My name is Janelle Hodge, and I'm from Indiana University, and I'm going to be speaking to you today about the next generation sequencing education gap. And this talk will cover the current state of the genomics field and a survey that asked people who are laboratory directors, what do they feel are their education needs? I have nothing to disclose. So NGS is clearly becoming relevant to everyone. So from the cytogenomics laboratory perspective, it started out as a whole genome view, but low-resolution with karyotype. And there's been increasing resolution with microarrays down to the CNB level, but nothing like the high, high-resolution molecular diagnostic laboratories started out with looking at indels and point mutations, but very targeted, but both of them are now moving towards NGS, which allows us a whole genome view at a high resolution. There are challenges to universal adoption of NGS. So we have a lack of reimbursement and field guidance, which is getting better. Laboratory silos where we have technology isolated in one lab versus another. There's also significant development costs for these complex tests, and this is especially challenging for smaller labs. There's also limited access to bioinformatics support. So currently, this technology is becoming increasingly accessible because we do have more robust out-of-the-box solutions and resources, but a significant issue is also the emerging fields of cytogenomics and molecular genetics. And really, you need to understand both of these areas to have the breadth of expertise to fully interpret all different genomic alterations. And this is irrespective of the technology. So, yeah, NGS is what we're looking at today, but it could be other technologies. So from the cytogenomics perspective, you know, bringing that knowledge of the structural chromosome implications, as well as copy number genome patterns. And then we have molecular genetics that can apply small variant interpretation and understanding NGS technology. So really, I think you need to have both to fully interpret alterations of the genome in both the proband, as well as the implications and recurrence risks for family members. There's an additional challenge, which is needing to speak the same language, because in molecular, we have HGDS, and this has been independently evolving from the cytogenomics, the ISCN. So if you want to describe a copy number variant, these are different. So the good news is that the field of laboratory director training has been evolving and recognizing this issue. So you can no longer train as a laboratory director in cytogenetics or molecular genetics. It's combined into one, which is the Laboratory Genetics and Genomics Fellowship, or LGG. In addition, if someone is certified only in one or the other, they can have an alternative pathway to certification where they gain knowledge when they are not certified in and they can sit for the same LGG boards. So in this context of what's happening with the field, let's talk about a survey to assess how people are really feeling about their knowledge level. So a survey was conducted by Hutton Kearney, and it was sent to the Cytogenetics Listserv. And the feedback was very interesting because education gaps and understanding of NGS technologies at the fundamental level were felt by clinicians, laboratory directors and technologists. And many of these individuals are also ones that are expected to validate and review these kinds of cases for patients. So let me describe the population of individuals that took this survey. So of the 133 that participated, 65 percent were from university teaching hospitals, but also a number of individuals from private hospitals and commercial laboratories. Most of the individuals were from medium sized labs, but there was a good spread of small to very large laboratories of individuals that participated. Interesting data. I received my last formal degree within, and what you can see is 39 percent more than 20 years ago and 32 percent in the last 20 years. So if you overlay the data of when NGS came in the clinical laboratory, we're talking mid 2000s and on. So what this tells us is that many currently practicing laboratorians completed their formal education before NGS really came into the clinical labs. So certainly the people that trained more than 20 years ago, but also many of the people that trained in the last 20 years. And the thing we have to remember is this isn't just cytogeneticists. These are actually also people that are trained in molecular genetics, but they didn't have formal training in NGS. But yes, so many are now asked to validate and report on these assays that they're learning on the fly. Which is a big ask of people. So in terms of certifications of these participants, the majority were certified as cytogenics, but also 40 percent are certified in clinical molecular. And what you'd expect from cytogeneticists, banded chromosomes, fish microarrays, but also the 43 percent sign out general molecular and 34 percent NGS. So here's the big number. When people were asked what training do they think would be beneficial, 63 percent said that they have significant education needs in NGS. That's a really high number. Here's some of the quotes from people who filled out the survey. It is our responsibility to stay current, to provide the best answers as inexpensively as possible. It will be diagnostic genomics combination of many technologies. It's a firehose. Hope we're all ready. I think the changes are exciting, although dizzying. Education needs are great from technologist to director to clinician level. So you might recognize something you agree with, if not everything in here. So this is something that's being relatively universally felt. So that's the problem. So then how do we address this education gap? This is not an easy thing to solve. There's not one thing and it's going to be done. But one way that we wanted to start addressing this was to make a short course for this ACMG 2020 meeting. The difference is that we wanted to target the very fundamentals from basic terminology on. Because there's not many resources out there that do that. It's hard to go to these different talks on NGS and you're gluing little pieces. But to put the whole picture together, because if you have no knowledge of NGS, hopefully this will be a helpful course. But also for people who have been learning on the fly. I think it's helpful to get pieces that might help a complete picture or understanding of, oh, that's why we do that kind of feelings and thoughts. OK. So this course has multiple pre-recorded talks. So in addition to this one, we have four more. And then we're also there's a subsequent live online portion. And there are many learning objectives. But I described to you what I think is really the big point of this course is giving the true fundamentals and a picture to solidify a lot of the knowledge people already have. So Elaine Martis from the Institute of Genomic Medicine at Nationwide Children's Hospital has recorded a talk on next generation sequencing technologies. So she's giving a detailed overview of NGS, including principles and methods and comparing platforms. You know, when do you use different platforms? What are the errors that happen in one platform versus another? And various applications of NGS as well will be described. We also will have Susan Chow from Columbia University will take you through the basic bioinformatics steps, and this is going to be including terminology and file formats. So if someone says you pile up or they say read depth or they say, oh, is it a BCF BAM, CRAM, SAM file? You'll know what those mean and at what point in the process they're used. And she'll include explaining quality control metrics, because obviously it's very, very important, and troubleshooting. They will move into validation. So Mark Ewald from the University of Colorado will talk about how do you select the appropriate NGS assay based on the strategy you're implementing? And then how do you validate different NGS assay types? So if you're going to be looking at FFPE, that's very different. You know, if you look at this paraffin embedded sample, then a different kind of specimen and what kind of NGS assays would you use? And then what is the quality control for validations and technical artifact identification, which obviously is important because you need to understand what are the issues with your specific platform before you start using it on patients. And then the final talk will be again by Elaine Martis. She'll be talking about what's new in NGS. So she'll be touching on long read technology, single cell sequencing, immunogenomics, as well as something that's becoming very common, which is NGS on not just DNA, but concurrent RNA to look at the impact of the variants you're finding by DNA on the expression in the RNA. Where you find these recorded talks, we are also uploading a definition sheet that you can use hopefully in the future to look back when you see a definition you don't recall. Okay, finally, subsequently, we're going to have a case based audience interaction. It'll be a live portion. This is currently scheduled for June 17. And it's going to be noon to 1.30 p.m. Eastern. Please check online just to confirm in case anything changes, but this is when it's currently scheduled. And the idea of this is that all the speakers will be available and we'll be going for the first half through cases to apply the knowledge that you've learned by watching the recorded talks. Also, when you fill out the surveys after the talks, that can include a place where you can put questions and we'll see those questions and hopefully be able to answer them during this live portion, in addition to people asking questions live during the online session. So I hope that this course is very useful to you and that you're able to attend the live portion. All right, well, thank you very much.

education gap

next-generation sequencing

cytogenomics

molecular genetics

bioinformatics support