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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.
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