WTHealth. Beyond genome sequencing

rc3 preroll music

Herald: Welcome back in Halle with Chaos
Zone TV, the next talk, will have

interactive elements, so here are the
hashtags again. We're on Mastodon with

@Twitter with the hashtag RC3 Chaos
Zone and on the IRC channel in Heckint and

which is RC3 Dash Chaos Zone. All right. Lisette
will now speak to us with a talk called

"What the Health Beyond Genome
Sequencing". Since the 80s, the Human

Genome Project set goals to technical and
ethical goals to understand the human

genome. In recent years, these goals have
been achieved, and humanity could profit

immensely from what the sciences and the
technology the methods could be developed

through the project. Lisette works at the
bleeding edge of what it is now a hard

data science. We are very excited to hear
about the considerations and the

practicalities of advancing the biology
even further.

Lisette: OK. Yeah, thank you very much for
the introduction. It's my pleasure to give

some insights into what I've learned
throughout my studies and what I'm now

actually also working on. So thank you for
providing me this slot. I was a little bit

surprised when I thought, Oh, OK, now I
actually have to give the talk. So please

forgive me if I'm sort of nervous, but
stay with me and thank you everyone for

watching and for filling in the survey
beforehand, and you will have another

option to participate in the poll later
on. So I have some things to announce

first, which would be about the content.
So it will all be very abstract. So we are

talking more about concepts than
about actual disease and suffering. So

there will be no photos. But yeah, the
general theme is about medical

examination, everything clinical, about
the patient assessing somebody's disease

and disease risk, and also going into the
more severe conditions of which you might

die. And we also touch upon family
relationships. So just so you know, yeah,

it will come back every now and then. So
just for everyone to be aware. And then

also, yeah, I need to disclose that I'm an
employee of a company that does work on

marketing genetic tests. So that set
aside, this is not this is not any kind of

advertising talk. It's really about what
is actually happening technology wise. So

I want to give you the insights into a
little bit of the technology, how it came

about and where we are now, and also try
and give you an overview of what are the

options in terms of genetic testing for
various utilitys and raise awareness just

for also the ethnical issues that might
arise from what we can learn from our DNA.

So this is enough of the prolog. Let's go
right into looking at a patient which is

classically done from the outside. So we
want to know what is different about this

person or a patient. And yeah, there are
really layers of information, and you

always assume that there's a relationship
with a condition. So be it a rash that you

see on the outside or as swelling that the
doctor can't feel or something that they

learn from interrogating the patient. And
then there's a bit of a borderline outside

inside test, which would be bodily fluids.
So if you test urine, saliva, blood, yeah,

you already look on the inside. So what's
happening inside of the patient and the

metabolome? Yeah, what's what's going on
in terms of small molecules that you might

detect with the one or the other test? And
also what you can see on the inside is

broken bones or cysts that shouldn't be
there. So for that, we use imaging which

where x-ray is the oldest, and then
there's magnetic resonance and pet

scanning. So these are like the cool,
advanced additional layers where you can

look inside of the of the patient. And
then of course, there's DNA. So if we look

even deeper and inside each cell, you will
have the genetic code of this person, so

to tell how they are different on a very
small scale. So that is the dogma of

molecular biology that you go from DNA,
which is your genetic blueprint, and then

certain parts are transcribed so the cell
makes copies of the DNA, which what I'm

called RNA, because it's a different
chemistry and these are then translated

into chains of amino acids, so there's a
code which amino acid should be attached

to which one. And then you fold it
properly and then you have a functional

protein. And then now why you sequence the
DNA is because you assume that there's a

mistake made, which then leads to a faulty
protein. And then in the end, something in

your body doesn't work. So, yeah, it's a
very simple concept, if you will. And

then, yeah, when we check in the DNA and
in the RNA is about 20000 protein coding

genes. And then there's also a different
types of RNA that do not code for proteins

that regulate other stuff so that the
correct genes are actually transcribed and

translated. So that's an additional 20 to
30 thousand, potentially more. And so if

you combine any of these two, see like a
certain signature of a person, you already

have billions of combinations. So as you
can imagine, there are many, many, many

signatures possible. But yeah, which of
these will actually tell you something

about the patient? So. Let's go back to
how we sequence the DNA. So it is actually

very simple. All of our usually 46
chromosomes so that 23 pairs are made of

at double stranded code, which is the DNA.
And then you see here in the unfolded

region that where a gene is starting, it
usually starts with A T G and these are

ciramated bases. So you have here in the
chemical metal insert and the A and the T,

which form a pair. So the red thing is in
between are hydrogen bonds that keep them

together. And A and T always want to be
together. And C and G always want to be

together. C and G actually form three of
those bonds. So in a little bit more

stable. And so as you can see, this double
stranded DNA is hands always inverted on

the other strand, so we call it the
complementary strands. So if you have ATG

on one strand, you always have TAC on the
other. So you only sequence one and we

defines the direction of the gene because
we know in which direction it makes sense

because, you know, only in one direction
you can then make a protein out of this

code. So enough for the chemistry and the
principle. So we really want to know and

to map where on each chromosome, which
letter occurs. So you can imagine that

this is quite an adventure and takes a lot
of effort. And actually, it has also

started very early on in the 70s. So maybe
you have heard of Sanger sequencing. So

that was the first generation of
sequencing from 1977, where you

essentially cut the strand in little
pieces and you know which one ends with an

A, ends with a T.. So you have all kinds of
fragments with different lengths which run

over a gel, which is not that important.
But it's it is also called capillary

sequencing, which then helped finding the
first human disease gene, which is called

the Huntington team. You might heard of the
disease where it belongs to Korea,

Huntington's. And so this was the first
association that was really confirmed

that, OK, you have a defect in a certain
gene, which directly translates into a

disease phenotype, but this is very rare.
So usually it is a lot more complex and we

will also get to that. So the capillary
sequencing still lasted for a while, so 10

years later, you had really cool
instruments for the first time from

Applied Biosystems so that you can
sequence a little bit quicker, but still

far from looking at the whole genome. So
that was then planned starting in 1988.

They defined the goals for the Human
Genome Project, which would then take from

1990 until 2003 to complete one full human
genome. So full in the sense that it still

had gaps. So there are some regions which
are tricky to sequence, so these gaps were

filled later on. But still, yeah, this was
a huge undertaking which cost about two to

three billion US dollars. And eventually,
in 2000, they announced that they had a

first draft of the human genome, and then
it got published in 2001 in the two big

scientific journals, Nature and Science,
both on the cover the human genome. So

that was and is a big step. So it's yeah,
that's just crucial to know, what we are

looking at to have a map of our complete
genome, where then you can map other

people's sequences to as well. So that's
what started also in 2005. But then for

different types of cancer, it's called
TCGA from the genome, the Cancer Genome

Atlas, and it also lasted for a couple of
years. But then they were much quicker in

sequencing, because 2005 was also the year
of next generation sequencing machines. So

nowadays we don't do Sanger sequencing
anymore or rarely. We usually rely on

heavy, high throughput parallel sequencing
so that you can sequence a lot more

different pieces, so to say, at the same
time and with very high accuracy. So

essentially, this means, that we now have
access to 3.1 billion base pairs, which

were first collected during this human
genome project. And this nice

advertisement when they were looking for
volunteers is really cute, actually,

because they also say here that this photo
of the project will have tremendous impact

on future progress of medical science and
lead to improved diagnosis and treatment

of hereditary diseases. Volunteers will
receive information about the project and

sign a consent form. No personal
information will be maintained or

transferred, and a small monetary
embarrassment will be provided. So, yeah,

they were promised that their data would
be kept anonymously and also they

collected blood from female volunteers or
sperm from male volunteers. And then they

collected a lot more samples than what
they would need so that in the end, you

couldn't tell anymore from whom the genome
was actually derived. And there was one

volunteer at Roswell Park and hence called
RP11, who had happened to have

exceptional quality sequencing reads. And
then so the first human genome was mainly

based on this one person, and we have
multiple new versions published of the

human reference genome today. Its version
38 and still about 70 percent are

untouched from this first genome assembly.
And a small thing about the cost. So I

mentioned that this was a really costly
project. Two to three billion dollars. And

now we have actually cracked the $1000
threshold. So it is possible to sequence a

full human genome for about a thousand
bucks, which is remarkable. So this is

really an enormous drop in the cost just
because the technology made such a big

leap when we came to the next generation
sequencing. And also one genome. If you

have it sufficiently covered so that you
are sure about which base pairs and which

position, then you have about 180
gigabytes of raw rids. And if you align

them to the reference genome, which is, of
course, now your atlas, if you will, so

you can put all our rids to the correct
place. And then this is called an

alignment file, which is about 80
gigabytes. And if you then only keep the

positions where something is different
from the reference genome and you compress

it, you are left with about 5 percent
of that. So 4 gigabytes per person.

Storable, nice little genome. OK. So this
takes me to the first poll, which is on

simple vote. A couple of people
already have participated in the monkey

survey. Then, yeah, you don't have to do
it again now, but the vote link will also

be in. And you also just fill in any name
combination of letters, click OK, and then

you can answer the first question, which I
present here. So this is just three

statements about sequencing a full human
genome. Whether you believe that it has

replaced fingerprinting in forensic
investigations, where do you think that it

gives you all the clinically relevant
information for any patient and whether

you think that it is cheaper than a full
body MRI scan? So yeah, we will get to the

results in a bit. I will just continue
with a couple more slides and then we can

see. What do you guys think, and I'm
really curious to actually hear that. And

see it for myself. Let's see. So if you
think in terms of complexity, we have

already touched upon Korea, Huntington,
which is a single gene, essentially that

gives you a full blown disease if it's not
encoded properly. And then you could think

of other diseases that are encoded by a
couple of genes, where you can think of

breast cancer over a couple of mutated
genes can give you a much higher risk than

average population. And also in
Alzheimer's disease, we see that

hereditary component. Brought about by a
couple of genes again and then more

general in terms of unknown diseases, you
can ask gene panels or full genome

sequencing to help out. And it gets more
and more fuzzy, but more and more also,

tests are available if you want to go to a
prognosis for this or that condition or to

the correct treatment choice. So I'll try
and give you a couple of more examples,

but only after we have talked about the
Cancer Genome Atlas, the PCGA . So here

that's also a lot of data. So they claim
2.5 petabytes were collected in the place

it was running from 2006 to 2014. And
yeah, in total, 33 different tumor types.

And they did not only look at the DNA and
all the mutations, but also RNA and also

proteins, and also different info on the
patient's survival and treatment data. So

that is a huge pool and resource of data
where people are looking at and finding

signatures of patients with less or more
advanced cancers with patients that

progress through treatment or not. But
it's all. Yeah, you still really need to

take it with a pinch of salt because, for
example, since 2006, treatment of cancer

has changed tremendously, and you cannot
just use any signature that you took from

the data from PCGA and extrapolate for
today's cancer patients. So that's a bit

tricky. PCGA still vastly used. But then,
yeah, I would propose that you should

rather use it for validation so you find
something in current data from today's

patients and then you can check whether
this was also seen in the PCGA data and not

the other way around. But let's get to the
results of the poll. See? Can we go there?

What happens? Oh, nice. What's the score?
7.3 So you mostly agree that full body MRI

is more expensive than the full genome
sequencing, which is true. So like I said,

the whole genome is now about 1000 dollars,
also 1000 euros, and the full body scan in

the MRI will cost about two to six
thousand euros, roughly. And then this one

with the fingerprints I have made up. So
sorry to fool you. This is not done yet.

And it also cannot potentially give you
all clinically relevant information about

the patient. So nice. Thank you for
participating. And also, I check the

survey monkey and also there. I have
managed to fool some people into believing

that. It's possible to replace
fingerprinting with full genome

sequencing, where that's not true. Sorry.
So let's go to another level. So not only

the DNA sequencing is interesting. So then
you have the map and on the property,

sorry, on the DNA strand, you know, for
example, where there's a different letter,

if you will. And then in the reference
genome, and then this mutation might be in

one of the regions where the DNA has
stored the code for a certain protein like

protein one or protein two. So the code
might be different, but also it might be

different how many copies are made. So
this is an example here where gene one and

two are equally often transcribed. And
then there's these transcripts, which we

call messenger RNA about equal amounts.
And this is, let's say, the state how it

should be in the healthy adult. And if you
think about any condition like a cancer

tumor, then it might get deregulated and
the cancer, for example, then there's this

and only makes very few copies of gene
one. And a lot of copies of gene two,

which might lead to effects like bigger
growth, faster faster growth, bigger

spread into the tissue, which would
normally confine the tumor. So that is

also one level of regulation and that you
cannot usually capture with DNA sequencing

or whole genome sequencing. For that, you
need to check for the expression which you

do on this level, on the RNA level. And
then you have they call in differential

expression, which gives you this kind of
picture analysis. So you have some

samples, vertical and then horizontal are
the genes, and you see that if you compare

the samples, some genes are more
expressed, which is red and some genes are

down compared to the others, which is
green. And then you can find clusters of

genes, a group of genes here in the red
bar, where Group one, in that case, a

certain kind of breast cancer is highly
upregulated and most of the people I

belong to, group two different kind of
breast cancer have lower expression of

that team and and the blue cluster is the
other way around. So that gives you an

idea of OK, you can maybe use one of these
genes to differentiate between the two

groups. And if that helps you to determine
what treatment they should get, that's of

course, super useful. And then you have
something like a genetic biomarker. If you

have multiple genes, then you usually call
it a signature. And so these genetic

signature tests can tell you, are you at
risk of a certain disease? They can help

diagnose or get to the exact subtype of of
your disease. They can help you with the

correct treatment or monitor whether the
disease actually responds to the

treatment, whether anything changes back
to normal. And also, it can sometimes be

useful to give a prognosis for a disease
progression. So in the end, you always

need to wonder what is the added value of
such kind of testing on top of the

clinical variables that are already
existing and does give you something

actionable? What can you do something with
the knowledge that you gained from this

testing? So there we are already at the
problems with genetic testing. So that

would be the second question that you can
answer again on Simple Vote. Please feel

invited to help me understand what you
think. And here it's just. For you

personally, the question whether you would
want to know whether you are at risk of a

genetic disease and would you want to know
if you had to pay for it and then slide it

to the right, if you're willing to pay or
slide it to the left, if you're totally

not willing to. And then the second slide
is the same question when you want to know

if you got the results for free? And then
to the right is yes, and more to the left

is no, absolutely not. So again, I will
just move on and you can take your time

answering that one. So to give you a bit
of a feeling for what is at stake is the

get WHO into testing for genetic risks.
It's, of course, good to know your family

history of disease. And also, if you're
planning to have children, for example,

would you want them to know that they
potentially carry a certain risk or not?

Then health or life insurance might have
an interest in knowing what people's risks

are, what they have to expect. So there
are certain instances where they are

eligible to know and certain instances
where at this moment in time, they

absolutely are not. So this is something
that's probably going to change in the

future. The more we know, the more we want
to use that knowledge. And then there's

the problem that some genes are very often
found to be up and downregulated, and

there seems to be a difference. But it's
just yeah, in the nature of those genes,

and we have sometimes multiple signatures
for the same problem. And then, yeah,

doctors and patients just don't know what
to choose from. So I'll go through some of

those issues in more detail. I have
mentioned the TCGA before, and this cancer

genome atlas is really a limited source
that is now exhausted, but it's still

oftentimes used as the silver bullet. So.
Let's see if we already have votes. Well.

So that would be. Yes. OK, so if you if
you could know your genetic risk and you

would get it for free, then most people
are inclined to say, yes, I would like

that very much. And if they had to pay for
it, then it seems to go more towards no,

but it's actually kind of neutral, which
was surprising. Yeah, I would have thought

that you would all say, no, I don't want
to know. But that was just my assumption,

and I was apparently wrong. Cool, thank
you. Poll number three third question is

about a commercially available DNA test,
which is not actually sequencing, but they

use a panel of mutations that are now
known because we have already sequenced

thousands and nearing a million complete
full genomes. And yeah, I was wondering

whether you would know. So that's quite a
number three. What institutions they

partner up with. So this DNA test is goal
23 and me. And if you don't know what it

is, then there's also an answer option for
this one. No clue what it is. It does. And

for the rest, yeah, I propose that they
work together with Broad Institute, that

they work together with GlaxoSmithKline,
GSK and they got 300 million US dollars

from them, that they work together with
general practitioners in the US, that they

got subsidy from Google 4 million US
dollars or and Amazon 9 million US

dollars. So, OK, let's see what you think
or how many of you don't know the text.

And in the meantime, I'll present two
cases to you, where genetic testing would

play a role like, for instance, in the
case of inhealthy adult, where the dad was

diagnosed with this heart condition,
hypertrophic cardiomyopathy, where the

heart tissue gets scars and at some point
it cannot pump properly anymore. And so if

you have one parent with that disease, you
have a 50 percent risk that you have

inherited those genes from your parents.
So this healthy adult and their siblings

got the offer to get tested. So the costs
are covered by the health insurance, but

there is no cure for this condition. So
you can. Yeah, have a stricter

surveillance, and you can get access to
early treatment if you develop symptoms,

but yeah. Other than that, yeah, it's
still just a risk gene. So to say so if

you know you have the gene, it doesn't
mean you will get the disease. It just

means you have an elevated risk. So it's
really hard to grasp. And this is one case

where at least in the Netherlands, the
life insurance would be eligible to know

if you got tested and you do have that
gene. So in the end, this person said, No,

no test, please. I will just go see a
cardiologist every now and then, have it

checked nonetheless. But I don't want to
know if I have those things OK. A second

case? Yeah. So that's an infant delayed in
development. It was still a bit fuzzy.

Like what should an infant be able to do
or not do at the age of one? But then the

parents started observing seizures in the
in that case, it was absences, so it was

not cramping, but just very absent. So
eventually, they got access to tests,

genetic tests where distinct genes were
analyzed. Nothing was found. Then panels

of genes with increasing size and nothing
was found. And then the whole genome

sequencing was done. And then you always
have to compare to the parents. And

essentially, parents and child who trust
that and the child had a mutation in a

gene where the parents had nothing and it
was just the very rare X-linked mutation.

And eventually they now know what is going
on, which was only due to the possibility

of whole genome sequencing. And in the
end, the parents also said, Yes, I want to

know what else is found in this whole
genome sequencing. So that isn't actually

case free, where one of the parents is the
carrier of a mutation in a in a protein,

that when it's faulty or when you get a
faulty version from both parents, then you

will develop this condition. Cystic
fibrosis. So that is really good to know

when you are a carrier of this and also
your future kids can get tested to see

whether they got this faulty version
from you. So let's have a look at the poll

number three. This is here. So the DNA
test 23 and me. Let's see where's the. I

have no clue what this test is. So this is
just a four. OK, so not that many people

voted for this one. Twenty nine votes. Oh,
well, actually. Twenty nine votes. And

then what you thought it would do. So
you'll have here, you approve of it,

working in conjunction with general
practitioners in the U.S., which is not

true. Sorry. Yes, it did get subsidy from
Google, 4 million US dollars in the

very beginning. No, no, no. Sanger
sequencing Yes. GSK 300 million. They want

to use their data to find new drug
targets. And I also made this one up. So

Amazon did not give any money to 23 and
me, but you can order through Amazon. So

that's possible. OK, thank you. And I'll
think I will wrap up after just presenting

this problem here quickly. So breast
cancer is one of the pioneering fields of

genetic testing. So you have five
commercially available tests that can tell

you what type you have, what treatment
options would be best for you and what

your prognosis is. So you really need a
well-informed team of doctors if you want

to make use of this. OK, I'll skip a few
slides. Mean, validation is important.

Takes a lot of time. And I think in the
future, it's not only going to be a whole

genome sequencing, but there will be a lot
more to it, like the immune system and

your gut microbiome and everything, which
is in there is also, of course, influenced

by outside factors what you eat, how much
sunlight you get, how much you move. So

this is also already available, this data
from your smart watch, for example. So I

think in the end, if we get to
personalized medicine, this will also play

a role. And to recap, if you sequenced the
whole genome, this is not the same as

ordering any tests online, where you also
might run into data security issues with

tests like 23 and me. And that's also not
the same a deceases signature. And then, yeah,

if you have a new cool diagnostic
signature that is published, it might

still take a long time and couple of
validation studies before it actually

enters the everyday clinic and you get it
reimbursed from your health insurance. And

for this, it also needs very well trained
physicians and informed patient and

family. I think there's no way in stopping
this. But that's just my take. So we will

see a lot more from the molecular side of
things in the future, and these are also

to be retrieved online. So everything all
the tests that are registered also you can

filter for countries, for Germany, for
example. And then you see even which

university clinic offers which kind of
testing. And if you ever hear the term

liquid biopsy, that's usually a black
sample where, yeah, all kinds of things

are measured, so you have DNA in there,
but you also have metabolites in there,

you can have little fragments of cancer
cells and cancer derived DNA. So this is

something that's coming forward more and
more that you just need a blood draw. And

then, yeah, you have a lot of insight, not
only the whole genome, but even more RNA

sequencing data, for example. So thank you
very much for inviting me, for listening,

and I'm happy to take your questions now.
Herald: It's again, the social media

hashtags on Mastodone and Twitter
RC3ChaosZone without a dash and then on

IRC unchecked, and the channel is RC3
with a dash. Chaos Zone.

Lisette: Do we already have any specific
questions?

Many think people would like to know.
Herald: And targeted gene modification

with CRISPR and Cas9 is not even allowed
on plants and animals in the EU. Do you

think there will ever be gene therapy for
humans?

Lisette: There was gene therapy. So, for
example. I'm not sure whether it was a

typo, low key a or an immune defect where
they tried to cure children with gene

therapy, so there were clinical trials,
but something went horribly wrong, and I

think actually one of the children
suffered so much from how they inserted

the gene that it developed a type of
cancer. But I'm still hesitant to say that

this is the end of gene therapy. So it has
potential in very severe cases where

there's no other option. But yes, it's
also true that we don't really know what

we're doing at the moment. So there's a
lot more research needed to make sure that

there's no off target effects if you cut
out a gene and put in a new sequence. So,

yeah, no, I don't think we can guarantee
that as of yet, but it's it's not

unthinkable.
Herald: All right. Huh, interesting.

Sounds like the technology isn't there yet
for a couple of years or decades.

Lisette: Oh, well, I think the technology
is there, it's just not secure enough.

Herald: All right. I see.
Lisette: So, yeah, it's done in the lab

big time, but then we don't usually use
humans. Only a cell line or yeah.

Something that is easy to control.
Herald: All right. Um, and then a dynamic

methods for tests, for example, for
diseases such as COVID, our target

tests, for example, the PCR test. Do you
think now the testing for infections might

shift to be more exploratory approaches,
for example, through sequencing instead of

targeted PCR?
Lisette: Yeah, that depends if you have a

suspicion that the infection has reached
the bloodstream and you're close to

sepsis, then it might be your last resort
to make a hole. Yeah. Just sequence

everything that is in the blood, but then
you need to be, of course, aware that the

majority will be human, so you need to
filter out a lot. And then what is left,

you might be able to map to a certain
microbe genomes, which are also pretty

well annotated. So I'm not sure about
nasal swabs or something like that, where

you can find out which flu you have
received. So that doesn't really make too

much sense to me unless you have a good
treatment options. But for example,

tuberculosis is one disease where if you
do sequence the germs now more and more

because a lot of strains of these bacteria
have multiple antibiotic resistances.

And then if you start treating with the
wrong antibiotics, you are really screwed.

So there, yeah, it's already well-
established that the university clinics at

least sequenced the strains before the
patient gets treatment.

Herald: Interesting, yes. Sounds very
cool. All right. Thank you so much,

Lisette. Very inspiring.
Lisette: You are welcome.It was a

pleasure. I hope I could convey the
message. Just be aware of, yeah, your

genes and your data. So yeah, that's
that's just there's a lot of potential in

there. But of course, we shouldn't be. We
should not be careless.

Herald: So, yes, definitely.
Lisette: That's all from my side. Thank

you.
Herald: Thank you so much.

rc3 postroll music

Subtitles created by c3subtitles.de
in the year 2022. Join, and help us!