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  • Contains 1 Component(s) Includes a Live Web Event on 06/01/2022 at 12:00 PM (EDT)

    Alexandre Bolze will discuss their recent HGGA paper.

    Alexandre Bolze, PhD, will discuss their study to identify genetic factors that help explain interindividual differences in reactions following COVID-19 vaccination. Results of the study show that the HLA-A*03:01 allele was associated with more side effects following vaccination with Pfizer-BioNTech BNT162b2 vaccine. The study of the genetics of response and of reactions to different vaccines could be used to better understand the immune response following vaccination and improve future vaccine design.

    Overview of Presentation

    • Vaccination side effects and other COVID-related phenotypes were collected by online surveys sent to individuals in the United States previously sequenced, including participants in the Healthy Nevada Project.
    • A minority of individuals have severe difficulties with daily routine following COVID-19 vaccination. Replication of known risk factors: younger age, female sex and a personal history of COVID-19 prior to vaccination.
    • GWAS identifies HLA region associated with strong side effects after COVID-19 vaccination.
    • HLA-A*03:01 association is specific to vaccine type.
    • Analysis of four local and 20 systemic symptoms showed that HLA-A*03:01 was most strongly associated with increased risk of fever and chills after receiving the vaccine.

    Alexandre Bolze, PhD

    Senior Staff Scientist

    Helix

    Dr. Alexandre Bolze is a senior staff scientist at Helix. He did his Ph.D. at the Rockefeller University in New York, in the laboratory of Human Genetics of Infectious Diseases, and completed a postdoctoral fellowship at the University of California San Francisco. During his training, he discovered the genetic cause of Isolated Congenital Asplenia, a condition where patients are born without a spleen and are predisposed to life-threatening bacterial infections. At Helix, Alexandre studied the impact of rare and common variants in different diseases including mitochondrial disorders, maturity-onset diabetes of the young and hereditary cancer. His interest in genomic medicine and infectious diseases led to his current work to identify genetic factors involved in differences in immune response following vaccination, as well as differences in common side effects or rare adverse events following vaccination.

     

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    Human genetics and genomics drives discovery and new applications across all facets of research, medicine, and society.

    Human genetics and genomics drives discovery and new applications across all facets of research, medicine, and society. How do you discuss these advancements with your neighbors, community, or general public? This webinar provides experiences, lessons, and best practices from your peers to support ASHG members who want to begin or supplement discussions with the public to translate their research. 

    • Identify common obstacles when sharing research with public audiences  
    • Provide resources to navigate obstacles when talking to the public
    • Connect this work with the benefits to both you as a scientist and the public 

    Michael Anton Bauer, PhD

    Bioinformatician, Assistant Professor

    Department of Biomedical Informatics at the University of Arkansas for Medical Sciences

    Michael Bauer is an assistant professor in the Department of Biomedical Informatics at the University of Arkansas for Medical Sciences. He obtained duel bachelor of science degrees in computer science and biology at New Mexico Institute of Mining and Technology. He then went to the University of Arkansas Little Rock and obtained his Masters and PhD in Bioinformatics. He specializes in the use of extremely large heterogeneous datasets, coined as Big Data. His work focuses specifically on furthering the understanding of cancer biology with the inclusion of multiple types of molecular data. These data types include epigenetic information, whole genome and RNA sequencing and combining these genomic modalities to get a more complete picture of the cancer biology. Recent work has involved investigating the largely unexplored process of alternative splicing of mRNA and long noncoding RNA and their role in Multiple Myeloma. In addition to research, he feels that it is important include public outreach and public education as part of his activities. An informed public about cancer genetics and genetics in general can better advocate for their own health and request cutting edge diagnostic tests and treatment. He believes this is one way to combat health disparities. In his free time, he is playing his 21st season of rugby for the Little Rock Rugby Club.

    Arvind Kothandaraman, MBS

    Managing Director, Specialty Diagnostics

    PerkinElmer. Inc.

    Arvind Kothandaraman is the Managing Director of Specialty Diagnostics at PerkinElmer. His primary interest is in equipping clinical laboratories with the tools needed to meet their technical and operational goals. Prior to PerkinElmer, Arvind held positions at Thermo Fisher Scientific, BioReference Laboratories and Advanced Analytical Technologies. Arvind holds a Master’s degree in Science and Business from the Claremont Colleges in California, USA.

    Kenneth Ramos, MD, PhD (Moderator)

    Professor of Translational Medical Sciences Alkek Chair of Medical Genetics Executive Director

    Institute of Biosciences and Technology Associate Vice President for Research Assistant Vice Chancellor for Health Services, Texas A&M University System

    Kenneth S. Ramos, MD, PhD is an accomplished physician-scientist with designations in the National Academy of Medicine and National Academy of Sciences. He is a transformational leader recognized throughout the world for his scientific contributions in the areas of genomics, precision medicine and toxicology.

    With formal training in pharmaceutical sciences, chemistry, biochemistry, pharmacology, and medicine, Dr. Ramos is helping to steer the changing landscape of medicine, biotechnology and healthcare. In this context, he leads several translational, clinical research, and educational programs that integrate diverse approaches to elucidate genomic mechanisms of disease and to develop novel therapies for several oncologic, pulmonary, and vascular diseases.
    Dr. Ramos has provided academic, executive, administrative, and scientific leadership in the areas of genetics and genomic medicine and toxicology at various academic institutions and over the course of his career has positively influenced the career of numerous clinicians and scientists engaged in medical, veterinary and pharmaceutical practice. He is deeply committed to initiatives that advance modern technological applications to improve quality of healthcare and reduce disease burden and health-associated costs.

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    Chiara Auwerx discusses their recent AJHG paper.

    Chiara Auwerx will discuss the role of individual CNVs and the total CNV burden on modulating over 50 medically relevant complex trait in the UK Biobank. Results of the study expose the pleiotropy and polygenicity of CNVs and highlight the complex and nuanced role of this mutational class at odds with the classical dichotomy between common diseases and Mendelian disorders.

    Overview

    • Call CNVs from genotyping microarray data in the UK Biobank.
    • Perform CNV-GWAS between the copy number state of CNV-proxy probes and 57 medically relevant complex traits.
    • Identify 131 independent CNV-trait associations across 47 phenotypes.
    • CNVs signals colocalize with SNP-GWAS signals and Mendelian disorder loci.
    • Total CNV burden negatively impacts health, socio-economic status, and longevity.
    • Data suggest a polygenic CNV architecture for many assessed traits.


    Chiara Auwerx, MS

    PhD candidate

    University of Lausanne

    Chiara Auwerx obtained a Bachelor (2017) and Master (2019) degree in biology from the Eidgenössische Technische Hochschule (ETH) Zürich (CH). She completed her Master thesis in Prof. Coleen Murphy’s group at Princeton University (US), where she investigated the effect on short-term memory of the loss-of-function of novel Alzheimer’s disease candidate genes in C. elegans. In 2020, she started a PhD in human statistical genetics under the supervision of Profs. Zoltán Kutalik and Alexandre Reymond at the University of Lausanne (CH). She has since been investigating the role of copy-number variants in shaping complex traits and common diseases in the general population. In 2021 she was awarded the Young Investigator Award (Lodewijk Sandkuijl) for the best talk in complex disease genetics and statistical genetics at the European Society of Human Genetics Conference. 

    Alexandre Reymond, PhD

    Director

    Center of Integrative Genomics, University of Lausanne

    Alexandre Reymond carried out his thesis in the laboratory of Dr. Viesturs Simanis at the Swiss Institute for Experimental Cancer Research (ISREC) and received his Ph.D. from the University of Lausanne in 1993. After completion of his postdoctoral training with Dr Roger Brent in the Department of Molecular Biology, Massachusetts General Hospital and in the Department of Genetics, Harvard Medical School in Boston, he moved to the Telethon Institute of Genetics and Medicine (TIGEM) in Milan in 1998 to lead a research group. He joined in 2000 the Department of Genetic Medicine and Development, University of Geneva Medical School. He moved to the Center for Integrative Genomics in October 2004 and became its Director in 2015. He is the Vice-President of the European Society of Human Genetics and the Chair of its Scientific Program Committee.

    Zoltán Kutalik, PhD

    Principal investigator

    Statistical Genetics Group, University of Lausanne

    Zoltán Kutalik is a statistical geneticist, associate professor at the University of Lausanne, heading the Statistical Genetics Group. His main research interest lies in developing statistical methods integrating various omics data in order to better understand the genetic architecture of complex human diseases. He is a council member of the Swiss Institute of Bioinformatics (SIB), scientific programme committee member of the ESHG, EMGM, BC2, ISCB conferences and evaluation committee member of the Swiss National Science Foundation (SNSF). Zoltan is on the advisory board of the LongITools EU project, science council member of the Health 2030 Genome Center, an editorial board member of PLoS Genetics, Human Molecular Genetics and EJHG. He won the Early Career Bioinformatician Award of the SIB, the Investigator-in-training award of the University of Lausanne and shared the Leenaards Prize. He published over 180 peer-reviewed articles (>40,000 citations, h-index >80) in international scientific journals. 

    Bruce Korf, MD, PhD (Moderator)

    Editor-in-Chief

    American Journal of Human Genetics

    Chief Genomics Officer, UAB Medicine 
    Wayne H. and Sara Crews Finley Endowed Chair in Medical Genetics UAB

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    Laura Schultz, PhD, discusses their recent HGGA paper.

    Laura Schultz, PhD, will discuss the surprising lack of consistency between polygenic scores (PGS) computed from subsequent generations of consortia-produced discovery GWAS for height, post-traumatic stress disorder, and type-2 diabetes.  For a given trait, PGS are only modestly correlated at the level of the individual subject, and different individuals are identified at the upper quantiles of the PGS distributions.

    Overview of Presentation

    • PGS calculated from pairs of same-ancestry discovery GWAS show only modest correlation with each other despite there being near-perfect genetic correlation between the discovery GWAS.
    • A series of height GWAS in the UK Biobank suggests that correlation between PGS is strongly dependent on the extent of sample overlap between the discovery GWAS.
    • Focusing on the upper tail of the PGS distribution, different discovery GWAS do not consistently identify the same individuals.  The degree of overlap decreases sharply as higher quantiles, less heritable traits, and different-ancestry GWAS are considered.
    • PGS computed from different discovery GWAS have only modest correlation at the individual level, underscoring the need to proceed cautiously with integrating PGS into precision medicine applications.

    Laura Schultz

    Data Scientist

    Department of Biomedical and Health Informatics at the Children's Hospital of Philadelphia (CHOP)

    Dr. Laura Schultz is a Data Scientist in the Department of Biomedical and Health Informatics at the Children's Hospital of Philadelphia (CHOP) who is also affiliated with the Lifespan Brain Institute (LiBI) at CHOP and the University of Pennsylvania. She earned her A.B. in psychobiology from Ripon College and her Ph.D. in psychology and neuroscience from Princeton University, and she completed a postdoctoral fellowship in computational neurobiology at the Salk Institute for Biological Studies.  After a previous career teaching statistics at Rowan University, she earned an M.S. in Analytics from the Georgia Institute of Technology and joined Laura Almasy's statistical genetics research group.  In addition to contributing statistical computing expertise to a wide range of collaborative projects at CHOP, LiBI, and beyond, she is interested in developing new methods for analyzing genomic data.

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    This webinar, the first in a series, will explore high-level approaches to finding work-life balance with ASHG member experts and a full-time career coach.

    COVID-19 has disrupted scientific workplaces and the way in which we work. With return-to-work efforts ramping up, what does work-life balance look like now? 

    This webinar, the first in a series, will explore high-level approaches to finding work-life balance with ASHG member experts and a full-time career coach. 

    Future webinars in the series will take a deep dive into specific work-life balance topics like parenting, networking, career choices, and remote working, based on what attendees’ say they want to hear about the most. Join us as we explore the necessary art of balancing your science with your personal life in this new age of work. 

    This webinar series is available to current ASHG members only. Please join or renew your membership today to register for the event.

    Jim Gould, PhD

    Director of the Office for Postdoctoral Fellows

    Harvard Medical School

    Dr. Gould is the Director of the Office for Postdoctoral Fellows as well as the Program Director for the Responsible Conduct of Research course at Harvard Medical School. He has been implementing research, career, and professional development programs and policies for HMS trainees since 2011. He has spoken and published on career and professional development topics in a variety of forums, locally and nationally, including articles covering CV to resume conversion, interviewing strategies, and manuscript writing. Prior to HMS, Dr. Gould completed two postdoctoral fellowships at the National Cancer Institute of the National Institutes of Health where he chaired the Fellows & Young Investigators Association.

    Marylyn Ritchie, PhD, FACMI

    Professor of Genetics and Director of the Institute for Biomedical Informatics

    University of Pennsylvania School of Medicine

    Dr. Marylyn D. Ritchie is a Professor of Genetics and Director of the Institute for Biomedical Informatics at the University of Pennsylvania School of Medicine. She is also Associate Director of the Penn Center for Precision Medicine, Director of the Center for Translational Bioinformatics, and Co-Director of the Penn Medicine BioBank.  Dr. Ritchie is an expert in translational bioinformatics, with a focus on developing, applying, and disseminating algorithms, methods, and tools integrating electronic health records (EHR) with genomics. Dr. Ritchie was appointed as a Fellow of the American College of Medical Informatics (ACMI) in 2020 and was elected as a member of the National Academy of Medicine in 2021. She is also the host of two podcasts: she co-hosts The Biomedical Informatics Roundtable podcast with Dr. Jason Moore and she is the solo host of The CALM Podcast: Combining Academia and Life with Marylyn.  

    Nadya Ali, MD

    Manager, Global Medical Information

    Seagen Inc.

    Dr. Nadya Ali is a Global Medical Information Manager and lead for a recently approved cervical cancer antibody-drug conjugate drug at Seagen, Inc., a biopharmaceutical company. Previously, she collaborated with Dr. Latrice Landry on a population-based research project focused on exposing racial disparities in biomarkers for diseases in early and late phase immunotherapy clinical trials. As the 2016/2017 United States Surgeon General David E. Satcher, M.D., Ph.D. Research Fellow, Dr. Ali analyzed two nationally used genomic catalogues to assess the goals of President Barak Obama’s Cancer Moonshot Initiative. Additionally, she completed research at the Harvard Medical School Center for Biomedical Informatics, Laboratory for Personalized Medicine, and evaluated the accuracy of a breast risk prediction model supported by the National Cancer Institute, on a simulated US patient population. 

    Lucia Hindorff, PhD, MPH (Moderator)

    Lead Extramural Training Program Director

    NHGRI

    Dr. Lucia Hindorff is the extramural lead for training programs in the Office of Training, Diversity and Health Equity (TiDHE) at NHGRI. Previously, she led NHGRI programs at the intersection of diversity and genomic medicine, including the Clinical Sequencing Evidence-Generating Research (CSER) program, the Population Architecture using Genomics and Epidemiology (PAGE) program, the online NHGRI-EBI GWAS Catalog, and the Polygenic Methods in Diverse Populations (PRIMED) consortium. She has authored or co-authored over 100 publications and enjoys working with trainees and experienced investigators alike. In addition to her extramural portfolio, Dr. Hindorff is broadly interested in characterizing and improving health information disparities and in coaching to build strong and diverse teams. She is a member of the ASHG Career Development Committee and co-hosts its Trainee Paper Spotlight podcast.

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    Dr. Roger Reeves discusses their recent AJHG paper.

    This month's presentation is on the recent AJHG paper, “A transchromosomic rat model with human chromosome 21 shows robust Down syndrome features." Attendees will have the opportunity to ask questions in a live Q&A session. 

    Overview of Presentation

    • Trisomy 21 is among the most complex genetic challenges to development and function
    • Animal models are essential to understanding mechanisms underlying divergent features
    • New models provide improved genetic representation and expand opportunities for preclinical studies

    To read the full paper, check the Journal Paper tab.

    Roger H. Reeves, PhD

    Professor Emeritus

    Johns Hopkins University School of Medicine

    Dr. Roger Reeves is Professor Emeritus in the Department of Physiology and the McKusick-Nathans Department of Genetic Medicine at the Johns Hopkins University School of Medicine. He earned his B.S. from Bowling Green State University in Ohio and his Ph.D. at University of Maryland, doing his thesis research at the National Cancer Institute. He is noted for his contributions to development of animal models to understand pathogenesis and variable expression of Down syndrome features. His lab demonstrated a biological basis for the reduced frequency of solid tumors in people with trisomy 21; provided direct evidence disproving a “critical region” for Down syndrome; and established a reduced response to effects of the SHH growth factor as a major contributor to several features of Down syndrome. Patient-based studies uncovered genetic modifiers predisposing to congenital heart disease in DS and in the population at large, and support for the development of a Cognitive Test Battery that can be used to monitor effectiveness of drugs designed to ameliorate cognitive dysfunction specific to people who have trisomy 21. Recognition for his efforts includes the Int’l. Sisley Lejeune prize for research in intellectual disabilities.

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    Dr. Genevieve Wojcik will discuss the role of social determinants of health in genetic epidemiology.

    Dr. Genevieve Wojcik will discuss the role of social determinants of health in genetic epidemiology, specifically the need for careful consideration from study design to interpretation. She will present two vignettes to illustrate: (1) a study of enteric infections in Bangladeshi infants, which required homogeneity of SDOH to better isolate genetic effects, and (2) the role of heterogeneity within Hispanic/Latino populations and how this can influence our estimates of genetic risk. Together, these vignettes will show how both homogeneity and heterogeneity in SDOH can influence genetic studies of human health.

    Overview of Presentation

    • Human genetics are part of a complex system contributing to health.
    • This system includes both individual-level and structural contributors.
    • These structural influences can introduce heterogeneity both within and between populations.
    • Genetic studies must consider societal contexts in order to appropriately account for these contributions in analyses and ensure appropriate interpretations of results.

    Dr. Genevieve Wojcik

    Genetic Epidemiologist and Assistant Professor of Epidemiology

    Johns Hopkins Bloomberg School of Public Health

    Dr. Genevieve Wojcik is a genetic epidemiologist and Assistant Professor of Epidemiology at the Johns Hopkins Bloomberg School of Public Health. She obtained her BA in Biology from Cornell University, followed by an MHS in Human Genetics/Genetic Epidemiology and a PhD in Epidemiology from the Johns Hopkins Bloomberg School of Public Health. Dr. Wojcik then conducted her postdoctoral training at Stanford University in the Departments of Genetics and Biomedical Data Science. Her research program focuses on two major areas: (1) investigating the role of human genetics in infection and vaccine response, and (2) understanding the role of ancestry in genetic risk and developing solutions to address health inequities for diverse and admixed populations. Dr. Wojcik is involved in multiple NHGRI consortia, most notably the Population Architecture using Genomics and Epidemiology (PAGE) Study and the Clinical Genome Resource (ClinGen).

    Anne Slavotinek, MD, PhD, FRACP, FACMG (Moderator)

    Professor of Clinical Pediatrics

    UCSF

    Dr. Slavotinek is certified in Clinical Genetics and has worked as a Medical Geneticist at UCSF since 2002, specializing in dysmorphology and clinical genomics. She received her medical degree from the University of Adelaide and her Ph.D from Flinders University whilst studying in Edinburgh at the MRC Human Genetics Unit. She trained in Clinical Genetics in the U.K. and then did a postdoctoral Fellowship and a Genetics Fellowship at the National Institutes of Health. She has participated in leadership activities at the American College of Medical Genetics and Genomics and is currently Chair of the American Board of Medical Genetics and Genomics. Dr. Slavotinek is a Co-Editor in Chief for the American Journal of Medical Genetics and an author on more than 200 peer-reviewed publications. She is a Principal Investigator for the Program in Prenatal and Pediatric genomic sequencing grant at UCSF that is part of the Clinical Sequencing Evidence Generating Research (CSER) consortium and directs a laboratory that uses next-generation sequencing technologies and zebrafish as an animal model system to study the etiology of developmental eye defects and multiple congenital anomaly syndromes.

    Chris Gunter, PhD (Moderator)

    Senior Advisor to the Director for Genomics Engagement

    National Human Genome Research Institute, NIH

    Dr. Chris Gunter is the Senior Advisor for Genomics Engagement at the National Human Genome Research Institute, and the head of the Engagement Methods Unit in the Social Behavioral Research Branch. She earned her Ph.D. in human genetics at Emory University and then completed postdoctoral work at Case Western Reserve University. Following that, she worked in editorial positions for Human Molecular Genetics, Science, and Nature, and currently has editorial positions at the preprint server bioRxiv and the journal CSHL Molecular Case Studies. Her work has two major foci: scientific studies on autism genetics, and development and measurement of science communication methods.

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    Dr. Hannah Polikowsky discusses their recent HGGA paper.

    This month's presentation is on the recent HGGA paper, “Population-based genetic effects for developmental stuttering." Attendees will have the opportunity to ask questions in a live Q&A session. 

    During this webinar, attendees will: 

    • Analyze population-scale genetic susceptibility for developmental stuttering
    • Discuss potential functional implications of genetic associations with developmental stuttering
    • Learn about the complex genetic factors impacting stuttering risk in populations

    To read the full paper, check the Journal Paper tab.

    Developmental stuttering is best explained by listening to and observing the trait. The webinar speakers recommend viewing this video of the phenotype to prepare before the event.

    Please note, if the hyperlink above does not take you to a page with a video, please copy and paste this link into your browser: 

    https://sla.talkbank.org/TBB/fluency/Voices-AWS/interview/24fa.cha

    Hannah Polikowsky

    PhD candidate

    Vanderbilt University

    Hannah Polikowsky is a PhD candidate at Vanderbilt University in the Human Genetics department. Her current research involves population and familial-based analyses of speech and language traits with ongoing investigations into the full genetic architecture of developmental stuttering. Prior to graduate school, Ms. Polikowsky launched a data analysis services division within a software-as-a-service company to provide scientists globally with tools and processes for drug discovery and clinical data analyses.  Today, Ms. Polikowsky continues to develop and implement analysis pipelines, which leverage high-parameter datasets and machine-learning tools, as a tactic to improve our understanding of human traits and ultimately, give rise to the equitable treatment of everyone. 

    Jennifer E. Below, PhD

    Principal Investigator of Below Lab

    Vanderbilt University Medical Center

    Dr. Jennifer "Piper" Below, PhD is an associate professor of medicine at Vanderbilt University Medical Center. Her lab works to understand the genetic basis of human disease, with a focus on bringing computation to unmet needs. One focus of the lab is understudied speech and language traits, with ongoing research projects investigating genetic susceptibility factors in developmental stuttering, developmental language disorder, and prosody. Her team has leveraged data within Vanderbilt University Medical Center’s electronic health records and the linked DNA databank, BioVU to characterize comorbidities of these traits phenome-wide and build machine learning-based models for imputing speech and language traits in the health record, where they are significantly underreported. She has partnered with institutions across the world to collect biospecimens from people with clinically characterized speech and language disorders for genetic analysis, as well as with the direct-to-consumer genomics company, 23andMe, who have provided results of genetic analyses on >100k self-reported stuttering cases and >1M controls including analyses in Hispanics and Latinos and Caucasian, African, and Asian ancestry groups. Collectively these data have allowed her to investigate the genetic architecture of speech and language traits across global populations and make discoveries about the genetic etiology of speech and language in Humans.

    Douglas Shaw

    PhD Candidate

    Vanderbilt University

    Douglas Shaw is a graduate student working with Dr. Below at the Vanderbilt Genetic Institute. Doug’s research primarily focuses on phenotypic and genotypic risk modeling to better understand the biological etiology of speech and language traits, specifically developmental stuttering. Doug utilizes statistical modeling to develop machine-learning phenotyping algorithms to drive genetic discovery in large electronic health records linked to genetic biobanks and better understand the constellation of comorbidities associated with various language traits. These genotype risk models have also served to identify and better understand the common genetic etiologies that exist between stuttering and other commonly observed co-occurring neuropsychiatric and behavioral clinical phenotypes.

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    The Genome Browser is a valuable tool at all levels of genetics education and research, but this is not an introductory workshop. It is designed to show users who have at least a working familiarity with the Browser new features likely not seen before.

    The UCSC Genome Browser has been a workhorse providing data and visualization for genetics research and clinical professionals for more than 20 years.  The Browser continues to grow and add new features, and even experienced users frequently disclose that they have missed important innovations.  The proposed workshop will feature some of the newest Browser offerings.

     We have recently revised our presentations of data important to the interpretation of variants in the clinical context.  Working with ClinVar, ClinGen, gnomAD and others, we now make the details of items displayed in the Browser more available via mouseover in the main Browser graphic.  In this way, multiple variants in a region can be investigated more quickly, without a required click-through. 

     We have also implemented a new feature called "Recommended Track Sets" -- one each for copy-number variants and single nucleotide variants.  Using this feature, users may, from any location in the genome, launch a pre-configured session with important data automatically displayed.

     A new data type has been introduced to aid in the display of ClinVar SNV variants with phenotypes in the five clinical classes (pathogenic > benign), simultaneously showing the variant classes and the number of reports of the variant in each class.

     We also now display a data track of exon-capture kits from various manufacturers. This allows users to evaluate the coverage of the genome both when choosing kits for use and to assist in the interpretation of whole exome sequencing experiments.  

     We will also briefly present our coronavirus resources, both as GWAS data on the genome and viral genome data.

     Participants should have experience with the Genome Browser and are encouraged to follow along with the presentation on a separate device.  Attendees with limited experience with the Browser should view the video tutorials at http://bit.ly/ucscBasics before attending. 


    Robert Kuhn, PhD

    Associate Director

    UC Santa Cruz

    Robert Kuhn received his PhD at the University of California, Santa Barbara in Biochemistry and Molecular Biology, where he studied the centromeres of yeast. Following a postdoctoral at UC Berkeley/USDA Plant Gene Expression Center, he taught biochemistry, molecular biology and genetics at UC Santa Cruz.  He joined the UCSC Genome Browser project in 2003, where he is now Associate Director, with a particular interest in clinical genetics.  The Genome Browser is a widely used visualization tool giving access to the genomes of human and more than one hundred other animals.  Dr. Kuhn's responsibilities include identifying important datasets for inclusion into the Browser, enabling researchers through teaching the Genome Browser in workshops and seminars and learning from them how to improve the Browser.

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    This workshop is ideal scientists who would like to find and use tools in the cloud for genomic analysis. Researchers interested in NHGRI data, such as the Human Pangenome Project, are especially encouraged to attend. Basic knowledge of Python or R is recommended but not required.

    Cloud-based analysis of genomic datasets is increasingly vital for portability, reproducibility, and multi-institution collaboration, but transitioning to the cloud can be daunting. We will offer a workshop that will serve to eliminate some of the barriers to the adoption of these tools. Specifically, we will teach researchers how to access and utilize The Analysis, Visualization, and Informatic Lab-space (AnVIL), an environment that provides access to hosted data, reproducible tools, and collaborative workspaces, and comprehensive documentation to enable users to conduct research in the cloud. This workshop will demonstrate how to access and explore data in AnVIL. Participants will also learn to search for analysis tools in Dockstore, a platform for sharing portable, container-based tools and workflows written to be interoperable across local and cloud environments. Finally, they will analyze data in a Terra workspace, which is a dedicated space where researchers can access and organize the same data and tools and run analyses.

     

    This workshop will specifically explore and demonstrate open-access data from the Human Pangenome Reference Consortium (HPRC), an NHGRI funded effort to create a more diverse and comprehensive reference human pangenome. We will present the data and methods produced and utilized within the first year of this project, which ultimately aims to release the assembly of high-quality diploid genomes from >350 ethnically diverse individuals across five years. Currently, raw data and assemblies from 45 individuals and associated Docker-based analysis workflows written in the Workflow Description Language (WDL) are available in the AnVIL for researchers to explore and utilize. Data and workflows will continue to be publicly released as early as possible to promote open science. These data make an excellent substrate for interaction with these data types and new workspaces and methods.

     

    Using data and workflows from the HPRC, participants of this workshop will follow along with instructors to learn how to:

     

    1. Register for a Terra account and set up a project using $300 in free Google Cloud credits
    2. Set up a collaborative cloud workspace in Terra
    3. Access and explore Human Pangenome Data hosted by AnVIL
    4. Search for bioinformatics workflows in Dockstore and export them to a Terra workspace
    5. Configure and launch a Docker-based WDL workflow to conduct a parallel analysis
    6. Monitor cloud costs associated with an analysis

     

    After completing the workshop, attendees will be able to leverage AnVIL to analyze hosted datasets and launch analyses that are reproducible and scalable. Attendees will also be familiar with Human Pangenome data and resources.

    Julian Lucas

    Senior Bioinformatics Systems Analyst

    University of California, Santa Cruz

    Julian Lucas is a Senior Bioinformatics Systems Analyst in the Computational Genomics Platform at the UC Santa Cruz Genomics Institute. He leads the data coordination for the Human Pangenome Reference Consortium (HPRC) and utilizes the NHGRI AnVIL cloud compute platform for sharing data and analysis methods for this open-access project with the research community.

    Beth Sheets, MS

    Program Manager, Computational Genomics Platform

    University of California, Santa Cruz

    Beth Sheets is a Program Manager for the Computational Genomics Platform at the UC Santa Cruz Genomics Institute. She currently works with two NIH initiatives, NHLBI BioData Catalyst and NHGRI AnVIL, which are bringing researchers to secure, collaborative, cloud-based workspaces that offer petabyes of hosted data and hundreds of scientific tools. She works with a collaborative team that builds Dockstore.org, the scientific tool-sharing repository for these two NIH initiatives, which providers researchers with features and training to publish their bioinformatics pipelines using FAIR (Findable, Accessible, Interoperable, Reusable) standards.

    Trevor Pesout

    PhD Candidate

    University of California, Santa Cruz

    Trevor is a Ph.D. Candidate in the Computational Genomics Lab at the UCSC Genomics Institute.  His work revolves around the use of third-generation long reads for phasing, polishing, and haplotyping.  He has developed many of the Quality Control workflows for the HPRC assembly group. His contributions are available in the Human Pangenome Reference Consortium organization on Dockstore for the community to reuse in the AnVIL cloud ecosystem.

    Mobin Asri

    PhD Candidate

    University of California, Santa Cruz

    Mobin is a PhD Candidate in the Computational Genomics Lab at the UCSC Genomics Institute. He works on comparative genomics and developing tools for evaluating diploid assemblies. He has developed the assembly workflow and read-based QC workflows for the HPRC assembly group. His contributions are available in the Human Pangenome Reference Consortium organization on Dockstore for the community to reuse in the AnVIL cloud ecosystem.

    Karen Miga, PhD

    Association Professor

    University of California, Santa Cruz

    Karen Miga is an Assistant Professor in the Biomolecular Engineering Department at UCSC and Associate Director at the UCSC Genomics Institute. She co-leads the telomere-to-telomere (T2T) consortium and is the Project Director of the Human Pangenome Reference Consortium (HPRC) production center at UCSC. Her research program combines innovative computational and experimental approaches to produce the high-resolution sequence maps of human centromeric and pericentromeric DNAs.

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