February 2021



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    PhenX Highlights
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PhenX Rapid Release: COVID-19 Research Collections
 

COVID-19 Research Collections were released in the PhenX Toolkit on October 30, 2020. Six specialty collections of protocols were selected by a crowdsourcing method and approved by the PhenX Steering Committee:

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  • Behaviors and Risks
  • Ethnicity, Race and Demographics
  • History, Treatment and Outcomes
  • Information Resources
  • Psychosocial and Mental Health
  • Socioeconomic

PhenX received funding in August 2020 from the Office of Behavioral and Social Sciences Research (OBSSR), National Human Genome Research Institute (NHGRI), the National Institute on Drug Abuse (NIDA), the National Institute on Minority Health and Health Disparities (NIMHD), and the National Cancer Institute (NCI) to establish recommended collections of measurement protocols to support research on COVID-19.

Use of these protocols will help researchers better understand the symptoms and treatments of COVID-19 diagnosis as well as the socioeconomic and mental health effects due to COVID-19. As part of these collections, 20 new COVID-19- related protocols were added to the Toolkit. As of February 1, 2021, the new COVID-19 protocols had been viewed 7,008 times and had been added to My Toolkit 2,807 times.

PhenX COVID-19 Protocol Library

In collaboration with OBSSR and the NIH Public Health Emergency and Disaster Research Response (DR2), PhenX was asked to participate in the NIH response to COVID-19. COVID-19 instruments submitted to NIH are carved into modules for inclusion in the PhenX COVID-19 Protocol Library. PhenX also shares the complete instruments and information about the source. One of the goals of the library was to encourage investigators to use COVID-19 protocols others were already using rather than creating additional ones. As of January 27, 2021, the library included 127 complete instruments and 511 modules in PDF format and had been viewed 41,043 times. You can access the library from any page in the Toolkit via the top navigation bar; pull down the menu under “Protocols” to “COVID-19 Protocol Library.”

 
 
 
 
Toolkit Releases
 
Cancer Outcomes and Survivorship Protocols

The Cancer Outcomes and Survivorship Working Group (WG) funded by a supplement from the National Human Genome Research Institute (NHGRI) and building on existing Toolkit content, released 15 protocols for cancer outcomes and survivorship research in the Toolkit on December 17, 2020. The WG was co-chaired by Dr. Roxanne Jensen of the National Cancer Institute (NCI) and Dr. Larissa Nekhlyudov of Brigham and Women’s Hospital. The PhenX Steering Committee liaison to this WG was Dr. Catherine McCarty.

Genomic Medicine Implementation Protocols

The Genomic Medicine Implementation (GMI) research domain, funded by a supplement from the National Human Genome Research Institute (NHGRI), was released in the Toolkit on September 10, 2020. The PhenX Steering Committee (SC) recognized this emerging research domain and the need to provide guidance and standard measures for investigators who are entering this realm. Co-chaired by Dr. Wendy Chung of Columbia University and Dr. Kyle Brothers of the University of Louisville, the GMI Working Group selected 15 protocols for GMI research for inclusion in the Toolkit. The PhenX SC liaison to the WG was Dr. Marylyn Ritchie.

 
 
 
 
PhenX Working Group News
 

The Smoking Cessation Working Group (WG) concluded community outreach on December 18, 2020. Protocols for smoking cessation research are scheduled to be released in the Toolkit in February 2021. Funded by the National Human Genome Research Institute (NHGRI) and 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 WG is co-chaired by Dr. Laura Bierut of Washington University in St. Louis and Dr. Gary Swan of Stanford University School of Medicine. Project scientists are Dr. Kay Wanke of Office of Disease Prevention, and Dr. Jonathan Pollock of NIDA. Dr. Beirut, Dr. Swan, Dr. Wanke and WG member Dr. Neal Benowitz will lead a symposium, “Biomarkers for Tobacco Dependence and Treatment: Promises and Pitfalls,” at the Society for Research on Nicotine and Tobacco (SRNT) annual meeting February 24-27, 2021.

 
 
 
 
Notes from PhenX Steering Committee Meetings
 

A webinar was held on October 8, 2020, during which the Steering Committee (SC) reviewed the results of PhenX COVID-19 crowdsourcing and the PhenX team’s plan for rapid release of the COVID-19 Research Collections. The SC also received progress updates from ongoing working groups (WGs), expert review panels, and research panels.

A webinar was held on September 9, 2020, during which the PhenX SC reviewed the results of COVID-19 crowdsourcing and provided input on the development of COVID-19 collections. The SC also approved recommendation of the Social Determinants of Health Core Collection.

A webinar was held on August 17, 2020, during which the SC received updates from the Genomic Medicine Implementation WG and the Office of Behavioral and Social Sciences Research (OBSSR) on the response to COVID-19 and related work by the PhenX team on the COVID-19 project.

 
 
 
    Explore the PhenX Toolkit
 
New Features
 
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Tutorial: Using the Browse Protocols Tree
A new three-minute video tutorial shows how to browse and view measurement protocols using the Toolkit’s new tree browser. The tree browser shows clusters of protocols related by scientific concept that may come from different research domains or collections in Toolkit.

 

Follow @PhenxToolkit on Twitter for More Updates

 Stay in touch with PhenX news by following @PhenxToolkit on Twitter.

 

 

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 October 1 to December 31, 2020. See PhenX Toolkit’s Use Statistics for additional data.

 
Funding Opportunities and Notices Encourage Use of Toolkit
 
The Toolkit’s FOAs & Notices pages list a total of 394 National Institutes of Health (NIH) Funding Opportunity Announcements (FOAs) and 28 Notices that encourage use of standard Toolkit measurement protocols in NIH-funded research. In 2020 alone, 30 FOAs and 14 Notices encouraged the use of the Toolkit protocols and collections.
 
 
 
    PhenX in the Community:

 

Helen Pan of RTI International presented a poster, “PhenX Common Measures for Collaborative Research: New Developments,” at the American Medical Informatics Association (AMIA) virtual annual symposium, November 14–18, 2020.

Michelle Krzyzanowski of RTI International presented “New PhenX Protocols for Social Determinants of Health Research and Introducing a PhenX COVID-19 Resource,” a poster at the American Society of Human Genetics (ASHG) virtual meeting, October 27–30, 2020.

Stephen Hwang, Lauren Gridley, and Michelle Krzyzanowski of RTI International presented “PhenX Consensus Measures for Phenotypes and Exposures,” at RTI’s 2020 Virtual Technology Showcase, September 3, 2020.

Erin Ramos of the National Human Genome Research Institute presented “The PhenX Toolkit” for the National Institute on Minority Health and Health Disparities’ Health Disparities Research Institute, August 6, 2020.

 
 
    Featured:
 
About
 
Cancer Outcomes and Survivorship Working Group Co-chairs
 
Larissa Nekhlyudov, MD, MPH
Dr. Nekhlyudov is an associate professor of medicine at Harvard Medical School and is a practicing internist at the Brigham and Women’s Hospital in Boston. She is also a clinical director of internal medicine for cancer survivors at the Dana-Farber Cancer Institute, where she offers clinical care for long-term survivors of childhood and adult cancers. Dr. Nekhlyudov is particularly interested in improving the care of cancer survivors and the interplay between primary and oncology care.

 

 
Roxanne E. Jensen, PhD
Dr. Jensen is a psychometrician and program director in the Outcomes Research Branch in the Healthcare Delivery Research Program at the National Cancer Institute. Dr. Jensen’s research interests include the use of patient-reported outcomes in clinical care settings, integration of patient-generated health data into electronic health records, and applying machine learning and other data science methods in cancer health care delivery. She is the scientific lead for the SEER–Medicare Health Outcomes Survey (SEER-MHOS) linked database on patient-reported outcomes.

 

 
Genomic Medicine Implementation Working Group Co-chairs
About
 
 
Wendy Chung, MD, PhD
Dr. Chung is a clinical and molecular geneticist and the Kennedy Family Professor of Pediatrics and Medicine at Columbia University. She directs National Institute of Health-funded research programs in human genetics of birth defects, including congenital diaphragmatic hernia, congenital heart disease, and esophageal atresia; autism; neurodevelopmental disorders; pulmonary hypertension; cardiomyopathy; obesity; diabetes; and breast cancer. She leads the Precision Medicine Resource in the Irving Institute at Columbia University.

 

 
Kyle Brothers, MD, PhD
Dr. Brothers is an associate professor of pediatrics and the endowed chair for pediatric clinical and translational research at the University of Louisville, where he directs the Division of Pediatric Clinical and Translational Research. Dr. Brothers is a pediatrician and bioethicist who conducts research on ethical issues in the translation of genomic technologies to clinical practice and on research ethics issues encountered in contemporary models of biomedical research. Dr. Brothers is a practicing primary care pediatrician and serves as a clinical ethics consultant at Norton Children's Hospital in Louisville, Kentucky.
 
 
 
    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
Co-Investigator

Deborah Maiese, MPA
Consensus Coordinator

Lisa Cox, MS

Steve Edwards, PhD

Michelle Engle, PhD

Lauren Gridley, MS

Stephen Hwang, MS

Michelle Krzyzanowski, PhD

Helen Pan, PhD

Mike Phillips, MS

 
 
National Human Genome Research Institute

Erin Ramos, PhD, MPH
PhenX Project Scientist

Jyoti Dayal, PhD
PhenX Program Director

Madison Goldrich
PhenX Project Analyst

 
National Heart, Lung, and Blood Institute

Phil Tonkins Jr., Dr.P.H.
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 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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