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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

    Sara Cullinan, PhD (Moderator)

    Deputy Editor

    American Journal of Human Genetics

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  • Upcoming
    Contains 1 Component(s) Includes a Live Web Event on 07/10/2024 at 12:00 PM (EDT)

    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.

    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 HNGRI-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.

    Jessica Chong, PhD (Moderator)

    Deputy Editor

    HGG Advances

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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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  • Contains 1 Component(s)

    Pengfei Liu will present on a novel workflow for rare disease diagnostics using RNA-seq. The workflow leverages patient cell transdifferentiation into induced neurons to improve molecular diagnostic yield of neurological genetic disorders.

    Pengfei Liu will present on a novel workflow for rare disease diagnostics using RNA-seq. The workflow leverages patient cell transdifferentiation into induced neurons to improve molecular diagnostic yield of neurological genetic disorders. 

    Overview of Presentation

    • Transcriptome RNA-seq using clinically accessible tissues does not provide comprehensive characterization of Mendelian disease genes involved in neurological disorders.
    • Cell transdifferentiation can be streamlined into a diagnostic RNA-seq workflow.
    • Induced neuron RNA-seq increases molecular diagnostic yield by activating neurological disease-associated genes and neuron-specific isoforms

     

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    Pengfei Liu, PhD, FACMGG

    Associate Professor

    Baylor College of Medicine

    Dr. Pengfei Liu is Associate Professor (tenured) at the Department of Molecular and Human Genetics at Baylor College of Medicine, as well as the CLIA Lab Director of the Medical Genetics and Multiomics Laboratory at Baylor. He is also the Director of the Baylor ACGME/ABMGG Laboratory Genetics and Genomics (LGG) Fellowship Program. Dr. Liu is a board-certified PhD clinical geneticist with a primary research interest in translating new technologies into clinical testing to advance the diagnostics and therapy of rare diseases. His clinical work has provided key evidence to recognize the necessity and importance of clinical reanalysis of diagnostic exome data. Dr. Liu has led the launch of clinical whole genome sequencing at Baylor Genetics as well as the clinical RNA-seq for the Undiagnosed Diseases Network (UDN). He has received multiple honors and awards, including the Michael Watson’s Genome Medicine Innovation Award from the ACMG, the Genomic Innovator Award from the NHGRI, and the Cotterman Award from the ASHG. 

    Alyson Barnes, PhD (Moderator)

    Assistant Editor

    American Journal of Human Genetics

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  • Contains 2 Component(s)

    Season 3, Voices in Genomics, with Iman Martin, PhD, MPH, MSc.

    In this episode, host Eli Roberson, PhD interviews Iman Martin, PhD, MPH, MSc, an epidemiologist and biostatistician. Dr. Martin shares her journey into science and epidemiology, emphasizing the importance of opportunity and preparation in one's career. She discusses her childhood and how the impact of chronic diseases on her community developed her early interest in science and health. The conversation explores Dr. Martin's career choices, the significance of diverse perspectives in science, and her commitment to serving through the United States Public Health Service.

    In the second half of the interview, Iman Martin, PhD, MPH, MSc, discusses her role in the US Public Health Service. Dr. Martin also delves into the concept of cultural competence and cultural humility, emphasizing the importance of understanding and bridging cultural differences in public health work. Additionally, she offers insights into the intersection of scientific research, cultural values, and more.

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  • Contains 9 Product(s)

    Season Three of Genetically Speaking

    This new season of Genetically Speaking explores perspectives and stories of genetic and genomic professionals who are balancing career work along with advocacy, allyship, or activism work around equity, justice, diversity, inclusion and more. The episodes feature in-depth interviews with individuals about their careers in science and research, as well as delving into their personal journeys, inspirations, and more.

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  • Contains 2 Component(s)

    Season 3, Voices in Genomics, with Daphne Martschenko, PhD.

    In part one of this episode, host Eli Roberson, PhD, interviews Daphne Martschenko, PhD, an assistant professor at the Stanford Center for Biomedical Ethics. Dr. Martschenko discusses her unconventional career path, leading to her current focus on the social and ethical implications of human genetic and genomic research. The conversation touches on the intersection of genetics and education, particularly examining how genomics research intersects with societal narratives, racial disparities, and historical beliefs. The discussion also highlights the importance of diversity, equity, and inclusion in scientific studies, emphasizing the need to consider diverse perspectives in the design, conduct, and communication of research.


    In part two, Dr. Martschenko discusses the harmful narratives and myths in science and her work to dispel these myths. She emphasizes the need to challenge long-standing harmful narratives about DNA and genetics. The conversation also explores the intersection of genetics, ethics, and societal impacts, acknowledging the importance of recognizing shared experiences and fostering interdisciplinary collaboration.

     

    Addendum:

    "Increasing equity in science requires better ethics training: A course by trainees, for trainees," published May 1, 2024

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  • Contains 1 Component(s)

    With the progression of genetic technologies, it is important to understand not only what technologies are available but also the range of results that they provide and how to interpret those results. From positive and negative results to secondary and novel findings, what information can these provide to patients and researchers/clinicians? Using anonymized clinical reports, the speakers will address this important next step in genetic technologies.

    With the progression of genetic technologies, it is important to understand not only what technologies are available but also the range of results that they provide and how to interpret those results. From positive and negative results to secondary and novel findings, what information can these provide to patients and researchers/clinicians? Using anonymized clinical reports, the speakers will address this important next step in genetic technologies.   

    This webinar is aimed at students, teachers, researchers and/or the general public with an interest in clinical genetics. 


    Overview of Presentation

    • Build upon the overview of genetic technologies and their uses previously addressed in the last PEAC webinar.
    • Share arrays, exomes, and genomes as part of the various clinical reports. 
    • Address results that span positive, negative, variants of unknown significance, secondary findings, and novel candidate genes. 

    Nara Sobreira, MD, PhD

    Principal Investigator

    Johns Hopkins University

    Nara Sobreira, MD, PhD, is an associate professor at the McKusick-Nathans Department of Genetic Medicine at Johns Hopkins University School of Medicine. Her area of expertise is rare Mendelian phenotypes, analysis of next-generation sequencing, and functional testing of candidate causative variants. She earned her M.D. at the University of Pernambuco in Brazil. She finished her Ph.D. in Human Genetics at Johns Hopkins followed by a one-year postdoc also at Johns Hopkins School of Medicine. She completed residencies in clinical genetics at both Universidade Federal de Sao Paulo and Johns Hopkins. Her main clinical and research focus is on identifying the genetic bases of rare phenotypes, mainly, phenotypes associated with cartilage tumors and vascular anomalies, and on understanding the physiopathology of these phenotypes to identify pharmacological strategies to treat them. She has worked extensively on developing strategies to better analyze the variants identified by next-generation sequencing and on novel strategies for data sharing. She is one of the creators of GeneMatcher, VariantMatcher, and one of the co-founders of the Matchmaker Exchange, all intended to share next-generation sequencing data.

    Arvind Kothandaraman, MBS

    General Manager of Multiomics and Specialty Diagnostics

    Revvity

    Arvind Kothandaraman’s work has revolved around development and deployment of tools that are vital for the improvement of human healthcare. He serves as the General Manager of Multiomics and Specialty Diagnostics at Revvity (formerly PerkinElmer) and has previously held positions at Thermo Fisher Scientific, Advanced Analytical (now Agilent Technologies) and BioReference Laboratories (now OPKO Health). His experience spans business management, product development, commercial engagement, operations, research, and development across life sciences discovery and diagnostics.

    Kothandaraman is passionate about bridging the gap between credible, actionable information and public awareness particularly in multifaceted areas like medical science. He considers every interaction to be a learning opportunity, greatly enjoys knowledge exchange and considers it to be an extremely effective method to invigorate the mind.

    Kothandaraman holds a master’s degree in business and science from the Claremont Colleges, California. He is an active member of the American Society of Human Genetics (ASHG) Public Education and Awareness Committee (PEAC).

    Joseph Shen, MD, PhD (Moderator)

    Associate Professor

    University of California, Davis

    Dr. Joseph Shen is a geneticist with interests in neurodevelopmental disorders, clinical and molecular characterization of ultra-rare genetic conditions, and gene variant interpretation. He obtained his undergraduate degree from University of California, Berkeley, and his medical degree and doctorate in human molecular genetics from Case Western Reserve University in Cleveland, OH. His pediatrics residency and clinical genetics fellowship training was at Baylor College of Medicine in Houston, TX. Currently he is an Associate Professor in the Division of Genomic Medicine in the Department of Pediatrics at University of California, Davis.

    Dr. Nara Sobreira examines examples of negative and positive pathogenic exome sequencing results in the following highlights from this webinar.

     

    Negative exome sequencing result:


     

     

    Positive pathogenic exome sequencing result:



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  • Contains 1 Component(s)

    Season 3, Voices in Genomics, with Wylie Burke MD, PhD.

    In this episode, host Eli Roberson, PhD, has a conversation with Wylie Burke, MD, PhD, a professor at the Department of Bioethics and Humanities at the University of Washington. Dr. Burke, with a background in genetics and medicine, shares insights into her career journey, emphasizing the intersection of genetics, medicine, and bioethics. The episode explores her interests in the equitable use of genetic information, the impact of social determinants on health, and how inclusivity informs and changes genetics and research for the better.

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  • Contains 1 Component(s)

    Dr. Tianyu Zhang from Carnegie Mellon University will discuss a new polygenic score framework and how it may benefit underrepresented populations..

    Dr. Tianyu Zhang from Carnegie Mellon University will discuss a new polygenic score framework and how it may benefit underrepresented populations.

     
    Overview of Presentation

    • Genetic scores of individuals can be used to predict their traits, such as eventual disease status.

    • These polygenic scores work best in the ancestry from which they were developed. Lack of portability across ancestries violates fairness principles and could generate clinical harm.

    • We propose a computationally efficient method---Joint Lassosum---to improve the portability.

    • A systematic simulation study is presented to answer when and how much the proposed framework would improve the score prediction accuracy for underrepresented ancestry groups. 

     

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    Tianyu Zhang, PhD

    Postdoctoral Researcher, Department of Statistics & Data Science

    Carnegie Mellon University

    Dr. Tianyu Zhang is a postdoctoral researcher at Carnegie Mellon University (CMU), Department of Statistics & Data Science. He obtained his undergraduate degree, double-majored in Biology and Mathematics, from Peking University, and Doctor of Philosophy degree in Biostatistics from University of Washington. As a statistician with scientific training, his methodological research strives to achieve both statistical validity and real-world feasibility. His work has been published in high-impact journals across many fields including statistics, medicine and computational biology. Currently, Dr. Zhang works closely with Dr. Kathryn Roeder at CMU on developing novel inferential methods that can be applied to high-dimensional problems including genetic and single-cell data analysis. 

    Bernie Devlin, PhD

    Professor of Psychiatry

    University of Pittsburgh School of Medicine

    Bernie Devlin is a Professor of Psychiatry and Clinical and Translational Science at the University of Pittsburgh School of Medicine. His research has three major foci: the development or refinement of statistical methods for the analysis of genetic data; the implementation of such methods to discover the genetic basis of disease and related phenotypes; and placing these findings in neurobiology. Much of his empirical work characterizes the genetic basis and neurobiology of autism spectrum disorder and schizophrenia. In 2009 he was inducted as a Fellow of the Statistics Section of the American Association for the Advancement of Science (AAAS) for contributions to modeling genetic data. 

    Mike Bamshad, MD (Moderator)

    Editor-in-Chief of HGG Advances

    Chief of the Genetic Medicine Division of the Department of Pediatrics at Seattle Children’s Hospital, University of Washington (UW), Director of the Center for Clinical Genomics, Principal investigator the UW Center for Mendelian Genomics

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