May 2020

 
    PhenX Highlights
Visit The PhenX Toolkit
 
 
 
 
 
Social Determinants of Health Collections Released
 

The Social Determinants of Health (SDOH) Collections, funded by the National Institute on Minority Health and Health Disparities (NIMHD), was released in the Toolkit on May 11, 2020. Co-chaired by Dr. Barbara Entwisle of the University of North Carolina at Chapel Hill and Dr. Alicia Fernandez of the University of California, San Francisco, the SDOH Working Group (WG) selected 19 new protocols relevant to SDOH research for inclusion in the Toolkit. NIMHD, working in collaboration with the National Institutes of Health (NIH) SDOH WG, developed a core collection and two specialty collections including the protocols. The SDOH Core Collection includes measurement protocols deemed relevant for all research projects collecting comparable data on SDOH across studies. The Individual SDOH Specialty collection includes protocols for research about people answering for themselves or their family (e.g., access to health services and technology, job insecurity and spirituality). The Structural SDOH Specialty collection includes protocols at the structural or community level (e.g., concentrated poverty, food swamps, social vulnerability). The NIMHD Project Scientist is Dr. Nishadi Rajapakse.

 
 
 
 

PhenX COVID-19 Protocols Page

In March 2020, Bill Riley, director of the Office of Behavioral and Social Sciences Research (OBSSR), and Erin Ramos, National Human Genome Research Institute (NHGRI) PhenX Project Scientist, reached out to the PhenX team to contribute to the NIH response to COVID-19. The PhenX COVID-19 page provides a list of COVID-19 related measurement protocols (case report forms, instruments, surveys, questionnaires) that are currently in use. We hope that investigators will consider choosing from these protocols rather than developing new ones. The source of each protocol has been verified and contact information is provided in case additional information is needed. In the future, we plan to provide data dictionaries to enhance data interoperability and to support data harmonization. Please note these protocols have not been selected via the standard PhenX consensus process and cannot be considered broadly validated; investigators are encouraged to perform validation studies. Another important resource is the NIH Public Health Emergency and Disaster Research Response (DR2). The NIH DR2 provides a wide array of data collection tools and resources for use in public health emergencies and disasters, including the COVID-19 pandemic.

 
 
 
 
    Explore the PhenX Toolkit
New Features
 
Browse Protocols Tree

The Cross-Domain Concept Tree Browser allows users to intuitively browse protocols by scientific concept, organized by the National Library of Medicine’s (NLM)’s Medical Subject Headings (MeSH), the most widely used vocabulary in medical research. Users can identify conceptually related protocols across research domains and access protocols from multiple entry points. For example, cystic fibrosis is under both “Respiratory Tract Diseases” and “Digestive System Diseases.”

 
 
Research Using PhenX
 

Publications Citing Use of PhenX Protocols includes 86 publications that report using specific PhenX protocols. Twenty-six Linked Studies Provided by Investigators provide information about use of PhenX protocols submitted by study investigators. New publications and linked studies are updated regularly.

 
Social Media: Links to YouTube and Twitter on the PhenX Homepage
 
Icons linking to our Twitter feed and YouTube channel have been added to the Toolkit’s top navigation bar. Video tutorials on YouTube are also found under the “Help” menu and include “Searching the PhenX Toolkit” and “How to Use My Toolkit.” Follow us on Twitter @PhenXToolkit
 
PhenX Working Group News
 

There’s still time to participate in the Genomic Medicine Implementation WG community outreach. The WG has extended outreach through May 29, 2020. The WG is co-chaired by Dr. Wendy Chung of Columbia University and Dr. Kyle Brothers of the University of Louisville.

The Cancer Outcomes and Survivorship WG will conduct outreach in June to get feedback on measurement protocols recommended for inclusion in the Toolkit. The WG is co-chaired by Dr. Roxanne Jensen of the National Cancer Institute (NCI) and Dr. Larissa Nekhlyudov of Brigham and Women’s Hospital.

The Pediatric Development WG completed work on December 11, 2019, with the release of 18 measurement protocols in a new domain covering child development, lifestyle, and school and home environments. Dr. Michelle Bosquet Enlow of Boston Children’s Hospital was the WG chair.

 
 
 
Notes from PhenX Steering Committee Meetings

During a webinar on May 11, 2020, the PhenX Steering Committee (SC) heard updates from the PhenX Team, Working Groups, and Expert Review Panels. Of particular interest was collaboration between PhenX and NIH to provide COVID-19 protocols in the Toolkit. The SC recommended a crowd-sourcing approach to develop new COVID-19 collections for release in the Toolkit.

At a February 17, 2020 webinar, the SC heard updates from the PhenX team about Toolkit improvements and discussed emerging issues. Working Groups (WGs) for Genomic Medicine Implementation, Social Determinants of Health, Cancer Outcomes and Survivorship, and Smoking Cessation presented updates. The team also reported plans to expand the Sickle Cell Disease (SCD) Collections with co-funding by the National Heart, Lung, and Blood Institute (NHLBI).

At the October 28, 2019 in-person meeting in Bethesda, MD, the SC approved measures recommended by the Pediatric Development WG and received updates from ongoing working groups. Kay Wanke, deputy director of the Office of Disease Prevention’s Tobacco Regulatory Science Program, presented an overview of work planned under the new Smoking Cessation supplement. PhenX team members presented an update on a pilot project to link PhenX variables to the Observational Medical Outcomes Partnership (OMOP) common data model.

 
 
 
 
Top Domains and Protocols

 

Top 5 Protocols:

1.   Annual Family Income

2.   Current Age

3.   Ethnicity

4.   Current Educational Attainment

5.   Gender Identity

 

Top 5 Domains:

1.     Substance Abuse and Addiction

2.     Mental Health Research

3.     Tobacco Regulatory Research

4.     Alcohol, Tobacco and Other Substances

5.     Demographics

Rankings are based on downloads to “My Toolkit” from January 1 to March 31, 2020enX Toolkit’s Use Statistics for additional data.

 
    PhenX in the Community
 

Standard Measures for Tobacco Regulatory Research: The PhenX Toolkit Collections was published as a supplement to Tobacco Control in January 2020 (Vol. 29, Suppl. 1). The special issue includes eight papers focusing on the Tobacco Regulatory Research (TRR) Collections. An editorial describes the vision and goals of the project and TRR Core Collections. Five original research papers outline the Host, Agent, Vector, and Environment (HAVE) specialty domains in the collection, the consensus process for selecting protocols, research gaps in these fields, and an analysis of electronic cigarette research grants funded by the National Institutes of Health (NIH). A review of risk perception measures in tobacco control research concludes the issue.

Dr. Carol Hamilton of RTI International presented “The PhenX Toolkit May 2020: COVID-19 and Social Determinants of Health,” a webinar, May 15, 2020, as part of the Genetic Alliance’s Registry Bootcamp Series. 

Tabitha Hendershot of RTI International shared information about the PhenX Toolkit at the NIH Tobacco Regulatory Science Meeting on October 21, 2019, in Bethesda, MD.

Mike Phillips of RTI International presented “New Content and Tools in the PhenX Toolkit,” a poster, October 16, 2019, at American Society of Human Genetics (ASHG) Annual Meeting. The Toolkit Team also presented information about the PhenX Toolkit at a booth in the Exhibit Hall.

 
 
 
 
    Featured:
Social Determinants of Health Working Group Co-Chairs
About
 
 
Barbara Entwisle, PhD
Dr. Entwisle is a Kenan Distinguished Professor of Sociology and Fellow of the Carolina Population Center (CPC). Her research focuses on social, natural, and built environments and their consequences for demographic and health outcomes. She is a leader in the development of new tools, including methods for estimating multilevel models, integrating social and spatial data, and spatially explicit agent-based modeling approaches. Over her career, she has contributed to the design of innovative surveys around the world, including the China Health and Nutrition Survey, the Russia Longitudinal Monitoring Survey, and the Nang Rong (Thailand) Surveys of Social and Demographic Change.
 
Alicia Fernandez, MD
Dr. Fernandez is a professor of medicine at University of California, San Francisco (UCSF), a health services researcher, a practicing general internist at Zuckerberg San Francisco General Hospital, and the director of the UCSF Latinx Center of Excellence. Her research has primarily focused on improving the care of immigrants with chronic disease with a strong focus on understanding the role of language and cultural barriers in diabetes care. Dr. Fernandez has been awarded a national professorship from the Arnold P. Gold Foundation, a K24 award from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) and was elected to the UCSF Academy of Medical Educators
 
 
 

 

    Pediatric Development Working Group Chair
 
Michelle Bosquet Enlow, PhD
Dr. Bosquet Enlow of Boston Children’s Hospital is a developmental and clinical psychologist with training in infant mental health, the assessment and treatment of traumatic stress in children and adults, the development of child stress regulation, and the etiology and maintenance of anxiety. She received a PhD from the Developmental Psychopathology and Clinical Science program at the University of Minnesota. Dr. Bosquet Enlow completed an internship in clinical psychology and a fellowship in infant mental health at Louisiana State University Health Sciences Center and a postdoctoral fellowship at the Boston Consortium in Clinical Psychology.
 
 
    Current Research
Team Members
 
More
 

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

Lauren Gridley, MS
Stephen Hwang, MS
Lisa Kilpatrick, MS
Michelle Krzyzanowski, PhD
Meisha Mandal, PhD
Helen Pan, PhD
Mike Phillips, MS
Pat West


National Human Genome Research Institute

Erin Ramos, PhD, MPH
PhenX Project Scientist
Natalie Pino
PhenX Project Analyst

National Heart, Lung, and Blood Institute

Traci Mondoro, PhD
PhenX NHLBI Project Scientist

National Institute on Drug Abuse

Jonathan Pollock, PhD
PhenX NIDA Project Scientist


National Institute on Minority Health
and Health Disparities

Nishadi Rajapakse, PhD
PhenX NIMHD Project Scientist
Nancy Jones, PhD, MA


Office of Disease Prevention

Kay Wanke, PhD, MPH
PhenX Tobacco Regulatory Science Program Project Scientist

 
Previous PhenX Newsletters
 
PhenX Steering Committee
 
 
Funding
 
PhenX is funded by the National Institutes of Health (NIH) Genomic Resource Grant (U41HG007050) from the National Human Genome Research Institute (NHGRI) with current or prior funding support from 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), and the Tobacco Regulatory Science Program (TRSP).

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