Hufeng Zhou, Theodore Arapoglou, Xihao Li, Zilin Li, Xiuwen Zheng, Jill Moore, Abhijith Asok, Sushant Kumar, Elizabeth E Blue, Steven Buyske, Nancy Cox, Adam Felsenfeld, Mark Gerstein, Eimear Kenny, Bingshan Li, Tara Matise, Anthony Philippakis, Heidi L Rehm, Heidi J Sofia, Grace Snyder; NHGRI Genome Sequencing Program Variant Functional Annotation Working Group; Zhiping Weng, Benjamin Neale, Shamil R Sunyaev, Xihong Lin

Abstract
Large biobank-scale whole genome sequencing (WGS) studies are rapidly identifying a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant functional annotations play a critical role in WGS analysis, result interpretation, and prioritization of disease- or trait-associated causal variants. Existing functional annotation databases have limited scope to perform online queries and functionally annotate the genotype data of large biobank-scale WGS studies. We develop the Functional Annotation of Variants Online Resources (FAVOR) to meet these pressing needs. FAVOR provides a comprehensive multi-faceted variant functional annotation online portal that summarizes and visualizes findings of all possible nine billion single nucleotide variants (SNVs) across the genome. It allows for rapid variant-, gene- and region-level queries of variant functional annotations. FAVOR integrates variant functional information from multiple sources to describe the functional characteristics of variants and facilitates prioritizing plausible causal variants influencing human phenotypes. Furthermore, we provide a scalable annotation tool, FAVORannotator, to functionally annotate large-scale WGS studies and efficiently store the genotype and their variant functional annotation data in a single file using the annotated Genomic Data Structure (aGDS) format, making downstream analysis more convenient. FAVOR and FAVORannotator are available at https://favor.genohub.org.

• PMID: 36350676
• DOI: 10.1093/nar/gkac966
• Article on PubMed

“Precision Approaches for Health Communication with Vulnerable and Underserved Populations”

Suzanne Bakken, PhD, RN, FAAN, FACMI

Alumni Professor of Nursing and Professor of Biomedical Informatics
Director, Precision in Symptom Self-Management Center
Director, Reducing Health Disparities Through Informatics Pre- and Post-doctoral Training Program
Editor-in-Chief, Journal of the American Medical Informatics Association
Columbia University

Thursday, May 13, 12:00-1:00pm

Registration Required: Here

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The Role of Digital Health Technologies in Drug Development: A Workshop

This workshop will provide a venue to discuss challenges and opportunities in digital health technologies for improving the probability of success in drug development and enabling precision medicine. Workshop participants may consider key components for an evidence-based framework for applying digital health technologies towards drug research and development.

When: Tuesday, March 24, 2020; 10 a.m. – 4:15 p.m..
Where: Webinar only; Registration required

Genomic and Precision Medicine Weekly Forum

Svati Shah, M.D., MHS
Associate Dean of Genomics and Director, Duke Precision Genomics Collaboratory; Professor of Medicine; Director, Adult Cardiovascular Genetics Clinic
Duke University

When: March 19, 2020
Where: WebEx

Genomic and Precision Medicine Weekly Forum

Bryce Seifert, Ph.D.
ABMGG Laboratory Genetics and Genomics Fellow
Duke University
Clinical Validity Assessment of Genes Frequently Tested on Hereditary Cancer Susceptibility Sequencing Panels

When: March 5, 2020
Where: Duke University

5th Annual Precision Medicine Conference

A two-day series of interactive presentations and panel sessions will feature some of the nation’s leading experts on emerging topics in genomic medicine and pharmacogenomics.

When: Friday February 21 – Saturday, February 22, 2020
Where: Orlando, FL

Genomic and Precision Medicine Weekly Forum

Calum MacRae, M.D., Ph.D.
Vice Chair for Scientific Innovation, Brigham and Women’s Hospital; Associate Professor of Medicine
Harvard Medical School
Overcoming the barriers to clinical whole genome sequencing in routine acute care

When: February 20, 2020
Where: Duke University

Clinical Pharmacogenomics Preconference

These sessions will provide the latest update on emerging topics in pharmacogenomics. Attendees will learn from pharmacogenomics implementation leaders about their real world-experiences with using pharmacogenomics in the clinic, describe the regulatory oversight and need for evidence-based pharmacogenomic testing, as well as discuss the hottest topics in clinical pharmacogenomics today. The inaugural Clinical Pharmacogenomics Networking Reception to immediately follow.

When: Thursday, February 20, 2020
Where: Orlando, FL

Stakeholder Summit: Federal Regulation of Pharmacogenomic Testing

UF Precision Medicine Program and Precision Medicine Advisors will bring together stakeholders to discuss recent regulation by the FDA and formulate solutions for improving the safety and efficacy of pharmacogenomic tests.

When: Thursday, February 20, 2020; 8 a.m. – noon
Where: Orlando, FL

Genomic and Precision Medicine Weekly Forum

Elizabeth McNally, M.D., Ph.D.
Director, Center for Genetic Medicine; Professor of Medicine and Biochemistry and Molecular Genetics
Northwestern University
Genetic Variation In Heart Failure: From Rare to Common and In Between

When: February 13, 2020
Where: Duke University

Genomic and Precision Medicine Weekly Forum

Rebekah Ryanne Wu, M.D.
Assistant Professor of Medicine
Duke University
Impact of Family Health History on Understanding Genomic Risk in Singaporean Populations

When: February 6, 2020
Where: Duke University

Genomic and Precision Medicine Weekly Forum

Isaac Kohane, M.D., Ph.D.
Chair, Department of Biomedical Informatics; Professor of Biomedical Informatics
Harvard Medical School
What Can We Learn from Genomics Being the Leading Application of Clinical AI?

When: January 30, 2020
Where: Duke University

Precision Medicine World Conference

PMCW is the largest annual conference dedicated to precision medicine and brings together recognized leaders, top global researchers and medical professionals, and innovators across healthcare and biotechnology sectors.

When: January 21 – 24, 2020
Where: Silicon Valley, CA
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Genomic and Precision Medicine Weekly Forum

Cynthia Moylan, M.D.
Associate Professor of Medicine
Duke University
The Looming NASH Epidemic: Using -omics for risk stratification and prevention

When: January 23, 2020
Where: Duke University

IGNITE Steering Committee Meeting

IGNITE will conduct a a two-day Steering Committee Meeting

When: Wednesday, January 22 – Thursday, January 23, 2020
Where: University of Florida Research & Academic Center, Lake Nona, FL

Genomic and Precision Medicine Weekly Forum

Joe Grzymski, Ph.D.
Senior Director, Applied Innovation Center; Associate Research Professor of Microbiology and Computational Biology
Desert Research Institute
The Healthy Nevada Project Genetics Study and Linking Phenotype to Genotype

When: January 16, 2020
Where: Duke University

Genomic and Precision Medicine Weekly Forum

Lisa Bastarache, M.S.
Research Assistant Professor
Vanderbilt University Medical Center
How much more can we explain with genetics? Using EHRs to find Undiagnosed Patients

When: January 9, 2020
Where: Duke University

Genomic and Precision Medicine Weekly Forum

Opeyemi Olabisi, M.D., Ph.D.
Assistant Professor of Medicine, Division of Nephrology
Duke University
Patient-stem cell-derived podocytes as tools for modeling APOL1-associated kidney disease

When: Thursday, December 19, 2019, noon – 1 P.M.
Where: Duke University

Therapeutic Genome Editing: An ASHG-AJHG Webinar

Advances in the technology of genome editing offer major opportunities in the treatment of genetic disorders, but also raise complex technical and ethical issues. This webinar will explore these considerations both for somatic and germline genome editing and will explore the future research agenda for therapeutic genome editing.

When: Wednesday, December 11, 2 – 3 P.M.

More info

Genomic and Precision Medicine Weekly Forum

George Church, Ph.D.
Professor of Genetics; Director, PersonalGenomes.org; Harvard University
Reading and Writing Omes

When: Thursday, December 5, 2019, noon – 1 P.M.
Where: Duke University

Precision Medicine Insights: A Webinar Series

Kristin Wiisanen, Pharm.D., FAPhA

When: Tuesday, December 3, 2019, 12 p.m. EDT

University of Florida precision medicine leaders will highlight current knowledge and trends in this series, including professional and educational opportunities, to advance the future of health care. Join us as Dr. Kristin Wiisanen, online graduate program director, discusses challenges and approaches to patient education in the era of precision medicine.

AMIA 2019 Annual Symposium

Under the overall theme of “Informatics: From Data to Knowledge to Action” the Ameican Medical Informatics Association (AMIA) Annual Symposium will build on more than 40 years of sharing pioneering research and insights for leveraging information to improve human health.

When: Saturday, Nov. 16 – Wednesday, Nov. 20, 2019
Where: Washington, D.C.

More info

15th Annual Personalized Medicine Conference

The 15th Annual Personalized Medicine Conference will convene the world’s leading researchers, investors, industry executives, policy experts, payers, clinicians, and patient advocates to define the landscape and outlook for personalized medicine in science, business, and policy.

When: Wednesday, Nov. 13 – Thursday, Nov. 14, 2019
Where: Boston, MA

More info

Genomic and Precision Medicine Weekly Forum

Hakon Hakonarson, M.D., Ph.D.
Director, Center for Applied Genomics at the Joseph Stokes Jr. Research Institute; Professor of Pediatrics; Children’s Hospital of Philadelphia

When: Thursday, November 7, 2019, noon – 1 P.M.
Where: Duke University

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Genomic and Precision Medicine Weekly Forum

Rhoda Au, Ph.D.
Professor of Anatomy & Neurobiology; Boston University

When: Thursday, October 31, 2019, noon – 1 P.M.
Where: Duke University

Exploring the Current Landscape of Consumer Genomics – A Workshop

The Roundtable on Genomics and Precision Health will host a one day public workshop to explore the current landscape of consumer genomics and implications for how genetic test information is used or may be used in research and clinical care.

When: Tuesday, October 29, 2019, 8:30 A.M.
Where: Washington, D.C.

More info

Genomic and Precision Medicine Weekly Forum

Gregory Gray, M.D., MPH, FIDSA
Professor of Medicine, Global Health and Environmental Health; Duke University

When: Thursday, October 24, 2019, noon – 1 P.M.
Where: Duke University

American Society of Human Genetics 2019 Annual Meeting

ASHG 2019 featured invited presentations by the world’s leading geneticists, in addition to symposia, workshops, and abstract-driven sessions about new developments in basic, translational, and clinical human genetics research and technology.

When: Tuesday, October 15 – Saturday, October 19, 2019
Where: Houston, Tx

More info

Genomic and Precision Medicine Weekly Forum

Joanne Ngeow, MBBS, MRCP, MPH
Senior Consultant, Division of Medical Oncology, National Cancer Centre Singapore

When: Thursday, October 10, 2019, noon – 1 P.M.
Where: Duke University

Genomic and Precision Medicine Weekly Forum

Brian Sullivan, M.D.
Medical Instructor in the Department of Medicine; Duke University

When: Thursday, October 3, 2019, noon – 1 P.M.
Where: Duke University

NHGRI Stategic Planning Workshop

Genomics in Medicine & Health

NHGRI is in the middle of a new round of strategic planning that will establish a ‘2020 vision for genomics’ and culminate in the publication of a new NHGRI strategic plan in October 2020 and is soliciting input from the broader research and public communities to help shape the 2020 strategic plan.

When: Thursday, Sept. 26 – Friday, Sept. 27, 2019, 8 A.M. – 5 P.M. both days
Where: Bethesda, MD

More info

Enhancing Scientific Reproducibility through Transparent Reporting – A Workshop

An ad hoc committee of the National Academies of Sciences, Engineering, and Medicine convened a public workshop to discuss the current state of transparency in reporting pre-clinical biomedical research and to explore the possibility of improving the harmonization of guidelines across journals and funding agencies so that biomedical researchers propose and report data in a consistent manner.

When: Wednesday, September 25 – Thursday, September 26, 2019; 8:30 A.M.
Where: Washington, D.C.

More info

IGNITE Steering Committee Meeting

IGNITE conducted a a two-day Steering Committee Meeting and joint meeting with the Data and Safety Monitoring Board

When: Wednesday, September 25 – Thursday, September 26, 2019
Where: Silver Spring, MD

Genomic and Precision Medicine Weekly Forum

Richard Gibbs, Ph.D.
Director, Human Genome Sequencing Center; Professor of Translational Biology & Molecular Medicine and Integrative Molecular and Biomolecular Sciences; Baylor College of Medicine

When: Thursday, September 19, 2019, noon – 1 P.M.
Where: Duke University

Genomic and Precision Medicine Weekly Forum

Georgia Wiesner, Ph.D.
Professor of Medicine, Vanderbilt University

When: Thursday, September 12, 2019, noon – 1 P.M.
Where: Duke University

IGNITE Steering Committee Meeting

IGNITE conducted a a two-day Steering Committee Meeting

When: Thursday, July 25 – Friday, July 26, 2019
Where: Orlando, Florida

NIH Collaboratory Grand Rounds

Moving Beyond Return of Research Results to Return of Value

Speaker: Consuelo H. Wilkins, M.D., MSCI
Vice President for Health Equity, Vanderbilt University Medical Center
Executive Director, Meharry-Vanderbilt Alliance

When: Friday, June 28, 1 – 2 P.M. EST

NIH Collaboratory Grand Rounds

Good Clinical Practice Guidance and Pragmatic Trials: Balancing the Best of Both Worlds in the Learning Health System

Speaker: Robert J. Mentz, M.D., FACC, FAHA, FHFSA
Director of the Duke Cooperative Cardiovascular Society
Assistant Program Director of the Duke Cardiovascular Disease Fellowship
Associate Professor
Duke University Medical Center and Duke Clinical Research Institute

When: Friday, June 14, 1 – 2 P.M. EST
More info

Julie Johnson, PharmD, Carol Horowitz, M.D., M.P.H., and Josh Denny, M.D., were three of the presenters at the University of Florida Precision Medicine Conference, held March 6-7, 2019 in Orlando, Florida. This conference brings together clinicians, researchers and other thought leaders from medicine and pharmacy to receive cutting edge guidance from professionals with experience implementing genomic medicine and pharmacogenomics in a variety of settings.

The M.D. Program at Icahn School of Medicine combines the most progressive, technologically advanced, scientifically-based education with the goal of improving societal health care needs locally in New York City and around the world. We explicitly blur the traditional distinction between pre-clinical and clinical years by integrating the basic sciences across courses as well initiating students into to the clinical environment from their first day of school.Not only do our students acquire the medical, scientific and clinical expertise needed for a successful career, but also the skills to work in interdisciplinary teams, the analytic tools needed for research, the confidence to critically evaluate and apply new information, an appreciation for the social, ethical and cultural aspects of health and the life-enriching skills they require to become self-directed, life-long learners.