Hello, and welcome to our ACMG product showcase. Genominon is here to showcase the Mastermind Genomic Search Engine, and in particular, our speakers will highlight its clinical use for optimizing variant interpretation. We are so happy to have two excellent representative Mastermind users share their clinical experience with using Mastermind to curate the evidence for variant interpretation. Andreas Laner from MGZ Munich and Pippa Granger from LabPlus Auckland will be our speakers today as they walk through a couple of examples drawn from their own clinical work to highlight the features and value that they gain from use of Mastermind in their clinical workflows. For my part, I'm Mark Keel, the Chief Science Officer and Founder of Genominon. In my role as CSO, I supervise the comprehensive genomic landscapes that we produce for our pharma clients, drawn on the comprehensive data in the Mastermind Genomic Search Engine. In addition to which, I also oversee a lot of the product vision for the Mastermind Genomic Search Engine, which we will be showcasing today. The Mastermind Genomic Search Engine is a web-based software that variant analysts, geneticists, genetic counselors, pathologists, clinicians, and researchers can use to understand what their variant means, where it has been published before, and in what contexts, and what information they can take action on. It is the most comprehensive and up-to-date organization of all of this genetic information across 30 million titles and abstracts, and more than 8 million full-text articles, and nearly 3 million supplemental datasets. The indexing that underpins the Mastermind Genomic Search Engine identifies every disease, every gene, and every genetic variant mentioned across all of that information. And to date, Mastermind contains more than 7 million genetic variants. In addition to indexing this body of knowledge for diseases, genes, and variants, Mastermind indexes the mention of any one of many thousands of therapies, as well as a comprehensive ontology of phenotypes, and a battery of categorical keywords that can then be organized into genomic associations. So I'm illustrating that here in the diagram on the left, where you can see how if any one of these entities is associated with any one of the other entities, or more than one, the Mastermind Genomic Search Engine will identify those associations and can produce the evidence supporting those associations based on a user's query comprising any one of those nodes, be it a genetic variant, as our speakers will showcase, or a copy number variant, as one of the examples will highlight, as well as any one of the other nodes there, diseases, phenotypes, therapies, etc. Just to orient you quickly before I pass it over to our speakers, this is the landing page, the search page for the Mastermind Genomic Search Engine, and you can see here how a user can begin their search with any one of those terms, and Mastermind will recognize what terms are appropriate and prompt that user to select which of those entities they want to comprise their search. The most typical use case for Mastermind in clinical circumstances is to perform a search for a specific genetic variant, which you can see here. Just to orient you to the Mastermind interface on this detail page, on the right is the literature landscape, which includes all of the papers that mention this variant, as well as deep insight into the nature of those mentions in each one of those references. On the left is the landscape of all of the genetic variants in the gene that you have searched for, and at the top are various ways that you can configure your search, whether it be by adding a disease, phenotype, or therapy, or any one of those categorical key terms from the pre-canned set of key terms, or any full-text search terms that you'd like to include in your query. One last thing to showcase before I turn it over to our speakers is the recently released association page, where you can see here, as an example, for this variant that I have searched for, Mastermind is able to showcase all of those associations that I alluded to in the diagram on the previous slide. In this case, for this variant, I'm showcasing all of the diseases that were found to be co-cited in the context of the mention of the genetic variant I searched for. So immediately, you can see the value that this provides. If you're unaware of the disease association in this case for this particular variant, Mastermind will immediately show you which diseases are most frequently co-cited in the context of your search for variant. So this is particularly useful for labs that are expanding their test offering to include larger and larger gene panels, up to and including whole genome and whole exome sequencing. I'd invite anyone interested in trying the Mastermind Genomic Search Engine to follow that link below, where you will be afforded a trial of the Mastermind Professional version, which is used by our clinical users for the most comprehensive, most feature-replete view into the data, but for which you would be afforded access to the Mastermind Basic Edition after your trial ends. So with that, let me introduce again our speakers, Andreas Laner and Pippa Granger. Thank you for having me here. My name is Andreas Laner and I work for the Medical Genetics Center in Munich. We have a big human genetic practice with more than 15 physicians and molecular biologists and we make all kinds of genetic diagnostics in Germany. So I will start with a short prelude, speaking about variant classification in general and the ACMG-AMP classification system in general, and then I will walk you through a case, one of many, where we used Mastermind to gather ACMG-relevant information and where we were able to solve the case in a short time. When I teach about variant interpretation, this is usually my entry slide, which transports only one important message. So it's my first tool in variant interpretation and it says that you should refrain from uncritically adopt gradings or classifications from any database or the literature without checking the underlying evidence. So you might ask where the relevant evidence comes from and this is exactly where the Cornerstone publication from Richards et al. comes into play. So in this paper from 2050, the ACMG-AMP guidelines were published and as you can see in this table, the ACMGs contain 28 evidence codes sorted according to evidence strength from far left, very strong benign, to far right, very strong pathogenic, and they are grouped into different evidence categories like computational data, functional data and or de novo data and they also come with a table where you can count the evidence codes and calculate the final classification. So in this graphic, I aimed to see these evidence codes from a molecular biologist's point of view and try to display the sources where the evidence comes from. So to say where to look for the evidence and while it will probably not surprise you to learn that you can extract almost, if not all, ACMG-relevant information from the literature. So eventually, information from the literature ends up in databases, but the literature is always the primary source of evidence. And it's obvious that a thorough literature curation is the core of a robust and consistent variant interpretation process. But unfortunately, it is also the most time-consuming part and compared to other parts of modern high-throughput NGS diagnostics, it is not yet scalable. So this is where my prelude ends and the main theme starts, namely how we use masterminds to speed up the variant interpretation process from here to there. So I will show you in this slide a typical case we had in our lab. And so after a few variant filtering steps, I ended up with one clear-cut pathogenic variant in the ABCA4 gene. This is a splice variant, and I think we all agree that this can be classified as a class four here. And so in this case, the mode of inheritance is autosomal recessive, and I was looking for a possible second pathogenic variant in this gene. So the gene fits very well to my phenotype of the patient, but this is not of concern here. And what you may notice and what I marked here is that I found another missense variant in this gene. And this is the starting point of my case here today. So in our variant interpretation tool, we already have the mastermind link included, but you may have noticed that we also have information about ClinVar, and it says that it's pathogenic in ClinVar, but if you remember my first rule in variant interpretation, you should not take this as evidence, but look for the underlying evidence instead. So what will happen when I click on this link to mastermind? I will be navigated to the mastermind home page, and here the variant details are already in the search line, and it shows me that I have almost 60 articles with this gene and this variant. So this is way too much, and I don't want to read all of these. So this is what I like mastermind very much. You can ask the program the right questions, and we get the relevant answers. So mastermind is much more than just a variant search tool. So in my setting, I have three questions in mind. You remember that it is an autosomal recessive mode of inheritance here. So my first question would be, is my variant, has this ever been detected in compound heterocyclic states with another pathogenic variant? Another question could be, are there functional studies? So I can invoke the criteria PS3, or a third question maybe, do we have case control data? So is the prevalence in affected increased over controls, which would be the criteria PS4, and I show you how I do this. At first, I navigate to the filter categories, and then navigate to the ACMG interpretation bar. And so my first question I want to answer is, are there functional studies? So I click here on functional, go to in vitro, and invoke this filter for functional studies. And I can see here on the number what will expect me if I hit the submit button. I will have nine papers with this search terms. And this is how the search then looks like. In this, I will not go into detail about what the windows you see here, I think this will be explained in another presentations. But in this publication history chart, the big dot here represents the first paper here in this table. And by clicking on it, I will have this windows opens and I see the search terms highlighted. So functional studies and the variant I was looking for. So this does not mean that I can now at this point, take the criteria PS3 for certain, I still have to get the relevant information out of the paper, but the search time is extremely reduced here. So alternatively, I can ask the second question, this has my variant been detected in compound heterozygous state in an affected individual. So this would be criteria PS3. For this, I would look in the part inheritance pattern, zircosity, and then compound heterozircosity. And if I submit with the new filters, then the publication history window changes and also the papers here on top of the list. And if I click on this, then I can find just in the highlighted text that my variant has been found in a compound heterozygous state with another variant and so on. Again, I have to check the literature, but this is a nice shortcut. So what about the last question, the case control data? For this question, I would check this pedigree and case studies and go to cases and case control and I will have two papers. And these are the papers. When I click on the first one, it says that my variant here was actually found to be the third most prevalent disease variant in the study. And so again, I have to check the literature again, but I think this would be valid to check the point PS4. So this was a short and quick overview of how we use Mastermind to get the relevant information and as I said, we are roughly 15 molecular biologists and we are all familiar with the system and I must say it speeded up the process a lot and helped us a lot. Okay, now I'm at the end and if you ever come to Munich and you would like to see me, then you have to locate here, well, not in the church, but our building is, our lab is right behind the church and you have a high probability to find me there. And if I'm not there, then you might have clues where to look instead. Okay, thank you. Hi, I'm Pippa Granger from the Diagnostic Genetics Department at LabPlus. LabPlus is the tertiary referral medical laboratory for the Auckland City Hospital and a major referral laboratory for specialised laboratory tests for New Zealand and the Pacific Islands. In the Diagnostic Genetics Department, we have teams working on pre-processing, cytogenetics, fish, molecular hematology, molecular oncology, molecular genetics and microarray. Within our molecular teams, due to the expanding number of variants for curation and the increased time pressure to perform these curations, we have been looking for a literature searching tool that could give clarity to our complex and rare variants and reduce the time it took scrolling through the literature. We've decided to investigate mastermind due to the sheer number of variants recorded, full-text articles indexed and supplementary datasets indexed. Also, this is updated weekly rather than quarterly. We acquired our licence in January 2021 and have implemented mastermind searching as a standard practice for our constitutional SNVs and CMVs, with the somatic variants to come later in the year. In this presentation, I will take you through two cases in which we've used mastermind. One was an SMV and one was a CMV. In the first case, we received a request for a targeted sequencing of the familial KCNQ1 variant in a 44-year-old male with a clinical diagnosis of long QT syndrome. On returning a positive heterozygous sequencing result, we curated the familial variant to confirm its relevance. We classify our variants according to the American College of Medical Genetics guidelines, which I will be referring to for this case. This case was a little tricky, as at first glance, we had only one moderate ACMG criteria that we could apply. Although it was a frameshift variant, resulting in a premature stop codon, it's only predicted to disrupt the last 45 amino acids and was less than 10% of the protein. And it's not within a recognized protein domain. This variant has been associated with multiple cases of long QT syndrome in a homozygous or compound heterozygous state. And there are 15 heterozygous variants found in the NOMAD population database. As we only had one moderate criteria using the ACMG guidelines, we needed to find at least one strong to be able to call this variant a class 4, likely pathogenic or higher. We were unable to use PS4 due to the number of heterozygous carriers within the NOMAD database. And so we needed to find a functional study. Using our previous software, we found five articles covering phenotype and cohort studies, but no functional studies. Using the Mastermind software, we were able to identify 23 papers, including a functional study, that were relevant to our search terms. And within this list of papers, which are sorted by relevance, the second hit was a January 2021 functional study illustrating the recessive inheritance pattern of this variant and the molecular mechanisms of disease. The data is even more impressive as this variant was curated in five papers. And we were able to apply a strong and moderate criteria, giving us a likely pathogenic variant. This case was reported as a heterozygous carrier for the familial class 4 variant. Due to the recessive nature of the inheritance and no other pathogenic variants identified within this family, further investigation was suggested. The clinical feedback was that they no longer believed this variant to be the cause of disease within the family. And family members who had previously tested negative for the variant were now being clinically monitored. Our second case was a prenatal amniotic fluid, which was referred for polyhydraminose bilateral pleural effusions and prenatal edema, referred to at 28 weeks. In this case, the microarray results showed two clear deletions at both ends of the chromosome 10, suggestive of a ring chromosome. The two regions contained many genes, and according to our standard cytogenetics guidelines, both regions were analysed separately. We were able to copy and paste the coordinates straight from CHAZ, our analysis software, directly into Mastermind, as you can see here. From sorting the overlapping tab and looking for the percentage overlap, we were able to obtain a hit containing the same genes as our copy number variant, with a 90% overlap and a link out to the key papers. If you can see here, there were two papers that combined the region of interest, and the search also identified several intersecting and surrounding CMVs reported in the literature. By clicking on the titles on the side, it shows you the specific mention within the text for the variant of interest, and it allows us to quickly determine whether the papers are of interest or not. These journal articles were used to create the final clinical report. The beauty of Mastermind is that it can search our exact copy number regions using the coordinates straight from the software, efficiently finding the closest match to our CMVs in the literature to the nearest base pair with the same gene content. This does not seem to be possible with other search engines or curated databases. It is also able to filter out for specific papers of interest, such as functional studies, cohorts, although this was not required for this presentation as in case one, we were able to get a great number of papers on the original search. The other fantastic thing about Mastermind is their quick responses from their support people and the availability to speak to someone via a video call to go through difficult cases or run training sessions with our teams, with great feedback on how we could improve our searches or what's coming up in the quarterly updates. And I'd like to take a moment to just thank the Mastermind team for all of their great help and support, and my team at Diagnostic Genetics with specific reference to Jasmine Jiang and Natasha Hendon for supplying me with the details for case one and Elaine Doherty for supplying me with the details for case two. Thank you very much. Thanks again for attending our ACMG product showcase. As a reminder, you can sign up for a trial access to Mastermind Professional by following the link below. And in addition, I invite you to contact us should you have any questions about Mastermind or how it could be applied in your clinical workflows.

ACMG

Mastermind Genomic Search Engine

web-based software

genetic information

variant analysis

clinical workflows