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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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