do you do?

Trying to figure out what it is.

You might not even have-- if it's not a known disease,

you don't even have this heritability information

from twin studies.

So it can be very hard.

And there's a lot of these types of things.

And one thing that could be tried

is to try to sequence the individual.

And an approach that's often taken

is to sequence what are called trios

where you sequence the individual and the individual's

parents.

Now what do you do with that information?

Well, you could look up a database of known variants

that exist in human populations and you could say, well,

do these three individuals carry some variant

within an exon that's not known previously?

Maybe the parents are heterozygous

and the individual is homozygous.

So you try to get some candidate genes this way.

And an example, a powerful approach,

is to look for de novo mutations.

By de novo, I mean the parents don't have it.

So a mutation that arose in the generation of the gametes

or early in the development of this individual that

has this disease.

So you can identify these de novo mutations

and identify candidate genes that way.

Then if you find something, you have some knowledge

of these genes, you could also go look in other individuals

and try to find other individuals that

might have a similar rare trait and see do you ever

see mutations in that gene in those individuals.

There are a lot of human Mendelian diseases.

I list some famous ones here.

Huntington's disease, inherited forms of risk

for breast cancer.

Not all forms of breast cancer display a heritable risk,

but some do.

Polycystic kidney disease, Lou Gehrig's disease,

or ALS, cystic fibrosis, sickle cell anemia, hemophilia,

and many others.

So I'm mentioning there's lots of traits and diseases

that are non-Mendelian, but there are also

a lot of Mendelian ones.

Here are some examples of pedigrees with human Mendelian

traits.

Polydactyly displays the autosomal dominant pattern

of inheritance, which you can see in pedigrees.

Hemophilia displays X-linked recessive inheritance.

This is an inheritance from the royal family of England

and through Europe.

We can see Queen Victoria here passing on an allele

to the son Leopold, and so on.

You can go and look up statistics on Mendelian traits

in humans in the Online Mendelian

Inheritance in Man database.

So I looked this up yesterday, where

they say there are 6,900 something phenotypes for which

the molecular basis is known.

That's a lot, and it's been going up rapidly.

And then depending on how you break down those phenotypes,

if you just-- if you look at some set of them,

some Mendelian phenotypes, you can say, how are we

doing with identifying them.

So there's 8,500 in this data, Mendelian phenotypes.

So just focusing on Mendelian phenotypes here.

And about 67% of those have a known molecular basis.

So most.

These numbers are rising.

Of course, we're identifying new traits and diseases,

phenotypes, I guess, and then more and more getting

identified all the time.

Now there's lots of news stories about this kind of approach,

using sequencing to try to identify the molecular basis

of rare traits.

So you can see some example titles here

where you take one example here, like this one.

It was a de novo mutation in this child.

The parents didn't have it and they found it

by sequencing the parents and the child.

Here's an example paper where, if you look at the methods,

how did they do it, where they found de novo variants

in some gene causing some neuropathy.

They say three patients carrying de novo variants

were identified by a diagnostic trio exome sequencing.

So now if you see that kind of wording,

you know what it means.

Now individuals that are displaying some rare trait

can participate in studies.

This is a study the Rare Genomes Project being conducted

at the Broad Institute here at MIT, in collaboration

with Mass General Hospital and Brigham and Women's

where here's the process.

You submit your DNA, they extract it and process it

for either exome or genome sequencing,

depending upon the details of the study.

And they say in particular, participation

from both of the patient's parents

will increase our ability to find a genetic cause,

and this is the reason why.