CMD SciFam: Genetics of CMD

CMD SciFam: Genetics of CMD


I’m Alan Begs. Maybe we’ll just quickly go
down the row here and introduce ourselves and then I’ll tell you a
little bit about how the session will work. My name is Casey Gennette. I’m a
genetic counselor working with Alan on his congenital myopathy and rare disease
research at Boston Children’s. I’m Chris Tan. I’m a genetic counselor I worked
at Invitae, which is a genetics lab based in San Francisco. Hi I’m Soma Das
I’m at the University of Chicago and I direct the molecular diagnostic lab
there that does testing for congenital myopathies ..muscle diseases. Hi, I’m
Jody Westbrook and I work at Invitae with Chris. I’m a scientist. And I’m Sandra
Donkervoort. I’m genetic counselor working with Dr. Carson Bonnemann at the
NIH in the diagnostic research program OK, so we are going to start with a
little basics. Genetics is obviously a complex topic. It’s something that not
everybody is familiar with there’s a lot of terminology that’s used. And so we’re
going to have Casey Gennette and Christopher Tan, two licensed and certified
genetic counselors, give us a brief presentation. Kind of put us all on …Did I
get that right or not? .. and put us all on the same page about some of the
terminology. And then after that, we hope to open it up to questions. I know many
of you, not everybody here has a genetic diagnosis. So some of you may have
questions about how you get a genetic diagnosis. Others may have questions
about what it means once you get one. Well you can discuss questions about
what is vous or VOUS? And other questions about that you may have about
this topic. So I’ll turn it over to Casey. Do I click with this? Okay can I stay seated? Alright..no, I’m good right here. OK..So we’re going to do a really brief
overview. For some of you this may be a lot of review. But we’ll just get
ourselves on the same page in terms of some of the
terminology that we use . So just a little shout out to our National Society of
Genetic Counselor for the slides. When we are talking about our DNA, it’s good to
just put everything into perspective. So inside of all of our cells, which we have
in our muscle, but every organ of our body, we have our chromosomes which you can think of as kind of our little packages of DNA. Inside the chromosomes we have our strands of DNA which are made up of all of our genes. And you all
know that many of the names of the genes that we’ve been talking about this
weekend. And really that’s kind of the focus of a lot of the genetic testing that
we’ll be doing and that Chris will be talking about. But a good analogy, as
genetic counselors we love analogies, we think of our whole genome or all of our
DNA together as a book. Inside that book we have chapters. You can think of those
as the chromosomes. So little packages that make up the entire book or genome.
And then our genes are much more specific. Those are the sentences. And our genes, each one tells our body different directions in terms of how to grow
and develop. And a lot of our genes, when not working properly, can turn into human
disease. So specifically something you’re hearing all weekend or what we call
mutations or variants. So variants are just changes within the DNA. Mutation and
variant oftentimes are used interchangeably. But we like to stick to
the term variants because we know that for changes in DNA, not all of them are
actually causing some kind of problem with the gene itself. So a variant is a
little bit of a better word to use. And what a variant is, is just any change
from what we consider the reference or something that is different than the
general population. We all have many many, many, many variants in our DNA
and a lot goes into determining which variants are actually going to cause
health issues. So Chris is going to talk more about how we determine that but, you
can just think of those variants as spelling changes. And so here we you know you take a regular sentence and you change the H in Hall to a B, it turns
into ball, which changes the ultimate meaning. So something that you may have
been hearing a lot about are the types of genetic variants. So we use different
terms to discuss kind of the different ways that these changes are occurring. So
on top we just have the original DNA sequence or sentence. You may have heard people talking about missense changes. These are just single spelling changes
within a gene that don’t necessarily change the remainder of the sequence. We
have insertions, which would be adding one or more of those base pairs or a
whole word as the sentence would be. We have deletions, which in the same way
kind of remove a portion of the gene Again, that can be just a single base
pair or a larger number of base pairs Then we have a duplication, which again
would just be a repetition of a certain portion of that gene. And then a nonsense
mutation. Nonsense mutation is a change that actually truncates the entire gene
or protein. And so what that means is the particular change ends that gene early.
And in those cases, the remainder of the sequence is no longer there or functional . So another term that you have probably hear a lot or something called zygosity
So we just wanted to quick define what the different types of zygosity are. So
each of these little figures..Does this have a pointe? it should. Okay, perfect. Okay, so each of these little things blue
figures right here are representing chromosomes or alleles. And so we
would have two copies… everyone has two copies of the vast majority of their
genes. When someone is heterozygous, what’s that referring to is having one
variant or one change on one copy. When we’ll go into some inheritance models in
a second, but when we talk about someone who’s heterozygous, in certain cases and
dominant conditions, that could mean that they are actually affected with that
condition. But in the case of recessive conditions, that would be referred to as
a carrier and I’ll show that in a moment. When someone’s homozygous, that means
they have two of the same changes, one on each copy. And then we also have a
compound heterozygote, which would be someone who has a changed copy, on ..each copy has changed, but they’re just two different variants. And then the last
example is something called hemizygous and this is a special one that refers to
just x-linked conditions. Hemizygous means that there’s a change on the X
chromosome, but then that individual is a male, so they only have one X and they
have a Y. So that’s referred to as hemizygous . Whereas a female who has two x’s would be heterozygous. All right and then before I turn it over to Chris,
we’re just going to do a quick review of the different inheritance pattern. For
all of these that were going over, we’ll show you a pedigree up here. So pedigrees
are really helpful for us when we take a family history, to look at the pattern of
a disease within a family. And so when we see people, maybe multiple people in each
subsequent generation having a disorder, that’s a clue to us that it’s likely
dominant inheritance. So if you look down here at just a single family, when you
have a parent who’s affected with a dominant condition, there’s a 50% chance
that they would pass that on to their children. So if someone had four kids, the
likelihood that is that two would be affected
When we talk about recessive inheritance, oftentimes when you look at the pedigree
or the family tree, you have one affected individual but you don’t see any family
history of that. And that can clue us in to a couple things. We oftentimes think
that it could be recessive, but it also could be that it’s a brand new change in
that child. In this case, it’s a recessive change. And when we think of recessive
conditions, we know that both the changes have to come, one from mom and one from
dad. And those individuals are called carriers. Many of you may know about that
or be a carrier yourself. Carriers are typically not affected with the health
condition and they’re not expected to show symptoms over time. It’s just that
when two individuals are both carriers for the same conditions, there’s a 25%
chance that they could have a child affective with that condition, and also a
50% chance that their kids could be carriers, and a 25% chance that they
could have a child that didn’t inherit either one of those changes. And then the
last mode we’ll talk about is x-linked. So as I mentioned before x-linked has
to do is the X chromosome. Females have two copies of the X chromosome, whereas
males only have one. They have an X and a Y. So when a woman has a change on her X chromosome, she’s typically thought to be a carrier. And that’s similar to kind of
a recessive model. But when she passes that down to a son, they don’t have that
extra copy of the X chromosome to kind of help it out, and they typically show
symptoms. And so you can see here when we see patterns of males being affected and
coming from related females who are unaffected, that usually clues us into
x-linked inheritance. And you can see down here, when a female is a carrier, she
can have daughters who are either carriers or completely unaffected. And
then she can have sons, who are either unaffected or affected. It’s 50% chance.
All right so I’m going to go ahead and pass the mic on to Chris and he’s going
to talk about how these different variants. So I’m briefly going to talk
about the different types of results that you could get from a genetic test
result or genetic test in general. And in general there are
five different types of variant classifications that will be reported on
a test result. And I’m going to talk about those three main types of
results. So the first being a positive results. So a positive result is
basically a pathogenic or likely pathogenic disease associated variant
was identified. Right, this typically confirms or establishes your diagnosis and
predictive genetic testing is now offered to other family members. On the
other end of that spectrum is a negative test result. So typically a negative
result means that no disease associated variant was identified. Right, so this
does not rule out a suspected condition. It does not eliminate the possibility of
having a hereditary condition and predictive genetic testing is not
typically available for other family members. The last one is an uncertain
result. So has anyone had a genetic test that came back with a result that was
uncertain? I’m starting to lose people here so I need you guys to get like a
second wind here. No, no uncertain result? That’s awesome. So that’s then
typically refers to that there isn’t enough information to determine if that
variant could cause disease and this is typically called a variant of uncertain
significance, abbreviated either vous or vus, depending on who you speak to. VOUS in general are not recommended for use in clinical decision making and VOUS
are typically not recommended for predictive testing in at-risk
individuals. So how does the laboratory come up with these classifications for
these variants? So this involves typically a careful review of the
medical literature. You know to determine has this variant
conceived before. Have experimental laboratory studies been performed?
Re-review population data so if that variant had
been seen in lots of clearly unaffected individuals, one would make the
assumption that that variant does not cause disease. In the absence of
experimental laboratory studies, laboratories often use computer models
to predict whether or not a variant could be disease-causing or not. And often
laboratories request testing of other family members to help determine whether
or not that variant segregates or is transmitted with disease in a family.
It’s also important to keep in mind that even after all these investigations,
sometimes the lab is still not able to determine if a particular variant is
likely to cause disease and again that is a variant of uncertain significance.
So again I want to leave plenty of time for questions. So I’m going to skip, skip,
skip, skip, skip, skip, skip, skip to my loo, and end with this very last slide about
genetic counselors. For those of you who maybe aren’t familiar with genetic
counseling or seeing a genetic counselor, a genetic counselor is typically an
individual who obtains a detailed family medical history and reviews information
about inheritance patterns . We help to identify at-risk family members,
discuss options for testing, review the benefits and limitations of genetic
testing, coordinate and interpret genetic test results, and address psychosocial
implications of test results. There are three awesome genetic counselors sitting
up at the podium. There are some genetic counselors out here in the audience. If
you have questions for us, feel free to find us and ask us. And again, feel free
to visit the National Society of Genetic Counselors web page which is www.nsg.org
to help locate a genetic counselor in your geographic area if you aren’t
currently set up with one. Thanks I think some of you must have questions.
Can we have anybody, any thoughts or questions from somebody in the audience?
Raise your hand. I was wondering how important it is that
someone who has a known CMD, that their parents have genetic counseling and
identified the possible variants. Me, I think it’s very important to get the
complete picture of the whole family, to know exactly to trace it through the
family. And it also depends on the type of CMD. So what the diagnosis is. Is it the one
that you expect to be recessive or is it the type that started spontaneously new
in the patient. And all that can be clarified through parental testing . In
case the diseases is recessive and the genetics indicates that it’s
heterozygous, have you guys seen symptoms of the disease appear in that case? So
since I’m standing here with the mic, I can start to address that. It depends
when you say it seems heterozygous. There’s two possibilities. One is that
exhaustive testing has been done and that we’re certain there’s only one
variant mutation or disease-causing variant on one chromosome. And we are
discovering new things about diseases in these conditions. And occasionally ,in a
condition that we think is recessive turns out there may be certain genetic
variants that can operate in a dominant fashion. However, what’s much more
likely is the possibility that there’s a second variant on the other chromosome
that we have not been able to identify. And this is particularly true for
several of the very large genes that we talked about. for the ryanodine receptor,
for the nebulin gene ,and the nemaline myopathy, for the titan gene
These are very large and complex genes and the current state of genetic testing
only allows us to identify a certain proportion of the disease-causing
variants. And so in a number of cases, we have individuals who have a medical
condition that we believe should be associated with,
for example, a mutation in the nebulin gene, and we find one conclusive mutation
on one chromosome, we can’t find the other. So we say this patient appears to
be heterozygous, and yet,in reality, they probably have a second change. We just
can’t find it. Could you go into a little depth about like mosaic genetics. I
remember hearing a little bit about it but I would love some more information.
Sure . I mean mosaicism… you’re going advanced genetics here. In
terms of genetic concepts, but typically, so every single one of our cells has our
DNA. So if there’s a mutation, we expect it to be in every single one of
our cells, you know starting from conception it’s there. With mosaicism,
what happened is that part of the cells are completely normal and the mutation
is present and only a selection of the cells. So instead of being present in
every single one of your cells, a portion is normal and another portion has the
genetic change. So typically that happens dominant situations, where one copy is
enough to cause symptoms. And then with the mosaicism. It depends on what the
mutation load is. So if more cells have two normal copies, the expected milder
symptoms than if more cells have an abnormal copy and that can be completely
random. Some tissue can be random with the tissue. So some tissue can have more
normal or less normal randomly developed, you know. through out growth. Does that answer it? OK. And I should I should say that mosaicism is it’s a reflection of a
very normal process. So of our 3 billion bases that make up our DNA, every time a
cell replicates ,there’s an opportunity for a mistake to be made. And typically
during embryo, during spermatogenesis or oogenesis ,when our eggs or sperm or
formed, there’s several de novo changes, new mutations or alterations that occur.
And the vast majority of the time, these don’t have any impact.
on us. So if you sequence our DNA and you sequence the DNA of our parents, all
of us in this room have several…have a small handful of changes that our
parents didn’t have. What mosaicism reflects is simply one of those changes
that has occurred after the egg is fertilized and while the embryo is
developing. And so in one of those cells, a mistake has occurred. So some of the
cells of your body carry the result of that mistake and others don’t. And as I
said, our bodies are mosaics for all sorts of changes but the vast majority
of them don’t have anything to do with the way we look or function. It’s only
once in a while, when one of the effects of gene that’s important for us, that
then it becomes a medical condition. So more questions. Gustavo has a microphone
that works. This way people can suddenly become symptomatic. But is mosaicism a
reason why people suddenly become symptomatic? Generally not because by the
time you’re born, you. the mosaicism is already present,.. so ..we’ll let… who would
like to take on disease onset and what causes later onset for certain
conditions? Anybody..Depending on the biology of the
condition, there are certain things that can become symptomatic later on. So
there’s a group of conditions, central nuclear myopathy, that my group is very
interested in and one of these forms myotubular myopathy affects a gene that’s
important from birth. And so virtually all the boys with Myotubular myopathy
are affected, weak and hypotonic right from birth. There’s another gene
called Dynamine2, that also causes a form of central nuclear myopathy, and
individuals with Dynamin2 related myopathy often appear completely normal
at birth and it’s only later in life. So the difference is between these two
conditions really is related to the biology of what that protein does. I just
want to add to that there’s still a lot that we don’t understand when it comes
to genetics and how it plays out in the family. Sometimes we see some variability
in terms of disease onset and progression or even within the same
family, one patient may have more problems with contractures
and the other maybe more weak. So there are other factors at play that can
change disease progression a little bit. But in terms of whether there is
something that causes the onset of symptoms, there’s no like environmental
or exposure or anything that we know off that would like set off disease onset. So
Dr. Soma Das leads one of the premier genetic testing laboratories in the
country at the University of Chicago and has been involved in the development of
tests for many years. And I think many of you have undergone a bit of it
diagnostic Odyssey with tests that maybe initially asked about a single gene in
the single mutation. Maybe later on you had something called a panel test, and
maybe eventually some of you had whole exome sequencing. So we let her talk a
little bit for a few minutes about the process and the evolution of these tests,
and in particular, what it means to get a negative result, and what that
doesn’t mean because in some cases as we know, negative results are not so meaningful.
Thank you So our knowledge has really increased.
Okay.. Sorry Our knowledge has really increased these
past several years . So when way back when, we would do testing for a single
gene. Like if a patient is suspected to have myotubular myopathy, our lab
…gosh.. it was about 20 years ago now, or 17 years ago, we did testing for one gene,
the MTM1 gene, which is known to be involved in Myotubular Myopathy. And so
the tests that we developed in the lab was to sequence that gene, to look for a
mutation. We now know that there’s a lot of genetic heterogeneity and there are a
lot of genes that can result in similar phenotypes. So in Myotubular myopathy,
for example, it’s not just the MTM1 gene. There are now ,we know, several other
genes that, when defective, can also result in Myotubular Myopathy or
phenotypes that we resemble Myotubular Myopathy. Right. And so
as we get this information, as researchers are identifying these additional
genes in the diagnostic lab, what we can do, is we can develop more comprehensive
tests. So that we now are not just sequencing the MTM1 gene, we’re sequencing the
MTM1, the Dynamine2, the RYR1, the Titan, so all the other genes that can
also result in this sort of a broad phenotype, we now do testing for a panel
of genes. So that’s when we, when now testing has gone from doing single gene
testing to doing panel gene testing, where we are sequencing many genes at
the same time. And there’s a technology that the labs all used now. It’s called
next-generation sequencing, which is a more high-throughput method of
sequencing these genes that allows us to sequence many more genes at the same
time. So for example, in in our lab, we have different panels for different
subtypes of muscle disease. So we would have a congenital myopathy panel. We have
a congenital muscular dystrophy panel. We have a congenital myasthenic syndrome
panel, limb girdle muscular dystrophy panel, and these panels all contain
genes that are associated with these different phenotypes. Right. Although it’s
important to also understand that many of these genes that result in ..say…
congenital myopathy, also does result sometimes in a phenotype of congenital
myasthenic syndrome. So you can have the same gene on many different panels
because they can result in different phenotypes. And on the other hand, labs,
we have this too, we can have a much broader panel that we call like a
neuromuscular panel that has a combination of all of these genes. For
example, ours contains like 130 neuromuscular genes in one panel, that
now does sequencing for all these genes. If the physician is not…if it’s a
patient …if they’re not quite clear that the patient has a particular sub class
of muscle disease, they may want to just do testing for a much
broader group of diseases. And so then that would be more beneficial to do a
more broad, a larger panel testing. And then, of course, so in the lab, we do the
sequencing and we analyze all the genes and the panel to see if we identify any
mutations. And if we, there are often times that we don’t. Right We’ve sequenced all
of these genes, but we haven’t found anything, it’s a negative result. We
haven’t found a mutation in any of the genes that we have sequenced. Now, of
course, what is that…negative is result. Sometimes it could be that the
mutation is actually present in one of those genes. We didn’t see it because in
the lab, these genes can be very large and in the lab we are sequencing
generally the coding region of the genes. These are the, these are the regions of
the genes it’s much easier to understand or interpret when we do find an
abnormality. That is, that what it means. But it could be possible that there
might be a mutation deep within an intron of the gene, which is a region of
the gene that’s non-coding, that we don’t sequence. It could be in the regulatory
region of the gene that we’re not sequencing. So a negative result doesn’t
always mean that it’s truly negative for those genes that we tested for. I would
say a large proportion are present in the regions that we sequence, but there
are going to be some that we are going to miss because of the limitations of
the technology. And then, and then the next phase after that, so,I talked about
single gene testing, then there’s panel testing and now there’s exome testing.
And exome testing is when we’re doing sequencing of all the genes in our in
our system . Right. So it’s not just genes for neuromuscular disease, but it’s all
our genes. And this is a, this is a test that is done when a physician may, we may
identify, you know, mutations in some other gene that’s not clearly associated
with your neuromuscular disease, so we might find something that was unexpected. And for patients who have a much, sort of broader, nonspecific
phenotype, doing exome sequencing might be a way to go. I also want to say that
though it’s really important to do, to have , to do this testing in
concert with genetic counseling. Because when we do these tests, we can sometimes identify lots of different sequence changes, some of which might be the cause of the condition, and some are what we call these variants of unknown
significance. We don’t know what this sequence change means, and this is where
it’s really important to have these test results interpreted by a genetic
counselor because they can really explain and go into detail as to what
all of this means. So based on the kind of condition or the situation, the
physician will really decide what’s the best kind of tests to do, whether exome
sequencing or single gene sequencing or panel testing, what might be the most
appropriate. So, yeah.. thank you very much Okay, we have one more online question
and then we’ll we’ll look for one last question and then let you guys get some
dessert. And this question online is from an individual with a ColVIa2
mutation, wanting to know, they’re overseas, what kind of tips could we provide to
get testing from overseas. And I think the first question, is for other family
members I should say. The first question really is, who is it appropriate to get
additional testing for. This is really a question that your physician needs to
think about and answer and discuss with you, because depending on the particular
form of the condition that you have, If it’s a childhood onset form and you have
like an older aunt or somebody, there’s not going to be much reason.. and this is
a family in Australia.. thank you, and so it may not be appropriate to test
everybody and that’s a decision that should be made by your physician. There
are genetic testing labs around the country that can do this. Certainly within Australia, there’s a very active one in Perth,
Midlands, Western Australia, run by Professor Nigel Lang. They can do ColVIa2
mutation testing. There is also group down in Melbourne and a group in Sydney. And
then in addition, there are labs here in the United States. There are of both
academic labs, like the one at University Chicago you heard about, and Invite in
San Francisco. And they will actually.. um.. I’ll let Jody Westbrook tell you what they
have to offer. Well sir, we do accept samples internationally as do many other
other labs in the U.S. It sounds like if you have other family members, you’re
interested in getting tested, it’s typically the most efficient to do that through the lab that did the initial testing for the affected individual. Were there
any more specific concerns from about that from online? Okay … Oh, okay
…. that’s probably unrelated. I have…. Hi
there, I have a question. No, it’s not working. Thank you. First of all,
congratulations on a truly fabulous meeting. I’m a genetic counselor from
Melbourne, Australia, so I might be able to help the person inquiring online…. Is it working. No it’s not. Hi there. I have a quick question. How do
you determine a gene is pathogenic, meaning it does relate to that disease?
How do you make that mutation of that disease pathogenic. Well, we look, we look at a lot of different kinds of
evidence. So if there’s a mutation in a gene and we’re just trying to decide is
it causing disease, the first thing we do is see is that mutation present in
healthy individuals? And if it hasn’t been seen in healthy individuals, that’s
one piece of evidence that it might be causitive. Then we look for other genetic
evidence. Has it been reported previously in other people who are affected with
the same disease? And then we look for experimental evidence. Are there
researchers who have done experiments about the specific mutation showing that
it is detrimental to that gene. And it’s really just dependent on how much information is out there. So when there’s a gene that’s not very well studied, you
could find a really rare mutation that may very well be harmful, but there’s
just not information out there and at that point, that’s when it ends up in
this bucket, this large bucket of things that we call
VOUS or variants of uncertain significance. And in addition to that, on
the clinical side, it’s also important to see does this fit with the symptoms like
does this variant in this gene fit with what we known clinically about this
patient. And what’s really tricky is we all have variants in our genetic
information. So if we run genetic testing on everyone here, we all going to end up
with a whole bunch variants, so there’s going to need to be clinical
correlation to see if it all fits together. It’s a complete picture Ok..So I think we have another session
starting in a few minutes on pulmonary care. Are there any last questions about
genetics anybody would like to ask? If not you, have a few minutes for a quick
bio break. Get some dessert. There’s delicious flan out there, coffee or tea
for anybody that likes and I think then our 1:15 is scheduled session on pulmonary care.

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