September 2021



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PhenX Highlights
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Sickle Cell Disease Curative Therapies Protocols Released
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The Sickle Cell Disease Curative Therapies Working Group (WG) selected 13 protocols that were released in the PhenX Toolkit on August 16, 2021. The Sickle Cell Disease Curative Therapies WG was co-chaired by Dr. Ross Fasano of Emory University, Children's Healthcare of Atlanta, and Dr. Matthew Hsieh of the National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH). The Expanding PhenX Sickle Cell Disease Collections project is funded by NHLBI. The project scientist is Dr. Phil Tonkins. The PhenX Sickle Cell Research and Scientific Panel, co-chaired by Dr. James Eckman of Emory University and Dr. John J. Strouse of Duke University, provides overarching guidance for the Expanding PhenX Sickle Cell Disease Collections project.

Smoking Cessation, Harm Reduction and Biomarkers Protocols Released

The Smoking Cessation, Harm Reduction and Biomarkers Working Group selected 11 protocols that were released in the PhenX Toolkit on February 23, 2021. This work was supported by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) under Award Number 3U41HG007050-07S1. This award was funded by the Office of the Director, National Institutes of Health (OD), the National Institute on Drug Abuse (NIDA), and the National Heart, Lung, and Blood Institute (NHLBI). The project scientists were Dr. Jonathan Pollock of NIDA and Dr. Kay Wanke of the Office of Disease Prevention (ODP), Tobacco Regulatory Science Program (TRSP). The cochairs of the working group were Dr. Laura Bierut of Washington University in St. Louis and Dr. Gary Swan of Stanford University School of Medicine.

Notes from PhenX Steering Committee Meetings

June 4, 2021, webinar: Special guests Dr. Jenna Norton of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) and Dr. Dan Vreeman of RTI International gave presentations to the PhenX Steering Committee (SC). Dr. Norton presented a rationale for developing Logical Observation Names and Codes (LOINC) codes for Social Determinants of Health (SDOH) Collection protocols, and Dr. Vreeman presented an approach to increase PhenX compatibility using LOINC and FHIR® (Fast Health Interoperability Resources). The SC considered community input on Toolkit usability, tools and features and provided direction for moving forward. The SC agreed that PhenX should prioritize support for long-COVID research and encouraged PhenX to collaborate with the Health Post-Acute Sequelae of SARS-CoV-2 infection (PASC) Initiative, now named RECOVER (Researching COVID to Enhance Recovery).

January 13 and 29, 2021, webinars: An update on the COVID-19 Protocol Library was presented, and the SC discussed the six COVID-19 Specialty Collections released in the Toolkit in October 2020. The SC approved a new process to evaluate and update existing Toolkit content using small groups called Content Expert Panels. The SC approved the scope for the new Bone and Joint Working Group (WG), which included such elements as arthritis/osteoarthritis, spine abnormalities and bone health. Updates were provided for ongoing WGs, including the Smoking Cessation, Harm Reduction and Biomarkers WG, the Sickle Cell Disease (SCD) Curative Therapies WG and SCD Pain WG.

Explore the PhenX Toolkit
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New Features and Tools

COVID-19 Variable Compare Tool

The Variable Compare Tool helps researchers better assess content of COVID-19-related protocols at the variable level. Nineteen full-length protocols from the COVID-19 Protocol Library and 20 protocols from the Toolkit's COVID-19 Research Collection are included to compare overlap and similarities.

The tool provides three ways for investigators to compare protocols:

  • Search for any variables (survey questions and associated responses) that are related to the search term or keyword entered.
  • Compare two questionnaires side by side. This view highlights the number of similar variables and their degree of similarity.
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  • See the number of similar variables in common among a set of selected questionnaires on a "heatmap" (shown above).

This tool can be accessed from the top navigation bar under the COVID-19 drop-down menu (shown at left).

Top Domains and Protocols

*Top 5 Protocols:
  1. Ethnicity and Race
  2. Current Employment Status
  3. Current Age
  4. Educational Attainment - Individual
  5. Annual Family Income
Top 5 Domains:
  1. Substance Abuse and Addiction
  2. Mental Health Research
  3. Demographics
  4. Tobacco Regulatory Research
  5. Alcohol, Tobacco and Other Substances

*Each of the top five protocols is included in the Social Determinants of Health (SDOH) Core Collection, which is recommended along with COVID-19 specialty collections on the COVID-19 Research Collections page.

Rankings are based on downloads to "My Toolkit" from April 1 to June 30, 2021. See PhenX Toolkit's Use Statistics for additional data.

NIH Funding Opportunities
According to the PhenX FOAs & Notices page, there are a total of 440 National Institutes of Health (NIH) Funding Opportunity Announcements (FOAs) and 29 Notices that encourage use of standard PhenX Toolkit measurement protocols in NIH-funded research. Recent announcements include:
  • Investigators applying to the HEAL Initiative: Novel Targets for Opioid Use Disorders and Opioid Overdose FOA (RFA-DA-22-032) are strongly encouraged to incorporate the Core and Specialty collections of the Substance Abuse and Addiction Collection of the PhenX Toolkit.
  • Investigators applying to the Role of Work in Health Disparities in the U.S. FOA (PAR-21-275) are strongly encouraged to incorporate measures from the Core and Specialty collections in the Social Determinants of Health Collection of the PhenX Toolkit.
PhenX in the Community:
newsletter_2021_terry.png Sharon Terry of the Genetic Alliance is the recipient of the 2021 Advocacy Award from the American Society of Human Genetics (ASHG), recognizing her contributions as an exemplary advocate at the Genetic Alliance on behalf of people with genetic diseases. Ms. Terry is a member of the PhenX Steering Committee.
The National Human Genome Research Institute's Expectation for Sharing Quality Metadata and Phenotypic Data (NOT-HG-21-022) strongly encourages the use of existing data standards and ontologies generally endorsed by the community of research areas. NHGRI recognized the PhenX Toolkit's "large collection of well-established and vetted phenotypic measurement protocols" in the notice.
PhenX Publications

Using the PhenX Toolkit to Select Standard Measurement Protocols for Your Research Study, Current Protocols in Human Genetics, May 26, 2021.

Genomic Medicine Implementation Protocols in the PhenX Toolkit: Tools for standardized data collection, Genetics in Medicine, May 10, 2021.

The PhenX Toolkit: Establishing Standard Measures for COVID-19 Research, Current Protocols in Human Genetics, April 27, 2021.

Featured:
About
National Human Genome Research Institute Management

Jyoti Dayal, MS

Ms. Dayal is a project scientist in the Division of Genomic Medicine (DGM), National Human Genome Research Institute (NHGRI). She is NHGRI project scientist for PhenX and is on the PhenX Steering Committee. She spent 17 years in a high-throughput DNA sequencing lab at the National Institutes of Health (NIH) Intramural Sequencing Center (NISC/NHGRI). She joined the Extramural Research Program at NHGRI in 2015, and her portfolio includes the NIH Common Fund Undiagnosed Diseases Network (UDN), a consortium to improve the level of diagnosis of rare and undiagnosed conditions. In collaboration with the National Institute of Child Health and Human Development (NICHD), she also leads the Developmental Genotype-Tissue Expression Project.

Madison Goldrich, BS

Ms. Goldrich is a scientific program analyst in the DGM at NHGRI. A May 2020 graduate of the University of Virginia with a bachelor of science degree in biomedical engineering and a minor in government, she joined the Extramural Research Program at NHGRI in July 2020. In addition to her work with the PhenX Toolkit, she provides support to various programs within the DGM, including the UDN, the NHGRI Genomic Medicine Working Group, and the Variation, Function and Disease and Advancing Genomic Medicine Research funding opportunity announcements. She is passionate about eliminating health disparities to uplift marginalized communities.

Smoking Cessation Working Group Co-chairs About

Laura Bierut, MD

Dr. Bierut is the Alumni Endowed Professor and Vice Chair for Faculty Development in the Department of Psychiatry at Washington University School of Medicine in St. Louis. As a physician-scientist, Dr. Bierut has built a successful research program devoted to understanding the genetics of nicotine use disorder. She served on the Advisory Council for the National Institute on Drug Abuse (NIDA) and is an active member of the NIDA Genetics Consortium, a group of scientists leading NIDA's efforts to understand genetic causes of substance dependence. She currently is a member of the Food and Drug Administration's Tobacco Products Scientific Advisory Committee, and she is co-chair of the National Comprehensive Cancer Network Smoking Cessation Guidelines workgroup.

Gary E. Swan, PhD

Dr. Swan conducted research at SRI International (formerly Stanford Research Institute) for 35 years and was director of the Center for Health Sciences, a group of MD- and PhD-level scientists studying the origins and consequences of health behaviors and diseases. His research areas of interest include treatment of nicotine dependence, genetic and environmental determinants of addiction and disease, brain aging, and pharmacogenetics. He was principal investigator or co-investigator on more than 20 National Institutes of Health-funded grants and has published more than 300 scientific papers. Dr. Swan was a national consultant to the Transdisciplinary Tobacco Use Research Centers, was a member of the NIDA Genetics Consortium, served on the steering committee for the National Cancer Institute's Women, Tobacco, & Cancer Meeting, participated in the 2005 review of NIH's portfolio of grants on the genetic epidemiology of drug abuse, was the senior scientific editor of a 2009 NCI Monograph, and was elected as the 2012-2013 president of the Society for Research on Nicotine and Tobacco.

Current PhenX
Team Members
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RTI International

Carol M. Hamilton, PhD

Principal Investigator

Tabitha Hendershot

Co-Investigator

Amanda Riley, PMP, MBA

Project Manager

Wayne Huggins, PhD

Investigator

Deborah Maiese, MPA

Consensus Coordinator

Lisa Cox, MS

Steve Edwards, PhD

Michelle Engle, PhD

Lisa Gehtland, MD

Lauren Gridley, MS

Stephen Hwang, MS

Michelle Krzyzanowski, PhD

Mark Nelms, PhD

Helen Pan, PhD

Mike Phillips, MS

Pat West

National Human Genome Research Institute

Jyoti Dayal, MS

PhenX Project Scientist

Erin Ramos, PhD, MPH

Deputy Director, Division of Genomic Medicine

Madison Goldrich

Scientific Project Analyst

PhenX Supplement Project Scientists

Nancy Jones, PhD, MA

National Institute on Minority Health and Health Disparities

Jonathan Pollock, PhD

National Institute on Drug Abuse

Erin Ramos, PhD, MPH

National Human Genome Research Institute

William T. Riley, PhD

Office of Behavioral and Social Sciences Research

Phil Tonkins Jr., DrPH.

National Heart, Lung, and Blood Institute

Kay Wanke, PhD, MPH

Tobacco Regulatory Science Program

Funding
PhenX has been funded by the National Human Genome Research Institute (NHGRI) since 2007. Current PhenX funding is a Genomic Resource Grant award (U41HG007050) from NHGRI. In addition, current or prior funding for PhenX has been provided by the National Institute on Drug Abuse (NIDA), the Office of Behavioral and Social Sciences Research (OBSSR), the National Institute of Mental Health (NIMH), the National Heart, Lung, and Blood Institute (NHLBI), the National Institute on Minority Health and Health Disparities (NIMHD), the National Cancer Institute (NCI), and the Tobacco Regulatory Science Program (TRSP) of the National Institutes of Health (NIH).


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