July 1, 2015

PhenX Newsletter - Information and Updates Issue 24. July 1, 2015


A Crowdsourcing Approach to Annotate Measures for use with Rare Genetic Conditions—Webinar July 8, 2015

We recognize that clinicians may already be using PhenX measures to assess rare genetic conditions, even though they may not be noted in the Toolkit as being appropriate for that particular condition. We would like to learn more about how measures are being used so we can note the PhenX measures that can be used with specific genetic conditions. PhenX has developed a crowdsourcing tool that makes it easy for clinicians to provide this information. To launch this effort, the Genetic Alliance is hosting a webinar, “PhenX Measures for Rare Genetic Conditions—Introducing an Annotation Tool and Crowdsourcing Approach,” from 11 a.m. to 12 p.m. EDT July 8, 2015. Presenters include Dr. Erin M. Ramos, PhenX Project Scientist, National Human Genome Research Institute; Dr. Carol M. Hamilton, PhenX Principal Investigator, RTI International; and Ms. Sharon Terry, President and Chief Executive Officer of Genetic Alliance.

Measures selected by the PhenX Rare Genetic Conditions Working Group will be highlighted, and a link to the annotation tool will be provided to webinar participants. A live demonstration of the annotation tool will show participants how to provide information relevant to specific genetic conditions. To register for the webinar, click on the banner below.


PhenX Measures for Rare Genetic Conditions—Released April 30, 2015

PhenX Featured Measure button
The PhenX Toolkit released 15 new measures selected by the Rare Genetic Conditions (RGC) Working Group (WG) at the end of April.. The RGC WG initially considered human organ systems as a way to help identify measures that are broadly relevant to rare genetic conditions. In addition, the RGC WG included some measures that are primarily applicable to specific conditions. PhenX is planning a crowdsourcing effort to acquire additional information about specific rare genetic conditions to further enhance the RGC measures in the PhenX Toolkit.


The RGC WG Chair was Dr. Peter Byers, and the SC Liaison was Ms. Sharon Terry.


New Tobacco Regulatory Research Measures—Released June 24, 2015

With the addition of measures for Agent, Vector and Environment, measures from all five Tobacco Regulatory Research (TRR) Working Groups (WGs) are now available in the PhenX Toolkit. The PhenX Measures for Tobacco Regulatory Research project is funded by the Food and Drug Administration and the Tobacco Regulatory Science Program (TRSP) as a Supplement to the PhenX Genomic Resource Grant award. Dr. Kay Wanke, Deputy Director of TRSP at the National Institutes of Health, is the Project Scientist. The Tobacco Regulatory Research Panel is co-chaired by Dr. Gary Swan and Dr. Jodi Prochaska.
PhenX Featured Measure button


Social-Cognitive (10 measures)

Biobehavioral (9 measures)

Agent (7 measures)

Vector (12 measures)

Environment (10 measures)


PhenX Steering Committee In-Person Meeting—April 8–9, 2015

The PhenX Steering Committee (SC) met in-person in Bethesda, MD. The SC provided guidance on emerging issues, including proposed changes to the PhenX Toolkit, the Expert Review Panel (ERP) process, and upcoming ERPs and Working Groups (WG).

At the meeting, the SC approved all measures selected by the Rare Genetic Conditions WG. The SC also recommended that ERP 2 review Toolkit measures selected by the Demographics, Environmental Exposures, and Social Environments WGs; that ERP 3 review measures selected by the Alcohol, Tobacco, and Other Substances WG with those selected by the Substance Abuse and Addiction WGs; and that ERP 4 review measures selected by the Psychiatric, Neurology, and Psychosocial WGs.

The SC decided that Pregnancy and Pediatrics will be the next research domain to be addressed.

The SC will meet for a teleconference on July 7, 2015, and again for an in-person meeting October 19–20, 2015.


PhenX on the Move

On May 29, 2015, the PhenX team met with the Sickle Cell Ontology Group of the Human Heredity and Health in Africa (H3Africa) Initiative to discuss ongoing work and potential collaboration. The H3Africa Initiative, funded by the National Institutes of Health and the Wellcome Trust, has established a network or African investigators to study the genomic and environmental factors that impact the health of African people.

On May 13, 2015, James M. Bjork, PhD, gave a talk that included information about PhenX measures and the PhenX Toolkit. The talk, “Impulsivity Measurement in the Big Data Era: Resources for Harmonization,” was presented at the 15th annual meeting of the International Society for Research on Impulsivity (InSRI) in Toronto, Ontario, Canada. Dr. Bjork was a member of the Substance Abuse and Addiction Scientific Panel and is currently an associate professor at the Institute for Drug and Alcohol Studies at Virginia Commonwealth University in Richmond, VA.

On March 25, 2015, Dr. Hamilton presented “PhenX Measures for Collaborative Biomedical and Translational Research” at the Data for Decisions (D4D) Conference and Exposition in Raleigh, NC.

On April 27, 2015, Dr. Hamilton presented “PhenX Overview and Updates” via webinar to the ClinGen Phenotype Working Group.


Explore the PhenX Toolkit

Featured Measure

The featured measure is the Ataxia Rating Scale, selected by the Rare Genetic Conditions Working Group (WG). The WG chose the Scale for the Assessment and Rating of Ataxia (SARA) to assess the severity of cerebellar ataxia. This condition is exhibited by uncoordinated body movements, unsteady gait, and loss of balance. SARA includes eight physical function tests that assess gait, stance, sitting, speech, finger-chase movement, nose-finger movement, fast alternating movements, and heel-shin movement. This scale has been shown to be a reliable and valid scale for measuring ataxia.


New Toolkit Home Page Buttons Provide Easy Access to Popular Features

New buttons on the PhenX Toolkit home page provide one-click access to popular features.

Explore these features by clicking the hyperlinked buttons below:


Top Domains and Top Measures


The Top 5 Domains and Top 5 Measures for June 2015 are listed below. The Top Domains and Measures are listed on the PhenX Toolkit home page and are recalculated and updated with each new release.


Top 5 Domains in the PhenX Toolkit
  1. Demographics
  2. Anthropometrics
  3. Alcohol, Tobacco and Other Substances
  4. Cardiovascular
  5. Environmental Exposures

Top 5 Measures in the PhenX Toolkit
  1. Current Age
  2. Gender
  3. Ethnicity
  4. Race
  5. Weight


Featured: Tobacco Regulatory Research Project Scientist and Steering Committee Members


Tobacco Regulatory Research Project Scientist


Kay Wanke, PhD

Dr. Wanke joined the National Institutes of Health (NIH) Office of Disease Prevention in March 2013 as the Deputy Director of the Tobacco Regulatory Science Program (TRSP), which coordinates the trans-NIH collaborative effort with the U.S. Food and Drug Administration’s (FDA’s) Center for Tobacco Products (CTP) to foster TRR. She first began assisting the FDA’s CTP in establishing its research programs while working as a program officer at the National Institute on Drug Abuse (NIDA) in the Epidemiology Research Branch. There, she co-led the development of the program for the Tobacco Centers of Regulatory Science and helped coordinate CTP’s collaborative efforts across the NIH Institutes. At NIDA, Dr. Wanke’s portfolio of grants covered the areas of tobacco control, tobacco regulatory science, genetic and behavioral epidemiology, and novel and improved phenotypes of tobacco and other drugs of abuse. She also previously served as a Health Scientist Administrator in the NIH Office of Behavioral and Social Sciences Research, where she developed programs to foster and support research in behavioral and social science genetics. Dr. Wanke received her PhD in clinical psychology from Southern Illinois University at Carbondale and completed her predoctoral internship at the University of Alabama at Birmingham School of Medicine. Her training and clinical experience include child psychology, forensic psychology, substance abuse, serious mental illness, marriage and family therapy, and developmental and neuropsychological assessment. She initially came to the NIH in 2001 as a Cancer Prevention Fellow at the National Cancer Institute. While in that fellowship, she completed her MPH at the Harvard School of Public Health and conducted research in tobacco use and depression, factors associated with adherence, strategies to improve smoking phenotype definition, and behavioral genetics of smoking cessation.


PhenX Steering Committee Members


Daniel R. Masys, MD, FACMI

Dr. Masys is an affiliate professor of Biomedical and Health Informatics at the University of Washington School of Medicine in Seattle. He joined the Department of Biomedical Informatics and Medical Education after retiring as professor and chair of the Department of Biomedical Informatics and Professor of Medicine at the Vanderbilt University School of Medicine in 2011. An honors graduate of Princeton University and the Ohio State University College of Medicine, he completed postgraduate training in internal medicine, hematology, and medical oncology at the University of California, San Diego (UCSD), and the Naval Regional Medical Center, San Diego. He served as chief of the International Cancer Research Data Bank of the National Cancer Institute, the National Institutes of Health (NIH), and was also director of the Lister Hill National Center for Biomedical Communications, a computer research and development division of the National Library of Medicine. He also served as director of Biomedical Informatics at the UCSD School of Medicine, director of the UCSD Human Research Protections Program, and professor of medicine. Dr. Masys is an elected member of the Institute of Medicine (IOM) of the National Academy of Sciences. He is a diplomate of the American Board of Internal Medicine in Medicine, Hematology, and Medical Oncology. He is a fellow of the American College of Physicians, and fellow and past president of the American College of Medical Informatics. Dr. Masys’s professional interests include development of informatics infrastructure for conducting clinical and translational research, genome-phenome correlation using phenotype data derived from electronic medical records data, and approaches to incorporating genomic data effectively into clinical systems. He is currently serving as advisor to the Office of the NIH Director for the Precision Medicine Initiative, is a member of the IOM National Cancer Policy Forum, and is a member of the IOM Committee to Review NASA’s Evidence Reports on Human Health Risks.


Sharon Terry, MA

Sharon Terry is president and CEO of Genetic Alliance, a network of more than 10,000 organizations, of which 1,200 are disease advocacy organizations. She is the founding CEO of PXE International, a research advocacy organization for the genetic condition pseudoxanthoma elasticum (PXE). PXE affects Terry’s two adult children. As co-discoverer of ABCC6, the gene associated with PXE, Terry holds the patent for ABCC6 that allows her to act as its steward, and she has assigned her rights to the foundation. She developed a diagnostic test and conducts clinical trials. She is the author of 140 peer-reviewed papers, of which 30 are PXE clinical studies. Terry is also a co-founder of the Genetic Alliance Registry and Biobank. In her focus at the forefront of consumer participation in genetics research, services, and policy, she serves in a leadership role on many of the major international and national organizations, including the Accelerating Medicines Partnership, Institute of Medicine (IOM) Science and Policy Board, the IOM Roundtable on Translating Genomic-Based Research for Health, the PubMed Central National Advisory Committee, the PhenX scientific advisory board, the Global Alliance for Genomics and Health, the International Rare Disease Research Consortium Executive Committee, and she also serves as Founding President of EspeRare Foundation of Geneva, Switzerland. She is on the editorial boards of several journals and is an editor of Genome. She led the coalition that was instrumental in the passage of the Genetic Information Nondiscrimination Act. She received an honorary doctorate from Iona College for her work in community engagement in 2006, the first Patient Service Award from the University of North Carolina Institute for Pharmacogenomics and Individualized Therapy in 2007, the Research! America Distinguished Organization Advocacy Award in 2009, and the Clinical Research Forum and Foundation’s Annual Award for Leadership in Public Advocacy in 2011. In 2012, she became an honorary professor of Hebei United University in Tangshan, China, and also received the Facing Our Risk of Cancer Empowered Spirit of Empowerment Advocacy Award. She was named one of FDA’s “30 Heroes for the Thirtieth Anniversary of the Orphan Drug Act” in 2013. In 2012 and 2013, Terry won $400,000 in first prizes in three large competitions for the Platform for Engaging Everyone Responsibly (PEER). PEER was awarded a $1 million contract from Patient Centered Outcomes Research Institute in 2014. Terry is an Ashoka Fellow. With her husband Patrick, she is an avid paragliding pilot, rock climber, and weekend farmer.


Research Team Members


RTI International NHGRI
Carol M. Hamilton, PhD Principal Investigator Erin Ramos, PhD, MPH Project Scientist
Tabitha Hendershot Co-Investigator Teri Manolio, MD, PhD Director, Division of
Amanda Riley, PMP Project Manager   Genomic Medicine
Deborah Maiese, MPA Consensus Coordinator Brenda Iglesias Scientific Program Analyst
Darigg Brown, PhD Investigator    
Wayne Huggins, PhD Investigator    
Destiney Nettles, MPM Investigator    
Michael Phillips, MS Investigator    
Helen Pan, PhD Toolkit Lead    
Pat West Communications Lead    


Link to Previous PhenX Newsletters




PhenX is supported by a Genomic Resource award (U41) funded by National Human Genome Research Institute (NHGRI) with co-funding by National Institute on Drug Abuse (NIDA).



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