August 19, 2021 @ 1:00 pm – 2:00 pm EDT

Dr. Perez-Palma is a bioengineer and a Doctor in Molecular Biosciences. After finishing his studies in Chile, he did a post-doctorate at the genomics center at the University of Cologne, Germany funded by the Dravet Foundation. Since then, Dr. Perez-Palma has specialized in the genetic study of patients with epilepsy and neuro-developmental disorders, focusing on the development of tools for the interpretation of variants. He was a research associate at the Cleveland Clinic until last year, and now he is at the Center for Genetics and Genomics, at the University of Development in Chile.

Here are our introductory comments:

Hello everyone, and welcome to today’s session. My name is Marta Dahiya; I’m a Syngap parent and a Director of the Syngap Research Fund.

We are very excited to continue the SRF Syngap research fund webinar series. The goal of the series is to empower your communications with clinicians as you get more clear knowledge of SYNGAP.

We also want to give a plug for our next presentation, “Treatments in development for epilepsy syndromes: opportunities for Syngap1”, which will take place on Thurs. Sept 2, 10 am PST/1 pm EST with Dr. Ana Mingorance.

Our talk for today is “Interpretation of SYNGAP1 Variants”. I have the pleasure to introduce today’s speaker, Dr. Eduardo Pérez Palma.

Dr. Perez-Palma is a bioengineer and a Doctor in Molecular Biosciences. After finishing his studies in Chile, he did a post-doctorate at the genomics center at the University of Cologne, Germany funded by the Dravet Foundation. Since then, Dr. Perez-Palma has specialized in the genetic study of patients with epilepsy and neurodevelopmental disorders, focusing on the development of tools for the interpretation of variants. He was a research associate at the Cleveland Clinic until last year, and now he is at the Center for Genetics and Genomics, at the University of Development in Chile.

Webinar Overview

Dr. Eduardo Pérez Palma is a bioengineer and doctor in molecular biosciences at the Universidad del Desarrollo in Chile. He starts the webinar with the basic concepts of the human genome and the main types of genetic variants. He goes on to talk about how a third of SYNGAP1 variants are variants of unknown significance (VUS) which is a problem when trying to treat disorders. In order to interpret a variant and its relationship with a disease, there are established criteria for determining whether variants are pathogenic, benign, likely pathogenic, likely benign, or VUS. Dr. Pérez Palma compares this interpretation process to solving a crime. He then talks about the bioinformatic methods used to interpret variants and how variants are re-interpreted as new information is discovered. He concludes with how this field is beginning to make predictions of the functional consequences and the phenotypes beyond the pathogenic variant, providing more information to understand neurodevelopmental disorders.

Other Relevant Publications by Dr. Pérez Palma

THIS IS FOR TRANSCRIPT ONLY:

:03hello everyone and welcome to today’s session my name is Marta I am a Syngap parent and director of

0:10Syngap Research Fund we are very excited to continue the SRF Syngap research fund

0:17webinar series the goal of the series is to empower your communications with clinicians

0:22as you get more clear knowledge of syngap we also want to give you a plug to our next presentation

0:30treatments in development for epilepsy syndromes opportunities for SYNGAP1 which will take place on

0:37thursday september 2nd 10 a.m pacific time and 1 p.m eastern time with dr ana minguranzi our

0:46talk today is interpretation of SYNGAP1 variant i have the pleasure to introduce today’s speaker

0:53dr eduardo perez palma dr perez palma is a bioengineer and a doctor in molecular bioscience

1:02after finishing his studies in Chile he did a postdoctorate at the genomic center at the

1:08university of Cologne Germany funded by the Dravet foundation since then Dr Perez palmer

1:15has specialized in the genetic study of patients with epilepsy and neurodevelopmental disorders

1:22focusing on the development of tools for interpretation of variants he was a research associate at the cleveland clinic until last year and now he is at the

1:34center for genetics and genomics at the university of development in Chile a recorded version of

1:42this webinar will be available on the SRF website under webinars on the family menu

1:49by the end of the presentation you will have the opportunity to get the answers to your

1:54questions we love to hear from you please write your questions in the Q&A for those of you just

2:02joining us welcome and again the speaker is dr eduardo perez palma and the talk today is

2:08interpretation of sync up one variant it’s now my pleasure to turn things over to dr palma welcomePresentation Contents

2:18thank you marta it’s my pleasure to be here today and thank you also for that kind introduction

2:26um well as previously announced my the title of my presentation is called

2:34interpretation of single single thing at one variance and well the contents of this talk

2:42first i’m going to introduce to you two basic concepts about genetic variation and SYNGAP1

2:50then i will continue with varying interpretation concepts the methodology variant interpretation

2:56and then and to describe to you some complementary methods that we can input to this process and

3:02help to aid in the identification of pathogenic variation then i will continue with an example

3:09of how to interpret SYNGAP1 variants and then some ideas and concepts that

3:16will try to describe to you where’s this whole field going and future projections

3:24so first let’s start with genetic variation and think of one Genetic variation

3:29genetic variation in the human genome is highly normal between two individuals you can expect

3:35between four and five five million nucleotides involved in genetic variation among these any

3:42normal individual with no apparent disease will have between 150 and 200 protein 2 truncating

3:48variants which these ones are usually diagnosed as pathogen variants but naturally we have between

3:54150 and 200 of these events also the most common type of variation is by far missus variation

4:05here we can expect normal individuals between ten thousand and twelve thousand mistransparent events

4:12of all of these genetic variants that one will carry between 40 and 80 events will be the novel that that means that it will be absent from both of our parents

4:23and among these one or two will be on the calling portion of the genome that means the genetic code that leads to protein production these numbers tell us the first message

4:36that any genetic test is going to find variance this is going to happen the key question here

4:43is which ones are the ones causing the disease which are the ones that are pathogenic variation Types of genetic variation

4:50we have many types of genetic variation we can expect in every gene in our genome to have

4:57at least two copies one from uh our mother and another one from our parent and nissan’s parents

5:04change a single nucleotide that leads to a change in an amino acid within the protein sequence this

5:13this may or may not leads to a chain of function we have also protein truncating variants that

5:21stop the protein production and then meeting to usually leading to a an apple insufficiency

5:28that means because we have only just one copy of this gene also we can observe within the human

5:34genome whole gene the lesions holding gene duplications the functional effects of this

5:41variation is very valuable too we have gain of function and lots of function from missions

5:47variance we have usually mostly loss of function variation within protein through

5:52the variance and from deletions also from duplications we can expect gain of function

5:58because we have multiple copies of the same gene of course in biology there is an exception for

6:04everything so if you go through the literature you can find exception for each of these cases

6:12missions variation by far are the most common type of variation and also the most difficult to predict if we go a bit more in deep into genetic variation and this is Relationship between genetic variants

6:23we can plot uh the relationship between genetic variants and this is in in this way

6:29in the y-axis we have penetrance which is how severe is the effect of the variant

6:35and then on the x-axis we have the frequency how common are variants within our population

6:41so whenever a variance is is associated to this use we can have a pathogenic effect

6:48that is mainly populated by rare variation that have a large effect these are the variants that

6:54by themselves can cause disease these are very rare they are not established in the general

7:00population but they have a high effect then on the other side we have common variations that

7:08contribute a small effect to the to the disease any disease and thus they can be establishing and

7:14be common population these variants are thought to have a collective effect a cumulative effect

7:21so on this side on the genetic spectrum we can start to talk about risk and an ethnic company

7:29naturally uh developmental epileptic encephalopathies and single one variation

7:34falls within the realm of mendelian variation of rare variants with large effects since one as you Risk

7:43all know it has a complex presentation but it’s it has a monogenic mechanism of inheritance usually

7:51when the novel variant can cause the disease by itself it has an incidence an incidence of one

7:57every 16 000 uh naturally born individuals and we can expect uh 400 new cases per year in latin

8:07America and in the united states this number it’s a bit lower is i think 366 individuals

8:15new cases per year the presentation of the disease is really complex we can have a lot

8:22of co-morbidities and and symptoms within SYNGAP1-related disorders and these symptoms

8:28are complex in a time dimension too they they evolve differently and they are they present

8:34themselves in different ways as long as the time moves and this is really important for the study

8:41of these disorders to know to manage expectations and and and see what we can expect from different

8:48mutations it’s always really heterogeneous for this type of syndrome but one important thing to

8:56know from the beginning is that not all sync up one variants will cause the same disorder

9:03but also not all think of one variance will cause a disorder by themselves most of the genes that

9:10have been associated with neurodevelopmental disorders they have naturally benign variation

9:17within them and it’s easy to find variants that do not cause any any harm at all and now in this

9:27parent interpretation is key so let’s move to the process of iron interpretation Interpretation

9:34this is a typical genetic test and from a gene panel you can see that we have 151 genes that

9:40we know that are commonly associated to disease and then the company tell us a

9:46clinical interpretation in this case will have a single one variant of uncertain significance

9:55this type of interpretation does not allow a diagnosis it doesn’t mean it’s wrong it’s not

10:00that it’s just that it’s not useful and why genetic diagnosis is so important you know

10:08way better than me that knowing the true cause of the disorder ends the diagnostic policy which

10:14is a source of stress psychological and economical stress for patients and their families knowing the

10:22genetic cause of the disorder allows for better better counseling genetic concentration management

10:29and lately in some cases you can lift to definitely solutions and treatments

10:36knowing what is happening genetically allows you to access support networks such as the singapore

10:43research fund and also to participate in clinical and genetic data aggregations that allowed

10:51that that allows scientific studies to be to be developed to understand better the disease

10:58the power comes in numbers naturally these benefits from genetic diagnostic diagnosis

11:05have a signage synergic effect the access to support networks improves clinical genetic

11:14data aggregation which in turn allows for more pathogenic variation to be identified allowing

11:22more patients and families accessing a diagnosis and also better counseling and patient management

11:29so it’s really important to access genetic diagnosis to reach a genetic diagnosis

11:35unfortunately for most of thing of one variance we have one-third that it will fall within

11:42the variance of uncertain significance realm and we can see that it’s the most populated

11:50category between clinical interpretation then if we move to the missing square inside the

11:56most common type of variants the variance of our non-significant rates goes up more than

12:03half of the variance being diagnosed with this state and personal communication with

12:13is i have heard that for each photogenic single vine that’s diagnosed choosing a variants

12:21are identified but not all is bad news right booze can be reinterpreted

12:30and in this matter what can we do when a warrant is pathogenic or benign how we can

12:36put our effort in our scientific effort to try to improve this procedure of interpretation

12:44what do you think what is an argument to say that my variance is pathogenic or not

12:50there are several criteria that can emerge for example has my parent been tested in a

12:56laboratory in a molecular setup do i know that the variant caused a change a deleterious change

13:02in the protein function is my variant established in the general population

13:08with no known effect has my variant been observing other patients these are all

13:14different arguments that arise when you sit on the table and discuss about varying interpretation Variant Interpretation

13:20so how to interpret the variant and its relationship with disease turns out that it’s quite similar to how to solve a crime if we consider the case mr barry

13:33mrs station we have a variant interpretation setup we have a variant that is a suspect

13:41accused of being causing the disease of the victim we have evidence and we have alibis

13:47of course the crime is the disease itself and the judge would be the interpreter

13:52the interpreter which can be any of us of course within this trial we have some rules

14:00the penal code and this was published in 2015 by the american college of medical genetics

14:08it was elaborated in agreement by clinicians scientists genetic counselors and laboratories

14:14it turned it consists of 31 criteria for viral interpretation that can be aggregated together to

14:22make a genetic diagnosis these are the criteria i don’t intend to show you each one of them but

14:30it’s very important to know that there are some criterias for pathogenicity that means

14:35the evidence and there are um criterias for the neutrality of the virus which are the alibis in

14:42this case we have strong arguments for for alibis we have supporting our arguments for alibis

14:49not all criteria have the same strength we have very strong arguments strong arguments

14:56moderate arguments for pathogenicity and just supportive arguments for pathogenicity

15:01together they can help us to make a call and make a judgment about the parenting question

15:09some examples of strong evidence a well-established in vitro or in vivo functional studies supporting supportive of damaging effect of the gene or aging product moderate evidence

15:22that means in a lower scale of interpretation is that my variant is located in a mutational hotspot

15:28and or a critical and when established functional domain an active site opens in for example without

15:36denying variation that’s also really important then on a supporting level evidence that means

15:44in a lower scale of confidence we have multiple lines of computational evidence here informatic methods available are plenty and i will show you a couple of examples later later

15:56on then we have alabas as i already mentioned if a variant is observed with a high frequency in

16:05the general population it’s unlikely to cause a severe syndrome so such such as a developmental

16:11epileptic and cellular encephalopathy normatives here the name of the database that aggregates

16:18variation from the general population it’s not the only one there are several

16:24then we have supporting alibis in frame deletions or in search insertions in a region known to be

16:30repetitive in different configurations and we don’t without any known function this is also an

16:39argument of supporting allies so having all these criteria and arguments in place

16:47is my very guilty or innocent naturally we have two states a pathogenic state a guilty state and then a benign code and my variance is innocent but

17:00very interpretation is a bit more complex it’s not binary we have five different levels of

17:07clinical significance from benign we have likely benign then we have uncertain significance in

17:14the middle when i cannot make a call for each side then lightly pathogenic and pathogenic

17:24how is the very the very code well the acmg suggests to make four different criteria

17:30combinations that allow us to make a call when one store one very strong argument alongside a

17:36strong argument will allow us to make a pathogenic call then only in the absence of benign arguments

17:45two moderate arguments alongside a strong a very strong argument will allow us to make the same

17:51call of identity on the other side if i find that this one supporting one or two supporting

18:00arguments for benign i can make a like united code also in the absence of photogenicity arguments

18:10in any case that these configurations are are not possible to make we will be obliged to make

18:18a variance of that known significance result and that is all other cases will be called as unknown

18:26significance which explains also why this category is so popular is it’s so populated in patient

18:34repositories and clinical laboratories some considerations about the interpretation different Interpretation Considerations

18:42interpreters might reach different conclusions or even oppose conclusions the information required

18:48for each criteria is difficult to access making a molecular history a functional experiment on

18:56one variant it’s usually really expensive and not many people can do this then information available

19:04evolves constantly which makes reinterpretation possible and it’s very important to keep in mind

19:11that these are guidelines not rules so it’s up to the judge at the end to make the call

19:20i’m coming back to all the 31 criteria i would like to highlight the computational methods available here which leads me to the complementary methodsComputational Methods

19:34bioinformatics criteria are considered among the acmg guidelines there are some strong computational

19:42criteria that say if i find my variant in patient variant repositories i can match my variant on my hand and see if it has been observed in other patients then we have

19:57other computational methods related frequency to mutational hotspot

20:02and then multiple scoring that i’m going to describe to you now

20:09basically the information methods can be separated into two categories the first one measures

20:18biological context that means measuring the effect on the chemical exchange observed if an amino acid

20:25changes with another that is similar is not very damaging if it changes completely in structure

20:32and we have structural damage conservation is my is my variant calling within the site that

20:38it’s conserved between species this is this tell us that the site is important if it is conserved

20:45we also have a meta scores that combines different scores and thresholds to generate a single score

20:51of pathogenicity and also machine learning associated methods here in each of these styles

20:57i can i show you some popular bioinformatics methods to score varying pathogenicity

21:03that’s just one category the other category is frequency evaluation when i use bioinformatics

21:11databases to carry my variant and see how it presents itself in the general population

21:18and also in patient variance repository as i already mentioned both of these categories come

21:24together in the variant interpretation process and we can use several multiple sources to analyse

21:31in the laboratory and as part of my research alongside with dr lao’s lab we have developed

21:38different also some specific methods for varying interpretation but also we lately realized that

21:47this is not only about generating fancy scoring pathogenicity methods we also need to understand

21:54what’s happening and make the information available to a broader audience and for for that

22:02matter i wanted to also highlight simple climber which is a method to reanalyze and and see how

22:09patient parents fall within the gene and put the information contained in an in a large database

22:16in a yeast-to-use context this is how patient variants look on timber we usually get access Simple Climber

22:24to a big table with a lot of information that is connected to multiple other databases but if

22:29you’re not close to the bioinformatic or genetic fields this table is difficult to digest i mean

22:37the hgbs format of varying coding you usually get the the result from a clinical genetic

22:44test company it’s difficult to understand it’s not straightforward so for this we developed

22:52a database called simple climber which i invite you to explore especially for singer and the

22:58the tools grabs the entire database climber and um lets you ask more questions that the ones that are

23:07possible to make in the original database it’s the same information but make it in a in a more easy

23:14to digest way if you type clipboard here if you type single you will see um a summary statistic

23:23for the variance that all within the gene you can automatically map the the variants that are known

23:31to be associated with Syngap related disorders we can see here there are a lot of them reported

23:37the latest release already contains 680 variants from SYNGAP1 and it’s um something that you you

23:47can use to explore to compare your your own variants and see if there are some trends there Resources

23:54of course the the tools that we have developed are not the only ones we have a lot of resources

24:01available in the internet i can i can share with you internally all of these sites

24:06and there are a lot of lot of resources lately to analyze variant

24:12so this is a world that is on development so we have a lot of

24:17resources to be integrated here especially just in the last couple of weeks we already had a report

24:23of all the protein structures available solved by this alpha fold computer super computer so a

24:32lot of studies can be performed right now that may aid in different in the future in the near futureExample

24:42so now i’m going to show you an example of how to interpret a single variant and

24:48again this is just an example idealist case but coming back to the example test

24:55we have a variant of unknown significance here and a clinical interpretation provided by the company we have the variant here in the https format that i was telling you aboutInterval Tool

25:11and then i would suggest to use the judge assistant which is called the interval tool

25:18and it’s designed to aid in the variant interpretation process this is an online tool developed by the oneglab it’s easy to use and makes all the

25:2631 criteria semi-automatic so you can fetch all the databases available in the internet

25:33in just one place and evaluate how the 31 acmg criteria behaves on a given environment

25:40we can input our variant from our own genetic test here and see what happens at the beginning we get

25:51a replication of the clinical interpretation but then if we go to details and adjust

25:57we can um obtain all the criteria and see what we can modify according to our own information

26:07here for example after studying the variant we realized that first this variable within

26:13a within a gene that has a low frequency of missing variation as we can see here on

26:18the nomad database in the whole database we can expect nearly 800 varying misses

26:28but we only observed 351 this tell us something that the gene doesn’t tolerate variation in the

26:34general population which means that it’s likely to be associated with six this is a supporting argument according to acmg criteria so we can check that out then

26:46we know that multiple lines of computational evidence supported by protogenicity i have

26:52selected here some popular scores that point into the direction of pathogenicity

27:01these are not the best scores these are the ones that we usually use and they

27:09they work really well in neurodevelopmental disorders but we can also check this out

27:16because multiple already multiple computational approaches are telling us that the environment

27:22might be auto unit so with these two arguments we can reinterpret the variant

27:27and we will obtain a likely pathogenic variation the same variation obviously but with different

27:32criteria included here because i as a judge have decided to include these former two arguments

27:40but this is not the only thing that we have in place we can we can study the parents this is Experimental Models

27:49available and we can determine the inheritance mode of the parent if it is absent from both

27:56parents we can conclude that the variant is the noble and being the noble is a strong argument for

28:01photogenicity so we can check that out if we have the resources and the know-how we can also make

28:09experimental models of my variants in vitro or in vivo to support the deleterious effect of my wire

28:16i have access to these or two repository repositories of experimental results i can

28:25check this out too so we have two strong arguments if we uh modify this on the platform we will

28:32get a pathogenic interpretation of the variant this time with more arguments of pathogenicitySummary

28:40then no more question your my variant is pathogenic

28:46as a summary of the varying interpretation process i would like to highlight that the interpretation is a continuous process it does not end once i make the call because

28:56new information is always appearing it’s bidirectional if i find a likely pathogenic

29:03variant today it might be a boost in the future because new information arises so it’s highly recommended to not consider the call the initial call and especially the

29:17the genetic test called uh i know called the clinical significance of my variant here

29:23keeping up with the literature is crucial of course each case is different and

29:29it’s highly recommended to be conservative innocent innocent until proven guilty right

29:36and this is really important because taking light in the pathogenicity code

29:44has some strong effects it helps on first on the on the environment because if i make a call on

29:52a variant that is pathogenic it will stay there and it will use as it will be used as a reference

29:58for future goals so it’s really important to be conservative and be entirely sure of the

30:06code that we’re making if not then it’s better to make a variance of a non-significant scope

30:14of course the interpretation is better in a multidisciplinary setup in collaboration

30:19interpretation requires clinical molecular and genetic expertise it is not a standalone process

30:28and then also i i would like to highlight that the adequate interpretation

30:33allows also accurate candidate selection for clinical trials and we all know that this

30:42is gaining importance as new therapies are being developed so as concluding remarks Conclusions

30:51for this talk i would like to talk to you to where this field is going

30:58we all know the complexity of neurodevelopmental disorders and until now i have only talked to

31:03you about two states of a possible variant a brand can be pathogenic or benign however

31:09all of these syndromes with different severity and stages and comparabilities are all caused by pathogenic virus so we need to go beyond the pathogenicity code

31:21some approach seeing that one is one good example of the complexity of neurodevelopmental disorders and pathogenic variants is not enough we need to know more

31:31we need to know how these comorbidities are related how how the syndrome evolves within time

31:39and genetics can can help in the study of this first beyond photogenic we can predict functional Predicting phenotypes

31:47consequences bioinformatically by training machine learning methods this is an example of a study

31:53that i have the privilege to participate to the story of henrik where she developed

32:00predicting a prediction model for gain or loss of function for sodium and calcium channels

32:06when this has very strong effects on the therapeutics and treatment that this patient

32:13can have so it’s really important to know the functional effect of pathogen parents

32:20then phenotype prediction some variants may lead to different phenotypes severe phenotypes mild

32:27severe mild penetrates this is seen in the syn19 when when we can have severe drug syndrome or mild

32:38epilepsy by studying more than a thousand patients we were able to model the pathogenicity

32:44of variants and developed a prediction model that was able to tell us the percentage of developing

32:50drug syndrome or guest plus and this is achieved just by data aggregation and statistical methods

32:59we created a tool to provide any person with a human science variant to develop a

33:06prediction for their own purposes and the other really important issue here is data aggregation Data aggregation and diversity

33:15and diversity i show you here the map of the epi-25 consortia the biggest genetic collaborative

33:23study epilepsy and we can see here the the source of patients that are studying

33:29currently more than 25 000 but we can see here a clear gap that i’m trying to reach but

33:39the the study of underrepresented populations in genetics may shed up some shed some light into

33:45the genetic mechanisms of the whole disease and also to uncover new mechanisms so it’s

33:50really important and we’re all part of this puzzle so finally i would like to end with the Conclusion

33:58mic uh words that pretty much summary what i would like to live with you don’t stop when

34:07you see a bus when you have a boost in your hands keep testing and keep asking asking

34:14with that i would like to say thank you to all the people that i worked with especially to denis

34:21lal and also to lisa marie who developed this nice allegory of [ __ ] of judgment the trial

34:30thank you that was great i think we have uh questions i have a few questions too but

34:36Victor is asking if you can see the journey what does he mean

34:42when a barrion is determined to be a boss based on a law problem scoreQuestion

34:51what does it mean for a variant to be yes

34:56do you see the Q&A questionnaire are you going out here

35:08i’m sorry i do not know what it’s probably and score i haven’t heard of this if somebody can help us out in the chat with the province score

35:20i don’t know jay i don’t know what is probably honest for i don’t know either

35:25yeah but none of the scores uh especially the bioinformatics ones are definitive scores uh

35:35scores can be integrated to the acmg guidelines as computational evidence but they do not have

35:43the power to determine pathogenicity by themselves that would be my comment

35:49for any score okay and i have a question how often um i know we talked before that initially when the

36:02companies started doing the genomic testing there was a lot of positive results and i want you to

36:07explain all that to people and when is the cut off when everybody was like a wait wait you are doing

36:13too many diagnosis and why that happened i want you to give a perspective what happened to people

36:22if if you take a look at the rates of pathogenicity delivered by genetic test companies at the beginning it was high and mostly because there was a

36:33positive pressure to establish clinical genetic testing in as a field as something that it’s

36:41useful this is this i don’t think this was intentional it’s just how it happened

36:48then as we went in to increase the volume of variance and clinical variants analyzed

36:55people started to be more conservative because initial pathogenic calls were not that pathogenic

37:03when you started to analyze more patients and that is one of the reasons that all

37:09the stakeholders gather together and establish these acmg guidelines to

37:15make the process systematic and most companies today they try to get close or even beyond

37:23the guidelines today to to be more precise in this process

37:30okay and then um the other question is uh how often you get second opinions of i mean how how

37:38that works because we know we have patients that come to our using god saying you know how i have

37:46a VUS for Syngap the kids look similar to our sync ups but it’s still they are in a VUS diagnosis how

37:54can you regular way or to recommend to railway for boss and how do you ask for a second opinion to a

38:01higher institution like yours that have somebody who work in this very hard second opinions

38:09um well i i think one of the most important things is to have access to genetic counseling

38:18after a genetic test because most of the processes done by clinical testing are automatic

38:25i know they provide most of the times a report evaluated by a scientist

38:32but still the genetic test is fixed in time it cannot update itself

38:39because it’s it’s paper right and you may stay with that and i do not recommend that

38:44i would recommend to revisit the interpretation um i don’t know once a year for viewers u.s uh

38:53information is growing and growing exponentially so reports are getting better and better

39:02so and and also there are the tools to study and i’ve seen how experts and how fast parents can become experts in the field and

39:16so you are able to do your own interpretation with all of these tools that are available

39:22and the community is quite active you you can always ask some scientists that it’s researching the gene who have the molecular expertise to make some calls to

39:33modify some criteria and i also recommend that to reach out to scientists who most of the

39:41times love to help and love to contribute to things that are quite important right

39:51have you seen diagnosis that you have revered from pathologic to benign

39:57or possible benign have you done that i i haven’t done it myself but i’ve seen it it’s

40:05mostly because when these general population databases they have like a new release and

40:12they report like twice the size you start to see variance that wasn’t in previous database but

40:19now you you see them and that’s a strong argument for perpendicular variants so that has to happen

40:28okay do you have oh i think we have more Victor and jazz are asking more of the q a and i think

40:38yeah JR may have some more important questions

40:43yeah well i wanted to talk a little bit more about victor’s second question so he had

40:48said that so provine is one of the i think it’s uh at the ventner institute it’s a

40:56it’s just one of the tools you can use to look for how how different you think the amino acid is

41:02basically um so it seems like for his questioning the idea is to go back maybe once a year

41:11and continue looking at the can continue inquiring about the VUS with the geneticist or the genetic

41:17counselor yeah um so a year sounds like a long ways away but we can also do some of our own

41:24research on it and try to bring this information to them i also think make sure we’re in citizen

41:30you know because they have a really top-notch genetic counselor and ellie brimble and she

41:36as far as i know she personally looks at each variant and uh tries to figure out what’s going

41:44on so i guess that’s i guess that’s maybe the opposite because you’re supposed to know that you have a pathogenic to go to citizen but i think my question for eduardo which might might have to do

41:56with victor’s question i’m not sure is how much weight is given when you have a small number of

42:04genes on the test so say you’re doing an epilepsy test an epilepsy panel with just 151 genes on it

42:12is there is the same weight given to that as when you do an entire exome

42:19right because because you’re only if you’re only looking at 151 and you have a vus what about the rest of the genome that wasn’t looked at how i’m just wondering how does does that have interplay

42:30in how these are scored or no well well um gene panels evolved constantly the literature reports a

42:42new lfc gene every month if not so so these finals are constantly changing and it’s a source of

42:51delay in the diagnosis process because when we have the exon the complete action we can do two

42:58things we first we can interrogate all genes possible and then we can bring revisit our exon

43:06with when time passes and see hey we have a couple of genes reported has my baron been there so exams

43:16tend to be uh of use for a longer time than panels of course the panels they have were the

43:27a relatively high chance in a cost cost effective strategy and what i’ve seen also is that patients

43:36who have a negative panel they go then to exome sequencing and this introduces a delay

43:45in the diagnosis with all the effects that this has so it’s really important to achieve

43:51diagnosis fast and for that i will always recommend if you have the access to an axon exon

43:59does not provide all the answers and there are several ways of identifying pathogenicity that are

44:05outside the axons and it’s um it’s part of the strategy um i i’ve seen so so you’re talking about

44:16also uh copy number variation and carry typing other tests that have other and even i guess

44:24uh mitochondrial testing yeah yes poison actions structural variants repetitions uh short tandem

44:32repeats all of these type of variants uh are not that easy to see on panels or exons so um is

44:42if you have a uas on the axon it’s does not mean that you don’t have

44:47that you don’t have a photogenic variant there are other tests that can determine alternative mechanisms that could be happening but we are just not seeing them

44:59yeah i have other questions but i think maybe oh i saw victor and jess are both

45:05here marta do you want to have them talk first i’ll ask i’ll ask when they’re done yeah victor do you want to ask your question sure thank you very much for the talk it was

45:16really really helpful and um i’m a parent my son was diagnosed with sin gap 1 based on a

45:23vus but with like the his his medical history and all in his the way he presents he was diagnosed

45:31um so this has been super helpful it’s i only understood a little bit of your talk i think but

45:37um oh i’m sorry no no it’s okay uh i i’ve been trying to learn it on my own and uh it’s it’s

45:45definitely a complicated world um and i actually work in medicine too so it’s a little i have some

45:50of a head start but um my question was around like where should we focus as like a patient

45:56group in terms of helping advance the science of classifying variants i i know we actually enrolled

46:04we’re enrolled in like this all of us which is like a us-based population um cohort where you

46:11contribute your your blood samples and they do genotyping i think whole exome sequencing and then

46:17you also contribute all of your your electronic health record data and surveys do you see those as

46:23being helpful for this or is it really you should we should be doing things like the citizen and

46:28things that are like really like more focused on like rare diseases i guess and what’s most helpful

46:37well um there is a limit in what you can do on a genome-wide level to determine pathogenicity

46:46not all genes are the same not our dna segments behave the same so i think

46:54moving into the gene wise direction uh is the it’s uh it’s a good strategy and and for that uh data

47:03aggregation is key we we need and to accumulate data to extract meaningful information um

47:13the more data and patience we have the more the more follow-up we do we can understand better how

47:20these variants behave in individuals in multiple individuals over time so as a group i think

47:30the a good strategy is to is to accumulate numbers and data um also also to develop more

47:39more robust statistical models specific to to certain phenotypes

47:46and for us that’s by joining citizen right yeah that’s the major work we are trying to do now

47:54is gonna be phenotyping all the uh genetic uh data that we have that’s that’s the

48:00short-term goal the long-term is different but the turn-turn goal is to get the phenotyping

48:06of all those variants and group them that you are doing a lot of that yeah is doing a lot of

48:12that that that work grouping and everything but yeah we are general that’s that’s the goal the

48:20are you able to enroll if you have a vus into citizen uh they we if you have a us we have i think uh they are like more than 10 by now and

48:36victor said he had a diagnosis though he had a diagnosis plus the genetic vos so that’s uh

48:42yes you should enroll if you have a diagnosis of singaporean you should enroll for 100 sure okay

48:48if i’m if i’m able to complement my my previous answer data aggregation is really important and

48:54also molecular studies the the molecular characterization of genetic variants found

49:02in patients i think this is key and also every functional characterization stays

49:11as a as a value of information for the future so it might be expensive to

49:17characterize uh every possible variant but every little step that we make in

49:23that direction will help to uh get the full picture of variability in singapore for example

49:33so can i ask you to elaborate on the molecular characterization are you talking about like biochemist biochemical assays in vitro you’re talking about mouse models

49:44yes any any any kind of characterization whether it’s in vitro and diva okay yes

49:52yes and any kind and for singap we were discussing before the talk that it’s quite complex because of

49:59its function interactions location it’s quite complex but every insight that we can

50:07make into the direction is valuable and it will be it will serve the future

50:17yeah thank you so just had a question martin yeah go ahead yes hi can you hear me hello hello

50:28um so my question is uh with the reinterpretation of the bus after a period of time um

50:37from my experience it really relies on the families pushing for the re-interpretation in many cases and i’m wondering if there is are we converging on a generalized approach

50:48to automatically re-evaluating um experience of unknown significance in the light of new evidence

50:58i know that some companies they provide reinterpretation amongst certain conditions um make it automatic uh it’s i’m not sure if that is possible because

51:13the nature of the new evidence is it comes from so many sources that it requires um

51:22the it requires on the table different people rather than a an automatic method um and on this

51:29table uh clinical expertise molecular expertise bioinformatic or genetic expertise are required

51:40so i i don’t think it can become completely automatic in the near future thank you so

51:53uh so as a follow-up to justice question you have you showed us a great website for looking

51:59at dravet that i think you guys run right is that from your lab yeah yeah yes we developed that with

52:08its own and revision currently so are are you developing the same thing for some gap

52:14one or are you developing the same thing for all genes or is that something that is a would need

52:20to be a funded project to do foreign we’re not developing something in those lines for symbol

52:27sync at one we are working on related sodium channels because it’s

52:34we have figured out that it’s easy to study them together so we’re working in that direction with

52:39scn2a and another sodium channels but not on zynga currently it will be possible with the with

52:50data available and that method was developed based on data aggregation from multiple patients

52:59variants age of onset clinical features like that if we wanted to try to set up a project like that

53:06how would we go about that as a patient advocacy group how would we figure out who should do that same kind of project for some gap that you’re doing for dravet

53:16right because we don’t want it we want to know we want to find the actual syngap patients we want to find the people that don’t have syngap you know if they think they do we want to know what the which

53:27parts of the gene do what and you know we want to know it all so it seems like this type of um

53:35this type of it’s it’s almost like a hunting you know gathering expedition to to find all this data from all these disparate sources and and interpret it

53:49well and uh we started the scm-1 project with one question can can we

53:57differentiate a mild presentation of the disease with severe and if we can do that we think of

54:07which i think we could on based on the data aggregation that you have might be possible

54:17okay so maybe you have a postdoc that might want to just sure we could okay

54:24okay we could talk about that more i i have a i don’t want to put you totally on the spot about that but we this is something we all need like our our patient community desperately needs us

54:33and we don’t we’re all kind of feeling around in the dark and i’m i’m you know maybe the leader of

54:39feeling around in the dark but i can’t you know people are like oh i don’t you know i i can’t do this this isn’t something i can do but it’s something that we all think about and that we need

54:47we need um concerted you know we need a concerted effort toward it so it’s very exciting to think

54:54um okay so i have a i want to ask you a question in a different realm if that’s okay um you talked when you showed us your the different types of mutations one type of

55:05mutation that wasn’t on your chart was uh sort of upstream very you know variations in the

55:11upstream regulatory regions so something that might change the expression level

55:17and i was wondering if you either for dravet or for sync gap if you look at upstream variation

55:27and um there’s there’s two reasons one is to want to know about how expression levels

55:34because if half is so severe maybe you know maybe less is is going to be some sort of mild

55:40right some sort of mild phenotype and then the second reason is as we get toward precise genetic

55:47therapies there are some times when we might want to distinguish between the two alleles and so knowing if there’s general variation in the population already that you could we is it likely

55:59that we’d be able to distinguish between the two alleles just by um normal population variation

56:07do you see what i’m saying not that we know a priori which it was but you know you might

56:12have to figure out which which one is which but is there a variation there that would

56:18allow us to distinguish between the two alleles in most humans

56:25well the the question has has several branches and it’s it’s complicated sometimes to differentiate

56:34that something is not there because it’s not there or because i’m using the wrong glasses let’s say

56:41or the wrong platform for utr’s structural variation repetitions sometimes there is a

56:49technical difficulty in seeing those variants to increase our own awareness that maybe we

56:58have some singaporeans that are increasing the expression on a non-coding region and

57:05non-coding regions are not tested in most of the clinical genetic testing approaches

57:13so that’s a technical uh difficulty if we have the resources we will test the whole genome and

57:21and we will explore everything and even that will not be enough to detect all pathogenic

57:26events and that we have we know that there are at the transcriptional level some some

57:33errors that can may lead to gain or loss of function of certain genes

57:39so it’s really important to be aware of the methods that we have um

57:47unfortunately is once the test is done it’s not possible to revise things that are not red so it

57:55might be difficult to evaluate that okay so in the in the epilepsy gene paddles they don’t look at

58:02some of the upstream because i thought in whole exome they lived at least a little bit outside the exo sure excellence sure in the collection we have uh we have some proofs that detect utr

58:17you can you can you can even design your own your own proofs to scan those regions more in deep

58:25but it’s we’re still learning how how genes are expressed so that’s also uh that’s also something

58:34that we need to consider the poison exons are a good example they are difficult to detect in

58:42in exome sequencing because you don’t have the proofs because you weren’t aware that this portion of the genomes were actually axons that appear suddenly and

58:54so we also have regulatory regions that are far away from

58:59from the gene itself so these regions in trance that regulate expressions and some eqgls

59:08it’s it’s not entirely reduced to the to the segment of the gene

59:19okay well i’ve of course asked something that can’t be answered so sorry about that um no no no it’s it’s an important discussion to discuss different mechanisms

59:34yeah i was part of a discussion with some people from some ring chromosome diseases

59:39and they were saying that their their diagnosis rate is going down because people don’t do carry

59:46type analysis as much anymore so as as all as you know things being diagnosed with panels and

59:53and whole exome are going up because of the increased testing uh their diseases are are being

1:00:00less diagnosed so i found that interesting that the right the things that we’ve known for a long

1:00:07time are starting to not be diagnosed as much just because the tests are falling out of favor um okay

1:00:13so it looks like mike would like to answer some questions live so i’m going to stop talking now

1:00:24i think that i think we answered all the ones that were in the q a but yeah i think all that

1:00:31you guys were talking about it goes to a relevance that uh for probably uh people that has bosses

1:00:38but uh going to the i mean genetic counselor once a year probably is very valuable because that’s

1:00:46the problem uh i mean this is a science that is just beginning this is it’s a lot to know

1:00:54and a lot of things that probably will come up in one year two years three years five years

1:01:00and for the ones we that we have the pathogenic diagnosis we probably will be a smart at least

1:01:07every three years i think what you think i think it revisited that diagnosis is probably important

1:01:16yes for sure for sure um ues are um

1:01:23must be so frustrating for for people having having that test in their hands and

1:01:32it’s a it’s a responsible claim to say that reinterpretation might give you hope uh if not now

1:01:42maybe in a year or so we might as the science community accumulate enough information to make

1:01:48the call yeah another thing is for example i have a sophia my daughter has um the the pathogenic for

1:01:58Syngap but also has two VUS in the in her genetic report then there is something now that is coming

1:02:06to evidence in the genetic that everybody has a different background too then how they will

1:02:13show the symptoms also the pain of the genetic background as a whole right yeah hey that’s uh

1:02:22that’s also really true because you have causing factors but you also have modifier

1:02:27factors that are maybe not entirely related to single one but just the background as you say

1:02:36for that matter i’m also really interested in gathering information from underrepresented population or also people with mixed genetics like admixture that it’s so common in latin

1:02:49american populations that background uh might explain why some patients uh react differently to

1:02:57drugs or manifest different this is progression um or other rare variants within them so

1:03:08yeah that’s really really true okay i guess any any other questions i think we are at the end of the hour any questions or

1:03:19it was great thank you so much Eduardo and this is i think very clear and very helpful for a lot

1:03:27of families thank you and i hope that santiago gets a little bit warmer too thank you for that

1:03:36anymore and we truly appreciate very much you are doing this for us yeah thank you stay connected

1:03:46we weren’t talking before about working together and we are still thinking about it yeah we are

1:03:52trying to do all these projects that are very important and of course your project is very important to us thank you so much thank you so much it’s really wonderful thank you