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This session will provide an interactive, guided demonstration of the public facing genomic tools, including the new PheWAS x GWAS data browser as well as an interactive, guided demonstration of our cloud computing platform, the Researcher Workbench. It will also provide participants a hands-on opportunity to replicate a research study with new genomic data types including structural variant and long reads data. Instructors will conduct an interactive Q&A session to engage attendees about the All of Us Researcher Workbench and the novel technology implemented to conduct genomic analyses.
The NIH’s All of Us Research Program is committed to collecting multiple types of health data from a million or more participants to create a diverse research resource that accelerates precision medicine. The All of Us Researcher Workbench is the free-to-access secure, cloud-based platform where registered researchers from both US-based and international intuitions access and analyze data using Python, R, or SAS coding languages. Currently the program has over 413,000 program participants with >245,000 whole genome sequence (WGS) samples and >314,000 genotyping arrays. Looking forward, we anticipate counts for both WGS and arrays to surpass 400,000 soon. The genomic data is combined with many types of phenotypic and auxiliary data types including electronic health records (EHR), survey data, physical measurements, and mobile health data (Fitbit). This session will 1) provide an interactive, guided demonstration of the public facing genomic tools, including the new PheWAS x GWAS data browser 2) provide an interactive, guided demonstration of our cloud computing platform, the Researcher Workbench 3) provide participants a hands-on opportunity to replicate a research study with new genomic data types including structural variant and long reads data and 4) conduct an interactive Q&A session to engage attendees about the All of Us Researcher Workbench and the novel technology implemented to conduct genomic analyses.
Please note, to participate in the interactive activities included in this workshop, please register for the platform. This process may take a few hours; registrants are strongly encouraged to complete this by November 15. Platform registration is optional but highly recommended.
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Hear from ASHG volunteers on how to navigate the Annual Meeting as a first-time attendee or trainee. We will cover a range of topics, from badge pick-up to networking opportunities and how to make the most of your experience. You will also have the opportunity to ask your questions during a Q&A period.
Hear from ASHG volunteers on how to navigate the Annual Meeting as a first-time attendee or trainee. We will cover a range of topics, from badge pick-up to networking opportunities and how to make the most of your experience. You will also have the opportunity to ask your questions during a Q&A period.
Overview of Event
- Summarize helpful tips and tricks for ASHG Annual Meeting attendees, especially those who are first-time attendees.
- Identify programming and networking opportunities for ASHG Annual Meeting attendees.
Helpful Resources
- First Time Attendees Guide
- Schedule and Online Planner. Be sure to login to save sessions to your schedule.
- Registration Rates and Ticketed Events
Kevin TA Booth, PhD
Laboratory Genetics and Genomics Fellow
Indiana University School of Medicine
Dr. Kevin T.A. Booth is a Laboratory Genetics and Genomics Fellow at the Indiana University School of Medicine. He obtained his undergraduate degree in Chemistry and his Doctor of Philosophy in Molecular Medicine from the University of Iowa. Dr. Booth went on to complete his postdoctoral training at Harvard Medical School, where his research focused on gene therapy for hereditary hearing loss. Dr. Booth has made substantial contributions to our understanding of the genetic, genomic, allelic, and phenotypic landscapes of hereditary hearing loss and the development of gene therapy approaches for genetic hearing loss. Dr. Booth's achievements have been recognized by numerous prestigious awards, including the Rex Montgomery Dissertation Prize in 2019 and the NIH Future Research Leader Award in 2021.
Maria Lalioti, PhD
Scientific Consultant
Pharma and Biotech Industries
Maria is a freelance scientific consultant for drug development in the gene therapy / gene editing space. She obtained her undergraduate degree in Biology from the University of Athens, Greece and her PhD in Human Molecular Genetics from the University of Geneva, Switzerland. She did her postdoctoral training at the University of Birmingham, UK and at Yale School of MedicineShe was an Assistant Professor at Yale doing translational research, before joining the biotech industry, where she served in positions of increasing responsibility (Biogen, Goldfinch Bio, Beam Tx). Her therapeutic areas of expertise include diseases of kidney, liver (metabolic), CNS, and reproductive system. She was an EMBO and HSFP postdoctoral fellow and has received numerous awards for her research including awards from the American and European Societies of Human Genetics (ASHG and ESHG).
Juliann Savatt, MS, CGC
Assistant Professor, Department of Genomic Health
Geisinger
Juliann completed her MS in Genetic Counseling at the University of North Carolina at Greensboro and has practiced as a certified genetic counselor in both cancer and pediatric neurodevelopmental clinical settings. She currently holds the position of Assistant Professor in the Department of Genomic Health at Geisinger where she is involved in multiple research efforts including the Clinical Genome Resource and where she co-directs the Geisinger MyCode Community Health Initiative (MyCode) Genomic Screening and Counseling Program that discloses clinically actionable results to biobank participants.
Beth Sullivan, PhD (Moderator)
James B. Duke Professor of Molecular Genetics and Microbiology
Duke University
Dr. Beth Sullivan is James B. Duke Professor of Molecular Genetics and Microbiology at Duke University and Associate Dean for Research in Duke University School of Medicine. She obtained her undergraduate degree in Biology, Chemistry, and Classics from Western Maryland College (now McDaniel College) and earned her Ph.D. in Human Genetics from the University of Maryland at Baltimore. Her lab studies mechanisms of human genome stability in normal and disease states, with a focus on the genomics and epigenetics of the centromere, functional characterization of alpha satellite DNA variation, and genome engineering of human artificial chromosomes and chromosome rearrangements.
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This workshop is for those passionate about human genetics who want to meaningfully impact the field through advocacy. You will gain foundational and practical skills to become an advocate, building on ASHG's ongoing efforts and highlighting available advocacy tools to the broader research community. This session is your invitation to step into the world of advocacy, armed with newfound knowledge and practical skills. Don't miss the chance to unlock your advocacy potential. No prior advocacy experience required!
This workshop is for those passionate about human genetics who want to meaningfully impact the field through advocacy. You will gain foundational and practical skills to become an advocate, building on ASHG's ongoing efforts and highlighting available advocacy tools to the broader research community. This session is your invitation to step into the world of advocacy, armed with newfound knowledge and practical skills. Don't miss the chance to unlock your advocacy potential. No prior advocacy experience required!
Participants can expect to cover the following topics:
- Demystifying Advocacy: Explore why advocacy matters and how it can be a powerful tool for shaping responsible and equitable practices in human genetics.
- Skills for Everyday Advocacy: This session is not just about theories, it is about practical skills you can apply in your daily work life. Walk away equipped with tools to effortlessly integrate advocacy into routines, highlighting the work already being done by ASHG.
- Hands-On Learning: Engage in interactive activities and discussions that make advocacy relatable and applicable to your career. Discover how easy it is to be an advocate in your community, workplace, or on Capitol Hill.
- Be the Change: Leave the workshop not just informed but inspired to be an advocate for responsible and inclusive practices in human genetics. Your voice has the potential to make a meaningful impact!
Learning Objectives:
- Summarize and identify context for policy issues affecting human genetics with ASHG Fact Sheets and Statements
- Formulate ways to be an ASHG advocate, contacting representatives and understanding bill language
- Examine communication strategies/practical tips in discussing human genetics
- Identify ASHG advocacy networks and professional development opportunities (i.e. ASHG Advocate Update, Advocacy Certificate Program for Trainees, Policy Fellowships)
Anna Capria, MS
Outreach Coordinator and Bioinformatic Analyst 2
J. Craig Venter Institute
Anna Capria is an Outreach Coordinator and Bioinformatics Analyst at the J. Craig Venter Institute, where she works on the NIAID-funded BV-BRC project. Her work is centered on making viral bioinformatics and genomics open and accessible to the broader scientific community. Anna holds a Bachelor’s in Biomedical Science from the Rochester Institute of Technology and an MS in Human Genetics and Genomic Data Analytics from Keck Graduate Institute. Anna volunteers at Rare Science in her free time, where she plays a key role in supporting the rare disease community from an outreach perspective. She has led efforts in patient group organization, social media strategy, advocacy, and the gifting of Rare Bears to patient organizations and families, bringing joy and support to those affected by rare diseases. She is also an active member of the San Diego Women in Bio Chapter, co-chairing the MAPS program. Driven by her deep interest in human genetics and rare diseases, Anna is passionate about advocating for research funding and empowering others in their advocacy journey. Her commitment to improving the lives of those around her is a constant source of motivation in her work.
Grace Tietz, BS
PhD Candidate
Baylor College of Medicine
Grace Tietz is a PhD candidate in Genetics at Baylor College of Medicine and an alumna of the ASHG Advocacy Certificate Program. Prior to starting her PhD, she worked at NIAID where she facilitated data sharing activities in the context of COVID-19 and obtained her B.S. at the University of Maryland College Park. Her current research aims to improve transferability of genetic testing across ancestries using population genetics approaches. Her policy interests are centered around the importance of improving diversity in genetics, both in the workforce, and in the cohorts that are studied. She additionally has interests in data diplomacy, sharing, and governance in genetics.
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Dr. Costain will discuss findings from systematically assessing rare canonical splice site variants in blood expressed genes in a cohort of individuals who underwent genome sequencing and RNA-seq. The team found that up to 1 in 4 variants may not cause loss-of-function, and that in silico predictions using established tools and published guidelines were often discordant with RNA-seq data.
Dr. Costain will discuss findings from systematically assessing rare canonical splice site variants in blood expressed genes in a cohort of individuals who underwent genome sequencing and RNA-seq. The team found that up to 1 in 4 variants may not cause loss-of-function, and that in silico predictions using established tools and published guidelines were often discordant with RNA-seq data.
Overview of Presentation
- Canonical splice site variants (CSSVs) are often presumed to cause loss-of-function and are assigned very strong evidence of pathogenicity
- We identified all 168 rare CSSVs in blood-expressed genes in a cohort of 112 individuals using genome sequencing, and studied their impact on splicing using RNA sequencing (RNA-seq).
- Approximately one in four rare CSSVs did not show evidence for loss-of-function based on analysis of RNA-seq data.
- Predictions from in silico methods were often discordant with findings from RNA-seq.
- More caution may be warranted in applying very strong pathogenicity evidence to CSSVs in the absence of functional data, especially when the pre-test probability is low and phenotypes are absent or variable (e.g., secondary findings; newborn genomic screening programs).
Gregory Costain, MD, PhD
Physician-scientist
Hospital for Sick Children (SickKids)
GREGORY (GREG) COSTAIN, M.D., Ph.D., is a medical geneticist and physician-scientist at The Hospital for Sick Children (SickKids), and an assistant professor at the University of Toronto. He co-leads various genetic medicine initiatives including the SickKids Genome Board, the SickKids Translational Genomics Node of Precision Child Health, and Can-GARD (Canadian Gene Cure Advanced Therapies for Rare Disease). His research program is focused on understanding the causes and consequences of rare variation in the human genome. His lab uses genome sequencing and computational approaches to discover new disease genes, genotype-phenotype associations, and pathways to precision treatments.
Jessica Chong, PhD (Moderator)
Deputy Editor
HGG Advances
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This workshop will use the ACMG/AMP standards and guidelines for germline SNV interpretation as a case study for developing classroom activities that engage learners, develop variant analysis skills, and build confidence in the curation process for students. Throughout the workshop, participants will gain hands-on experience designing instructional activities for clinical genetics concepts, assessing the effectiveness of the activities, and constructing an instructional scaffold to guide learners to mastery of the curation process. Participants will also discuss the benefits of teaching in a team-based, active modality.
Single nucleotide variant (SNV) curation is an important skill to develop for students in genetic counseling, genomics, and bioinformatics master’s programs. It is also a common subject for continuing education workshops for professionals working in clinical genetics roles. While the number of evidence categories and scoring criteria can be intimidating for new learners, the process lends itself well to team-based, active learning approaches in the classroom. This workshop will use the ACMG/AMP standards and guidelines for germline SNV interpretation as a case study for developing classroom activities that engage learners, develop variant analysis skills, and build confidence in the curation process for students. Throughout the workshop, participants will gain hands-on experience designing instructional activities for clinical genetics concepts, assessing the effectiveness of the activities, and constructing an instructional scaffold to guide learners to mastery of the curation process. Participants will also discuss the benefits of teaching in a team-based, active modality. While the workshop will focus on in-person educational formats, there will also be discussion of how to adapt the same activities to synchronous, online delivery and self-paced, solo learners.
Learning Objectives
- Design team-based, active learning activities for teaching genetics concepts
- Assess the effectiveness of active learning activities
- Plan an educational approach to develop students' skills in SNV interpretation
- Describe the benefits of team-based learning approaches for students
Barbara Kraatz Fortini, PhD
Keck Graduate Institute
Barbara Kraatz Fortini, Associate Professor of Genetics is currently Director of the Center for Training in Applied Genomics at KGI, and serves as the Program Director for >span class="NormalTextRun SCXW63644289 BCX0" data-ccp-parastyle="Normal (Web)"> Master of Science in Human Genetics and Genomic Data Analytics (MSGDA), an execute-education Certificate in Applied Genomics (CAG), and the Clinical Genetics and Bioinformatics (CGB) summer program for undergraduates. Within the KGI curriculum, Fortini teaches courses in Human Molecular Genetics, Human Genomics, and Functional Genomics. Fortini’s research is focused on how non-coding genomic variation affects colorectal cancer risk, using both bioinformatics and cell-based assays to understand the consequences of variants associated with colon cancer. Fortini completed her postdoctoral training at the Keck School of Medicine of USC in the Department of Preventive Medicine at the USC Norris Comprehensive Cancer Center. She received her BS in 2002 and her PhD in 2011 at the California Institute of Technology.
Emily Quinn, MS, CGC
Associate Professor
Keck Graduate Institute
Emily Quinn, MS, CGC is an Associate Professor and the Program Director for the Master of Science in Human Genetics and Genetic Counseling program at Keck Graduate Institute (KGI). Emily received her bachelor degrees in Biology and Psychology from the University of California Santa Cruz and her master degree in Genetic Counseling from the Icahn School of Medicine at Mount Sinai. Emily’s clinical background is in pediatric cancer predisposition and her academic research interests are in the topics of diversity, equity and inclusion, admissions processes, and educational effectiveness.
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- Life Member - $20
- Nonmember - $30
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This webinar will introduce attendees to the career-enhancing ASHG-NHGRI Genomics and Public Service Fellowship Program. Learn about the four different fellowship options, why they might be right for you, and how to make your application stand out. Hear from mentors and fellows about their experiences and get your questions answered!
This webinar will introduce attendees to the career-enhancing ASHG-NHGRI Genomics and Public Service Fellowship Program. Learn about the four different fellowship options, why they might be right for you, and how to make your application stand out. Hear from mentors and fellows about their experiences and get your questions answered!
Overview
- Gain awareness of the fellowship offerings from ASHG-NHGRI and the experiences of current fellows
- Learn who can apply to the different fellowships and what makes a candidate’s application stand out
- Get your questions about the fellowship programs answered
Please visit our website to learn more the ASHG-NHGRI Fellowships Program!
Kristin Lewis, PhD
Associate Director of Fellowship Programs
ASHG
Dr. Lewis earned a Ph.D. in Physics from the University of Michigan and has lived and worked in Washington, DC for over a decade. She is well-versed in the world of scientific fellowships after being a AAAS Science & Technology Policy Fellow at NASA and after serving as previous director of the AAAS Mass Media Fellowship. She currently manages the ASHG-NHGRI Genomics and Public Service Fellowship Program at ASHG.
Beth Tuck, MA
Education and Community Involvement Branch Chief
National Human Genome Research Institute (NHGRI)
Beth Tuck (she/her) is the chief of the Education and Community Involvement Branch at NHGRI. Previously she served as the executive director at Genspace, the world’s first community biology lab in Brooklyn, New York, where she oversaw the organization’s staff, programs, strategy, fundraising and finance. In her previous role as a genomics education specialist at NHGRI, she worked on enhancing K-16 genomic literacy, education and community engagement. Her achievements included designing curricular resources, engaging students and teachers in hands-on genomics activities, supporting teacher professional development and training scientists in public engagement skills. Beth was also the first ASHG/NHGRI Genetics and Education Fellow in 2014. Her graduate research at Washington University in St. Louis focused on the molecular mechanisms of neurological disorders.
Sofia Martín, BA
ASHG-NHGRI Post-Baccalaureate Genomics Analyst Fellow
National Human Genome Research Institute (NHGRI)
Sofia Martín is a current ASHG-NHGRI Post-Baccalaureate Genomics Analyst Fellow. She earned her BA at St. Edward’s University in Austin, TX, studying Biology with a concentration in Allied Health professions. She has conducted independent research in St. Edward’s Microbiology and Developmental Genetics labs. Most recently, she has completed a medical research internship with the Department of Nephrology at Washington University in St. Louis, MO, where she used light sheet fluorescence microscopy to identify patterns of structures in human kidney tissue. Sofia has a career interest in Genetic Counseling specializing in oncology and hereditary cancer screening. She feels grateful for the opportunity to work on a multitude of NHGRI projects to expand her knowledge of genetics and genomics.
Sarah Bates, MS, MA
Communications Director
National Human Genome Research Institute (NHGRI)
Christine Chang, MPH
Program Director
National Human Genome Research Institute (NHGRI)
Christine Chang is a program officer in the Division of Genomic Medicine, joining the National Human Genome Research Institute in 2014. She manages a portfolio of grants in genomic medicine research. She is also the co-manager of the NHGRI Scientific Program Analyst program.
Prior to joining NHGRI, Ms. Chang was a Cancer Research Training Fellow at the National Cancer Institute in the Epidemiology and Genomics Research Program.
Karina Miller, PhD
Manager of Advocacy & Public Affairs
ASHG
Karina A. Miller, PhD, is the Manager of Advocacy & Public Affairs at the American Society of Human Genetics. She obtained her undergraduate training from Rensselaer Polytechnic Institute and her PhD in cancer genetics from Roswell Park Comprehensive Cancer Center, affiliated with the University at Buffalo. During her graduate training, she was a founding member and leader of a science policy group and of a nonprofit organization to support professional development of women in STEM. At ASHG, she develops and manages programs and resources to support ASHG member advocacy, including the Advocacy Certificate for Human Genetics and Genomics Trainees (ACGT), serves as one of the mentors for the ASHG/NHGRI Genetics and Public Policy Fellowship, and supports ASHG’s Capitol Hill engagement. She also supports implementation of ASHG committee projects and activities in policy, advocacy, and professional practice.
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This webinar will introduce advocacy framed around U.S. policy-making, ASHG’s role in the biomedical research advocacy community, and why it is essential for scientists to take action.
Congress is charged with making decisions about funding science and agencies like the National Institutes of Health; however, it is impossible for Congress to be fully informed about the many facets of research funded by the federal government. ASHG members are in a unique position as subject matter experts to directly convey the benefits of human genetics and genomics research to policymakers. Advocacy is essential to raise awareness about the importance of federal science funding, its economic impact and translation into health advances, and the importance and benefits of human genetics research in dispelling misconceptions and improving health for all. This webinar will introduce advocacy framed around U.S. policy-making, ASHG’s role in the biomedical research advocacy community, and why it is essential for scientists to take action.
Overview of Presentation
- Understand how advocacy helps to explain the benefits of human genetics and genomics research to policymakers.
- Learn how organizations like ASHG and their member volunteers influence biomedical research and policy.
- Recognize the importance of scientists advocating for evidence-based decision making, robust research funding, and policies that advance biomedical science and the appropriate application of genetics in health and society.
Jon Judd
PhD Candidate
Stanford University
Jon Judd is a Genetics PhD candidate at Stanford University in the labs of Jonathan Pritchard and John Witte, researching the genetic and social causes of complex diseases. He obtained his undergraduate degree in Chemical and Biomolecular Engineering from Johns Hopkins University. Throughout his training, Jon has been a keen advocate at the local and federal levels. Beyond being a member of ASHG’s Government & Public Advocacy Committee, Jon staffed the Presidents’ Council of Advisors on Science and Technology at the White House and was a research assistant for the Association of Science and Technology Centers. At the grassroots level, Jon is a co-chair of the Stanford Genetics Advocacy Committee, president of the Stanford Science Policy Group, and assisted in organizing Stanford BioJam, a community-led camp devoted to the education of teenagers underrepresented in STEM.
Yvette Seger, PhD
Director of Strategic Scientific Program Advancement; Director of Science Policy; Deputy Director of the Office of Public Affairs
Federation of American Societies for Experimental Biology
Yvette Seger, PhD, is the Director of Strategic Scientific Program Advancement, Director of Science Policy, and Deputy Director of the Office of Public Affairs for the Federation of American Societies for Experimental Biology (FASEB), a coalition of 22 scientific societies collectively representing over 110,000 individual biological and biomedical researchers. In these roles she leads the Federation's strategic investments in diversity, equity, accessibility, and inclusion and data sharing and reuse while also contributing to overall strategic vision for FASEB’s science policy initiatives. Dr. Seger launched her policy career at the National Academies as a Christine Mirzayan Science & Technology Policy Fellow where she worked on a report examining processes for identifying and appointing scientists to key federal advisory positions. After leaving the Academies, Dr. Seger held senior policy analyst positions at the research advocacy group FasterCures, the National Institutes of Health Office of Science Policy, and Thomson Reuters before joining FASEB in 2013. Dr. Seger holds a PhD in Genetics from Stony Brook University and received a BA in Zoology (Genetics Concentration) and Politics & Government from Ohio Wesleyan University.
Jennifer Zeitzer
Deputy Executive Director; Director, Office of Public Affairs
Federation of American Societies for Experimental Biology
Jennifer Zeitzer was named Director of the FASEB Office of Public Affairs (OPA) in June 2018 and assumed the dual role of Deputy Executive Director in June 2022. She works with a team of policy analysts, legislative affairs specialists, and the elected leadership of the Federation and its member societies to develop and promote policies to advance biomedical research. Prior to her current role, Jennifer served as the Director of Legislative Relations/ Deputy Director of OPA. In that role, she represented FASEB on Capitol Hill, managed FASEB’s communications with the U.S. Congress, and developed legislative strategies related to funding for the National Institutes of Health and other federal science agencies. She also coordinated FASEB’s advocacy efforts with coalition partners in the biomedical and scientific research community. Previously, Jennifer was the Director of Congressional Relations at the Alzheimer’s Association. She has a bachelor’s degree in Political Science from the Pennsylvania State University.
Anthony Wynshaw-Boris, MD, PhD (Moderator)
The James H. Jewell MD (Med ’34) Professor of Genetics
Case Western Reserve University School of Medicine and University Hospitals
Tony Wynshaw-Boris received his MD, PhD degrees from Case Western Reserve University School of Medicine. In 1994, Dr. Wynshaw-Boris set up an independent laboratory at NHGRI, where he initiated a program using mouse models to study human genetic diseases, with a focus on neurogenetic diseases. In 1999, he moved to UCSD School of Medicine, where he became Professor of Pediatrics and Medicine, as well as Chief of the Division of Medical Genetics in the Department of Pediatrics. In 2007, he moved to UCSF School of Medicine, where he was the Charles J. Epstein Professor of Human Genetics and Pediatrics, and the Chief of the Division of Medical Genetics in the Department of Pediatrics. At UCSF, in addition to mouse models, his laboratory began to use patient-derived induced pluripotent stem cell (iPSC) models to study human disease. He returned to Cleveland in 2013 to become the Chair of the Department of Genetics and Genome Sciences, and is now the James H. Jewell MD (Med ’34) Professor of Genetics. His laboratory continues to use mouse and iPSC models to shed light on mechanisms of neurogenetic diseases with the ultimate goal of providing novel therapies.
Dr. Wynshaw-Boris was President of the American Society for Human Genetics for 2020 and is currently Chair of the Government and Public Advocacy Committee (GPAC). He was appointed to the National Advisory Child Health and Human Development Council of the Eunice Kennedy Shriver National Institute of Child Health & Human Development, NIH, in 2019. He has also been elected to membership in the American Society for Clinical Investigation, the Association of American Physicians, the American Pediatric Society, and he was elected as Fellow of the American Association for the Advancement of Science.
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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 SIG seminar. 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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Erin Thorpe Venti will present findings from an observational, retrospective analysis of 1,004 underserved individuals from 8 countries with suspected rare genetic disease who received clinical genome sequencing (cGS) through the iHope program, a philanthropic testing access program.
Erin Thorpe Venti will present findings from an observational, retrospective analysis of 1,004 underserved individuals from 8 countries with suspected rare genetic disease who received clinical genome sequencing (cGS) through the iHope program, a philanthropic testing access program.
Overview of Presentation
- The diagnostic yield of cGS was 41.4% across the cohort. Individuals from sites in low- and middle-income countries (LMIC) had a higher diagnostic yield compared to those from sites in high-income countries (HIC).
- cGS impacted the clinician’s diagnostic evaluation (DE) for 76.9% of individuals, with a higher rate in LMIC sites (87.4%) compared to HIC sites (70.1%). Positive test results led to a substantial increase in DE (64.2 times more likely), showing the impact of accurate diagnoses on clinical practices.
- cGS resulted in a change of management (COM) for 41.1% of individuals, including new specialty referrals, imaging, therapeutic interventions, and palliative care. The COM increased to 69.2% when genetic counseling and avoidance of additional testing we also considered.
- Individuals from LMIC sites were as likely as their HIC counterparts to experience a change in diagnostic evaluation and change of management, suggesting that increased access to genomic testing may support diagnostic equity and the reduction of global health care disparities.
Erin Thorpe Venti, MS, CGC
Director of Clinical Programs
Genetic Alliance
Erin Thorpe Venti is a board-certified genetic counselor with more than a decade of experience in clinical patient care, research, and genetic testing. For the past nine years, Erin has specialized in clinical whole genome sequencing for rare and undiagnosed genetic conditions, with expertise in variant interpretation, case analysis, clinical reporting, test development, reanalysis workflows, data analysis, provider education, and program management. She currently serves as the Director of Clinical Programs at Genetic Alliance, a nonprofit health advocacy organization dedicated to advancing health through genetics. In this role, Erin oversees the management and operations of iHope Genetic Health, an initiative focused on providing access to complex genetic testing for underserved children in low-to-middle-income countries.
Alyson Barnes, PhD (Moderator)
Assistant Editor
American Journal of Human Genetics
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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, PhD
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.
Jonathan Pugh
Director
Nanopore Education at Oxford Nanopore Technologies
Jonathan Pugh has devoted over a decade to Oxford Nanopore Technologies, advancing from a foundational role in nanopore research to currently spearheading the company's educational initiatives as the Director of Nanopore Education. With a rich career encompassing product management, marketing, and now education, Jonathan leverages his extensive expertise to bring sequencing technology to a wider student demographic across the globe. His current role reflects a harmonious blend of his adept communication skills and a deep-seated knowledge of nanopore sequencing, aiming to foster STEM engagement and education for the next generation of scientists.
James Melton, PhD
Senior Lecturer
Spelman College
Dr. James Melton is a Senior Lecturer in the Biology Department at Spelman College. He obtained his PhD in Biology from the University of Alabama and studied the diversity and organellar genomics of green algae. Previously as a CURE (Course-based Undergraduate Research Experience) postdoctoral fellow at Spelman College, he investigated the diversity and transcriptomics of Amoebozoa. He currently leads the ‘Phage Discovery and Genomics’ program at Spelman College and has incorporated Oxford Nanopore sequencing into the classroom for every student to be able to sequence their isolated phage.
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