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  • Contains 1 Component(s) Includes a Live Web Event on 09/17/2024 at 12:00 PM (EDT)

    In this webinar, Paul W. Hook, PhD, former leader of the Bioinformatics SIG, provides insight into his current work using cleavage under targets and release using nuclease (CUT&RUN) to measure protein-DNA binding with nanopore sequencing. Dr. Hook will introduce CUT&RUN, detail computational analysis while highlighting software used, present results, and explain how this method may be used in the future. A time for Q&A will follow the presentation.

    Join members of the Bioinformatics & Computational Approaches SIG for this series. In this webinar, Paul W. Hook, PhD, former leader of the Bioinformatics SIG, provides insight into his current work using cleavage under targets and release using nuclease (CUT&RUN) to measure protein-DNA binding with nanopore sequencing. Dr. Hook will introduce CUT&RUN, detail computational analysis while highlighting software used, present results, and explain how this method may be used in the future. A time for Q&A will follow the presentation.
     
    The focus of the Bioinformatics & Computational Methods SIG is on computational approaches for analyzing and interpreting genetics and genomics data. Topics include statistical genetics methods, polygenic risk scores, GWAS, RNA-seq, ATAC-seq, and much more.


    Overview of Presentation

    • Introduce CUT&RUN and outline a typical CUT&RUN analysis pipeline
    • Highlight how typical CUT&RUN analysis was adapted to CUT&RUN performed with nanopore sequencing
    • Emphasize potential future uses of this method

    Paul W. Hook, PhD

    Postdoctoral Fellow

    Johns Hopkins University

    Dr. Paul W. Hook received his Bachelor of Science degree in Biochemistry and Molecular Biology from the Pennsylvania State University in 2012. He went on to earn his PhD in Human Genetics from Johns Hopkins University School of Medicine in 2020, where his thesis work focused on pinpointing the genes and variants underlying genome-wide association signals through the use of genomic data from disease-relevant cell populations. Dr. Hook joined Winston Timp’s lab as a postdoctoral fellow in the Department of Biomedical Engineering at Johns Hopkins University in the summer of 2020. In this role, his work has focused on the development and application of new approaches for measuring different aspects of epigenetics by using long-read sequencing, including chromatin state, DNA methylation, and protein-DNA binding.

    Minna Kaikkonen-Määttä, PhD (Moderator)

    Professor at A.I.Virtanen Institute

    University of Eastern Finland

    Minna Kaikkonen-Määttä obtained her Bachelor's degree in Cellular Biology and Physiology from the Claude Bernard University Lyon 1, France, in 2002 and Master’s degree in Molecular Biology from University of Jyväskylä, Finland, in 2005. She obtained her PhD in Molecular Medicine under the supervision of Prof. Seppo Ylä-Herttuala in Kuopio in 2008. Her doctoral studies were focused on “Engineering Baculo- and Lentiviral Vectors for Enhanced and Targeted Gene Delivery”. She did her postdoctoral studies with Prof. Christopher Glass at University of California San Diego where she shifted her research focus into transcriptional gene regulation and enhancer RNAs supported by the Young Investigator Award from Leducq Foundation. She started her own lab in 2015 at the University of Eastern Finland with a focus on gene and cell level understanding of atherosclerosis using state-of-the-art next generation sequencing methods. Currently she is a Professor in Cardiovascular Genomics and runs a lab of 20 members while acting as a Director of the A.I.Virtanen Research Institute and Single Cell Genomics Core. She has published over 100 peer-reviewed articles with ~6000 citations (H-index 34). She has received over 8.5 million in research funding and is currently supported by the prestigious European Research Council Consolidator Grant, Academy of Finland, Finnish Foundation for Cardiovascular Research and Sigrid Juselius Foundation. She is the President of the Finnish Society of Atherosclerosis and member of the ESC working group on Atherosclerosis and Vascular Biology, Scandinavian Society of Atherosclerosis, and Membership Engagement Committee of the American Society of Human Genetics. 

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  • Contains 1 Component(s) Includes a Live Web Event on 08/28/2024 at 12:00 PM (EDT)

    This webinar introduces innovative methods for integrating hands-on genomics into high school and college curricula, demonstrating how affordable DNA sequencing can facilitate equitable STEM access and data literacy.

    This webinar introduces innovative methods for integrating hands-on genomics into high school and college curricula, demonstrating how affordable DNA sequencing can facilitate equitable STEM access and data literacy. Educators are increasingly able to access low-cost sequencing technologies, supported by freely available bioinformatics tools. This offers students the chance to work with the same data and tools as cutting-edge researchers. We will provide practical tips and strategies for hands-on genomics education, including teaching techniques and recommendations for free or low-cost equipment, reagents, and digital tools. The webinar will feature resources developed through collaboration among three Minority Serving Institutions (MSIs): New York City College of Technology, Spelman College, and the University of Puerto Rico-Río Piedras, along with the Cold Spring Harbor Laboratory DNA Learning Center. 

    We will also hear from diverse individuals and faculty-led genomics education networks, and industry as they devise methods to make genomics education accessible and inclusive. We will also highlight ethical and culturally relevant teaching approaches for responsible engagement with genomics research. Ultimately, making a wide range of genomics experiences available in any classroom will empower students, particularly those from resource-limited institutions, to gain a deep understanding of genomics and prepare for careers in research and the bioeconomy.

     

    Overview of Presentation:

    • Compare genomics sequencing curricula, experiment resources, and teaching strategies for college and pre-college audiences
    • Identify the ethical considerations, accessibility, and opportunities for inclusion in introductory genomics education
    • Summarise technical and pedagogical challenges in genomics education
    • Generalize and adapt the resources presented to local context and applications

    Jason Williams (Moderator)

    Assistant Director

    Cold Spring Harbor Laboratory DNA Learning Center

    Mr. Williams is Assistant Director, Inclusion and Research Readiness at the Cold Spring Harbor Laboratory DNA Learning Center where he develops national biology education programs. Mr. Williams has delivered professional development and training for thousands of students, researchers and educators in bioinformatics, data science, and molecular biology. His focus has been developing bioinformatics in undergraduate education and career-spanning learning for biologists. Jason is founder of LifeSciTrainers.org – a global effort to promote community of practice among professionals who develop short-format training for life scientists. Jason is advisory to cyberinfrastructure, bioinformatics, and education projects and initiatives in the US, UK, Europe, and Australia.

    Daniel Shay

    Teacher and IST Science Curriculum Director

    North Central High School

    Dan Shay is a non-traditional scientist. After graduating college with a Bachelor’s degree, Dan taught environmental education for several years before receiving his Master’s in Teaching in 2013. For the last 11 years, Dan has taught and directed a specialized Biotechnology Career and Technical Education program at a North Central High School. The goal of this program is to teach students the skills they need to enter into a career in biotechnology research. In the 5 years that he has directed the program, Dan has received over $100k in funding to update the technological infrastructure of his lab, some of this went towards purchasing the Oxford Nanopore minION and developing protocols for students to collect and analyze sequencing data as a class. Dan was the recipient of the 2021 Washington State Science and Engineering Fair Teacher of the Year award and the 2023 WA State Outstanding Biology Teacher Award. 

    Katharina Wolff

    Doctoral Student

    Plant Biotechnology and Bioinformatics, Technische Universität Braunschweig

    Katharina Wolff is currently a doctoral candidate at TU Braunschweig, working with Prof. Dr. Boas Pucker in the group “Plant Biotechnology and Bioinformatics”. Her research spans the realms of Synthetic Biology, Plant Genomics, and Bioinformatics, seamlessly blending wet lab and dry lab methodologies. Within the workgroup, Katharina oversees the operations at the ONT Sequencing Facility. Her role involves leveraging her expertise in both wet lab techniques and bioinformatics to conduct thorough and comprehensive genomic analyses. Additionally, Katharina has developed and supervised a practical Data Literacy in Genome Research course in collaboration with Prof. Dr. Boas Pucker.

    Laura Reed

    Professor of Biology

    University of Alabama

    Laura K. Reed is a Professor of Biology at the University of Alabama.  Dr. Reed received her BS in Biology (University of Oregon), her PhD in Ecology and Evolution (University of Arizona), was NIH-NRSA postdoctoral fellow (North Carolina State University), and joined the faculty at the University of Alabama in 2010. Her research focuses on the evolutionary genomics of complex traits and effective science education methodology. She directs the Genomics Education Partnership (thegep.org), a collaboration dedicated to bringing course-based genomics research experiences into undergraduate courses across the US.

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  • Contains 1 Component(s) Includes a Live Web Event on 08/21/2024 at 12:00 PM (EDT)

    Directors of four NIH funded projects that aim to train people from underrepresented groups in genomics and introduce them to future careers will present an overview of their program. Following this will be a panel discussion about opportunities and challenges in recruiting, training, and retaining a diverse and representative genomics community.

    A lack of representation within the genomics workforce limits the questions addressed, interpretation of the research, and uptake of actionable results into communities. While these limitations are well known, a lack of representation within the genomics community persists. Challenges include a lack of entry points along the educational and career pathway and barriers or hardships to continuing resulting in lower retention.

    Here, we bring together directors of four NIH funded projects that aim to train people from underrepresented groups in genomics and introduce them to future careers. Underrepresented groups include first-generation college students, people with disabilities, and students from Historically Black Colleges and Universities (HBCUs) and Hispanic Serving Institutions (HSI). Each program presents a different point of entry into the genomics community from undergraduate genomics research experiences and fellowships, to Master’s degrees in genomic data science, to career videos that foster science identity. In addition, these programs provide support to retain individuals including fostering identities as genomic scientists, building mentor networks, and cultivating a sense of belonging. After each director presents an overview of their program, there will be a panel discussion about opportunities and challenges in recruiting, training, and retaining a diverse and representative genomics community.

    Overview of Presentation:

    • Identify genomics training programs and career resources
    • Classify different points of entry into genomics careers
    • Identify best practices to focus on developing a sense of belonging and supporting building identities as a genomic scientist
    • Understand ways to build and support diverse communities and mentoring networks
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  • Contains 1 Component(s) Includes a Live Web Event on 08/14/2024 at 12:00 PM (EDT)

    Dr. Gabrielle Lemire will discuss exome copy number variant (CNV) detection, analysis and classification on a cohort of 6,633 families with undiagnosed rare genetic disorders. With the resolution provided by exome sequencing, they identified a causative CNV in 2.6% of families and assessed CNV pathogenicity by applying an advanced classification approach.

    Dr. Gabrielle Lemire will discuss exome copy number variant (CNV) detection, analysis and classification on a cohort of 6,633 families with undiagnosed rare genetic disorders. With the resolution provided by exome sequencing, they identified a causative CNV in 2.6% of families and assessed CNV pathogenicity by applying an advanced classification approach. 

     

    Overview of Presentation

    • CNVs can be difficult to identify by standard exome sequencing and challenges still remain in accurate classification of CNV pathogenicity.
    • CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics.
    • The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%).
    • To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework.
    • We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance.
    • Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing.

    Gabrielle Lemire, MD, FRCPC

    Research Fellow

    Boston Children’s Hospital; Broad Institute of MIT and Harvard

    Dr. Gabrielle Lemire is a medical geneticist certified under the Royal College of Physicians of Canada who currently trains at Boston Children’s Hospital and Broad Institute of MIT and Harvard. She completed her medical and residency training in medical genetics at Université de Montréal and a clinical research fellowship with the Care4Rare Canada Consortium at the University of Ottawa. She is currently a postdoctoral research fellow in Dr. Anne O’Donnell-Luria’s laboratory at Boston Children’s Hospital. Dr Lemire performs exome and genome analyses to identify rare disease diagnoses and novel gene discovery. Her research focuses on developing novel approaches to investigate undiagnosed rare genetic diseases, understanding their molecular mechanism, and improve phenotype delineation of rare diseases. 

    Alba Sanchis-Juan, PhD

    Postdoctoral Fellow at Talkowski Lab, Center for Genomic Medicine

    MGH and Broad Institute of MIT and Harvard

    Dr. Sanchis-Juan is a Postdoctoral Research Fellow at the Center for Genomic Medicine MGH, Harvard Medical School and the Broad Institute of MIT and Harvard. Alba completed her PhD in Biotechnology at the Polytechnic University of Valencia, in collaboration with the University of Cambridge, and joined the Talkowski laboratory in 2020. Her research has focused on the discovery of unknown etiological genes and variants in coding and non-coding regions of the genome of patients with rare diseases, with a particular focus on identification and resolution of structural variants and complex rearrangements using short- and long-read whole-genome sequencing technologies. Currently, she is leading large-scale population and clinical genomics efforts to aggregate the largest collection of rare disease cases to date to combine the full spectrum of genetic variants to empower gene and variant discovery causing rare diseases.

    Harrison Brand, PhD

    Assistant Professor

    MGH and Harvard Medical School

    Dr. Harrison Brand is an Assistant Professor in the Departments of Neurology and Surgery at Massachusetts General Hospital (MGH) and Harvard Medical School. He also serves as the Associate Director of the Broad Structural Variation Group. Research in his lab focuses on the development of novel methods for the analysis of structural variation (SV) from whole genome sequencing data and application of these methods to decipher the genetic architecture of structural birth defects and other developmental disorders. He served as one of the primary developers of the cloud-based GATK structural variant caller (GATK-SV) and has led efforts to generate robust SV reference databases for the genomic community in cohorts such as gnomAD, 1000 genomes, and All of Us. 

    Anne O'Donnell-Luria, MD, PhD

    Assistant Professor, Boston Children's Hospital and Institute Member

    Broad Institute of MIT and Harvard

    Dr. O’Donnell-Luria is an Assistant Professor in Pediatrics at Boston Children’s Hospital, Harvard Medical School and Institute Member at the Broad Institute of MIT and Harvard. Her research is focused on improving the diagnosis of rare disease. She obtained her MD/PhD degrees from Columbia University Medical School and residency training in Pediatrics, Clinical Genetics, and Medical Biochemical Genetics at Harvard Medical School, Boston Children’s Hospital. She is part of several collaborative studies in genomics including the GREGoR consortium, NeuroDev Project, gnomAD consortium, CAGI consortium, and ClinGen. Her research is focused on methods and technologies to improve rare disease diagnosis given that half of patients remain undiagnosed. 

    Sara Cullinan, PhD (Moderator)

    Deputy Editor

    American Journal of Human Genetics

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  • Contains 1 Component(s) Includes a Live Web Event on 07/31/2024 at 12:00 PM (EDT)

    Attendees will learn how to access HPRC data and resources. They will be able to conduct variant analyses using the pangenome and they will be able to utilize tools for mapping functional genomics data, such as RNAseq and DNA methylation data, to the pangenome.

    The NHGRI-funded Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. The project leverages innovations in technology and study design to construct the highest possible quality human pangenome reference. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve disease association studies across populations, expand the scope of genomic research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine. 

    The HPRC is poised to release another set of haplotypes before ASHG 2024. In addition to releasing these data, the HPRC is working across scientific communities to foster a new ecosystem of analysis tools. We aim to facilitate community engagement with the pangenome via outreach and education to create an expert user base of the pangenome reference to ensure that researchers are well-positioned to accelerate research. After completing the webinar, attendees will have learned how to access HPRC data and resources. They will be able to conduct variant analyses using the pangenome and they will be able to utilize tools for mapping functional genomics data, such as RNAseq and DNA methylation data, to the pangenome.

     Overview of Presentation:

    • Introduce participants to the pangenome project and its resources
    • Conduct Variant analysis using the pangenome
    • Provide instruction using alignment and analysis for functional genomics
    • Facilitate engagement with the pangenome and summarize the tools available to the community

    Heather Lawson, PhD

    Dr. Lawson received her PhD in Biological Anthropology from Penn State in 2008. She went on to do a postdoc with Dr. Jim Cheverud at Washington University where she focused on characterizing gene-by-environment interactions and parent-of-origin effects on metabolic traits in mice. She started her lab in 2015, using systems biology to elucidate the (epi)genetic architecture of complex traits. She is currently a member of the Human Pangenome Reference Consortium (HPRC), the Impact of Genomic Variation on Function Consortium (IGVF), and the Somatic Mosaicism across Human Tissues Network (SMaHT).

    Robert Fulton

    Mr. Fulton is an Assistant Professor of Genetics at Washington University School of Medical in St. Louis and the Director of Technology Development at the McDonnell Genome Institute (MGI). His role is to develop and deliver genomic solutions to a broad range of clinical and research questions based on his 30-plus years of experience in the generation of DNA sequence and analysis. Mr. Fulton holds bachelor’s (genetic engineering) and master’s degrees, both from Southern Illinois University, Edwardsville.

    Juan Macias-Velasco, PhD

    Dr. Juan F. Macias-Velasco is a postdoctoral research associate in the Department of Genetics at Washington University in St. Louis. He earned his B.S. in Biology from The University of Texas at Tyler, his M.S. in Biotechnology from The University of Texas Health Science Center at Tyler, and his Ph.D. in Computational and Systems Biology from Washington University in St. Louis. During his postdoctoral tenure in the lab of Dr. Ting Wang, Dr. Macias-Velasco has led the Collaborative and Integrative Genomics group at the McDonnell Genome Institute. He actively participates in the Human Pangenome Research Consortium and the Impact of Genomic Variation on Function Consortium, contributing to the development of pangenomic methods. Dr. Macias-Velasco’s work aims to enhance the understanding of the gene regulatory landscape and its implications for regenerative medicine. He has received recognition for his contributions to the field, including multiple presentations at national and international conferences, and has published extensively on topics related to functional genomics and systems biology.

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  • Contains 1 Component(s) Includes a Live Web Event on 07/24/2024 at 12:00 PM (EDT)

    This webinar will provide a typology of four novel service delivery models for genetics services and present real-world examples, providing attendees with an approach to analyzing and addressing the unmet need for genetics consultation in primary care at their own institutions.

    The supply of clinical genetics specialists (medical geneticists and genetic counselors) is insufficient to meet current demand for equitable genetic consultative services. To bridge the gap between primary care patients needing genetics consultation and the limited supply of specialists, health care organizations have implemented various alternative service delivery models. This webinar will provide a typology of novel service delivery models and present real-world examples of each: 1) a hub-and-spoke model in which a centralized “hub” offers specialty care to primary care and community “spokes”; 2) a train-the-PCP model, in which primary care providers receive the training and support needed for them to perform common genetic medicine services themselves; 3) a PCP extender model, in which new staff are added or existing staff trained to provide limited specialty care within primary care; and 4) a specialty integration model, in which specialists such as genetic counselors are integrated into a primary care practice. 

    After the presentations, a panel discussion with Q&A will allow speakers and audience members to discuss the relative advantages and limitations of each model and the factors organizational leaders should consider when selecting a model for their specific clinical context. As a result, this webinar will provide attendees with an approach to analyzing and addressing the unmet need for genetics consultation in primary care at their own institutions.

     

    Overview of Presentation:

    • Compare and contrast the characteristics of different genetics service delivery models in primary care
    • Identify key implementation strategies for different genetics service delivery models across diverse clinical contexts
    • List the resources and personnel required to implement different genetics service delivery models
    • Evaluate the impact of different genetics service delivery models on health disparities, access to care, and primary care provider genetics knowledge

    Jason Vassy, MD, MPH, MS

    Jason Vassy, MD, MPH, MS is an Associate Professor of Medicine at Harvard Medical School and clinician-investigator at the Veterans Affairs (VA) Boston Healthcare System. He is a practicing primary care internist and researcher in the implementation and evaluation of genomic medicine interventions. For the last decade, he has directed the Genomes2Veterans Research Program at VA Boston, where his research examines the clinical utility of genetic and genomic testing in various primary care clinical contexts, including clinical trials of pharmacogenetic testing, polygenic risk score testing, and return of unanticipated genetic results. 

    Kopika Kuhathaas, MS

    Kopika Kuhathaas is a Board Eligible Genetic Counselor. She holds a Master of Science in Genetic Counseling from the MGH Institute of Health Professions and a Bachelor of Science in Biology from the University of Waterloo. Kopika’s graduate thesis project examined clinicians' perspectives and their approaches to managing direct-to-consumer genetic testing in their practice. She has worked with a number of research programs, such as the Undiagnosed Diseases Network, where she contributed to various projects and provided compassionate support to participants with rare diseases and their families. Kopika is passionate about improving equitable access to genetic testing and services.

    Mylynda Massart, MD, PhD

    Mylynda B. Massart, MD, PhD, is a board-certified Family Medicine physician at UPMC, and associate professor at the University of Pittsburgh. She is the founder and Medical Director of the UPMC Primary Care Precision Medicine clinic, and as the Associate Director of Clinical Services for the Institute for Precision Medicine. Dr. Massart is a core director at the Clinical and Translational Science Institute (CSTI). Dr. Massart serves as one of the co-Investigators for the All of US Pennsylvania research project working on community education and engagement and as MPI of The Community Engagement Alliance Consultative Resource (CEACR).

    Pamela Ganschow, MD

    Dr. Pamela Ganschow is the Director of the Cancer Prevention and Survivorship program at the University of Illinois Cancer Center in Chicago transitioning to her position there in March of 2021 after 23 years on faculty at Cook County Health. She is an oncogeneralist who trained in internal medicine at Northwestern University and now focuses her clinical care and research primarily on cancer along the continuum of care from prevention and screening through survivorship. She has dedicated her professional life to work in cancer control research and education, building innovative programs that enable equitable, high-quality access to cancer screening and prevention services for underserved populations with a recent focus on embedding cancer survivorship and cancer genetic services into the primary care space.

    Adam Buchanan, MS, MPH

    Adam Buchanan is Associate Professor and Chair of the Geisinger Department of Genomic Health, an NIH-funded investigator, and board-certified and licensed genetic counselor with 20 years of research experience in assessing genetic counseling outcomes and risk management behaviors. He has clinical expertise in genetic counseling among, and genomic screening for, individuals at increased risk of hereditary cancer, inherited cardiovascular disease and other genetic conditions. Further, he is a master’s trained behavioral scientist and has completed mentored training in implementation science methodology at the National Cancer Institute. Mr. Buchanan is on the leadership group of the MyCode Genomic Screening and Counseling program, which conducts population screening for clinically actionable genetic disease risk.

    Leland E. Hull, MD, MPH

    Dr. Hull is an Assistant Professor of Medicine at Havard Medical School and clinician-investigator in the Division of General Internal Medicine at the Massachusetts General Hospital (MGH).  Her research focuses on designing, implementing, and testing approaches to bring genomic medicine to the front lines of clinical care to improve disease risk prediction and personalize clinical decision-making.  Clinically, she is a practicing primary care physician and also serves as Clinical Director of the MGH Preventive Genetic Counseling Service, which offers expedited genetic counseling for common guideline-concordant preventive genetics questions (e.g. obtaining breast cancer susceptibility testing, arranging for preconception carrier screening). 

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  • Contains 3 Product(s)

    This webinar series will describe responsible and meaningful community engagement approaches across the research lifecycle, in a manner that addresses health inequalities, avoids potential harms, builds trustworthy relationships, and increases the representation of underrepresented communities in genetics and genomics research.

    This webinar series will describe responsible and meaningful community engagement approaches across the research lifecycle, in a manner that addresses health inequalities, avoids potential harms, builds trustworthy relationships, and increases the representation of underrepresented communities in genetics and genomics research.

     

    Learning Objectives

    • To identify potential challenges and opportunities of community engagement practices.
    • To learn, through current scenario-based illustrations, how to effectively identify and design trust-building community engagement methods and practices.
    • To identify and learn how to integrate ethical, legal, and social implications (ELSI) frameworks into community engagement methods and practices.

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    Join us for a one hour introductory bioinformatics webinar to the GA4GH VRS standard, led by the specification maintainers.

    The Variation Representation Specification (VRS) is a nascent standard of the Global Alliance for Genomics and Health (GA4GH) Genomic Knowledge Standards Work Stream, developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories. VRS provides an extensible framework for standardizing the computable representation of biomolecular variation across complex data types and variant information in sequence variant knowledgebases, complementing contemporary human-readable (e.g. HGVS) and flat file (VCF) standards. 

    Join us for a one hour introductory bioinformatics webinar to the GA4GH VRS standard, led by the specification maintainers. The webinar will begin with an introductory overview of the features of VRS and its use in computational exchange of variant annotation and interpretation data. We will introduce you to open-source and online tools for generating and validating VRS variants, and work through interactive exercises demonstrating the use of VRS for small variants (e.g. SNVs and InDels), as well as complex variation such as haplotypes, genomic rearrangements, and copy number variants. The second half of the webinar will provide an overview of VRS as used for genomic evidence from databases such as gnomAD v4, MaveDB, ClinVar, and CIViC to computationally describe variant evidence for use in variant interpretation workflows. We will use VRS to find and collate data from these databases.

    Overview of Presentation:

    • Learn how to use the GA4GH Variation Representation Specification (VRS)
    • Describe variants with VRS using open-source community tools
    • Search genomic evidence resources using VRS
    • Collate genomic knowledge using VRS

    Alex Wagner, PhD

    Principal Investigator

    The Steve and Cindy Rasmussen Institute for Genomic Medicine (IGM) at Nationwide Children’s Hospital

    Dr. Wagner is a Principal Investigator at The Steve and Cindy Rasmussen Institute for Genomic Medicine (IGM) at Nationwide Children’s Hospital. He analyzed the content of multiple public knowledgebases of the Variant Interpretation for Cancer Consortium (VICC) and demonstrated the need for data standards and supporting tools for genomic knowledge sharing and reuse. From this work, he took on the development and application of genomic knowledge standards under the auspices of the Global Alliance for Genomics and Health (GA4GH). In 2021, Dr. Wagner was recognized by the National Human Genome Research Institute (NHGRI) as an NHGRI Genomic Innovator for his work in this area. He currently holds leadership and/or invited positions in multiple national and international consortia, including GA4GH, the NIH Bridge2AI program, the HGVS Variant Nomenclature Committee, and the Variant Interpretation for Cancer Consortium (VICC).

    Lawrence Babb

    Senior Principal Software Engineer

    Broad Institute of MIT and Harvard

    Since August 2018, Mr. Babb has served as a Senior Principal Software Engineer at the Broad Institute of MIT and Harvard. The last 20 years of his 40-year software engineering career has centered on creating software tools and interoperable data standards to enhance genetic testing in clinical settings. Mr. Babb specializes in data modeling and standards development, particularly in applying genomic knowledge to test results. Mr. Babb co-leads the GA4GH Genomic Knowledge Standards and the ClinGen Data Platform Workgroup, promoting open-data sharing in genomics. Additionally, Mr. Babb manages software teams for ClinGen and the Translational Genomics Group at Broad.

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    Dr. Appelbaum will discuss findings from a series of focus groups with patients, clinicians, and IRB members on return of polygenic risk scores in research. Despite strong interest in such results, they found multiple barriers to their effective use to improve health.

    Dr. Appelbaum will discuss findings from a series of focus groups with patients, clinicians, and IRB members on return of polygenic risk scores in research. Despite strong interest in such results, they found multiple barriers to their effective use to improve health. 

    Overview of Presentation

    • We conducted online focus groups, as part of the eMERGE-IV study, with patients/community members, clinicians, and IRB members to explore their views on return of polygenic risk scores (PRS) for common disorders.
    • Across stakeholder groups, there was strong interest in having PRS results returned to research participants.
    • However, there were significant differences in stakeholders’ views about resources needed for PRS data to translate into improved participant health. 
    • Issues identified included researcher-participant communication, health and genomic literacy, and a range of structural barriers such as financial instability, insurance coverage, and the absence of health-supporting infrastructure in poorer neighborhoods. 
    • The promotion of equity in genomic research and clinical applications will require measures to facilitate effective use of PRS and other genomic data in the real world.

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    Paul S. Appelbaum, MD

    Dollard Professor of Psychiatry, Medicine & Law

    Columbia University

    Paul S. Appelbaum, M.D. is the Elizabeth K. Dollard Professor of Psychiatry, Medicine, and Law, and Director, Center for Law, Ethics, and Psychiatry, Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University. For 13 years, he directed Columbia’s NHGRI-funded Center of Excellence in ELSI Research. His recent research has focused on the ethical and psychosocial impact of advances in genetics. Dr. Appelbaum is a Past President of the American Psychiatric Association and the American Academy of Psychiatry and the Law, now chairs the APA’s DSM Steering Committee, and is a member (and former chair) of the Standing Committee on Ethics of the World Psychiatric Association. He has been elected to the National Academy of Medicine. Dr. Appelbaum is a graduate of Columbia College, received his M.D. from Harvard Medical School, and completed his psychiatry residency at the Massachusetts Mental Health Center/Harvard Medical School.

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    Season 3, Voices in Genomics, with Michelle Takemoto, MS, CGC.

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