November 5, 2015

PhenX Newsletter - Information and Updates Issue 25, November 5, 2015


PhenX Toolkit Highlighted in ASHG Presidential Symposium

The PhenX Toolkit was noted as "a fabulous public good that NHGRI and NIH have brought us" during the Presidential Symposium at the 2015 Conference for the American Society of Human Genetics in Baltimore, Md. Dr. David Hunter of Boston’s Harvard TH Chan School of Public Health described it this way during his presentation on Oct. 6, encouraging the audience to visit the PhenX Toolkit web site. The mention brought increased attention to PhenX events at ASHG. (See PhenX on the Move below.)

PhenX Measures for Obesity Research—September 9, 2015

In September, Obesity became the 23rd research domain in the PhenX Toolkit. Led by WG co-chairs Dr. Nancy Butte and Dr. Steven Smith, the Obesity WG selected a total of 11 new measures. Recognizing the variety of measures that apply to obesity research, the WG also identified additional relevant measures found in other PhenX domains and collections. This additional list of measures can also be found under the Obesity domain.

PhenX Measures for Sickle Cell Disease Research — Released August 12, 2015

The PhenX Sickle Cell Disease Research and Scientific Panel (SRSP) and two Working Groups (WGs) released 25 new measures to the Toolkit in the Sickle Cell Disease (SCD) Research Collection in August. The PhenX Measures for SCD Research project is funded by the National Heart, Lung, and Blood Institute (NHLBI) as an administrative supplement to the PhenX Genomic Resource Grant. Dr. Ellen M. Werner, program director in the Blood Epidemiology and Clinical Therapeutics Branch at NHLBI, is the project scientist; Dr. James R. Eckman and Dr. Kathryn L. Hassell were co-chairs of the SRSP.
Sickle Cell Disease Research
The SRSP created the SCD Core Collections of measures. Core Tier 1 measures are relevant and essential to all areas of SCD research and are recommended for use by all NHLBI-funded investigators performing human subjects SCD research. Core Tier 2 measures, in contrast, are relevant to many areas of SCD research but are more specialized, require a greater time commitment, and are complementary to Core Tier 1 measures.
Each WG was responsible for creating a specialty collection of measures that focused on its specific areas of research and complemented the Core Collection measures. The WGs and the SRSP also reviewed relevant existing PhenX Toolkit measures for their applications to SCD.

Social-Cognitive (10 measures)
Biobehavioral (9 measures)
Agent (7 measures)
Vector (12 measures)
Environment (10 measures) --> Core Tier 1 (11 measures)
Core Tier 2 (16 measures)
SCD WG 1: Cardiovascular, Pulmonary, and Renal Specialty Collection (14 measures)
SCD WG 2: Neurology, Quality of Life, and Health Services Specialty Collection (10 measures)

PhenX Mental Health Research Eating Disorders Measures—Released August 7, 2015

The Eating Disorders WG released 10 new measures, completing the PhenX Measures for Mental Health Research (MHR) Collection funded by the National Institute of Mental Health (NIMH). An eight-member Mental Health Research Panel (MHRP) was convened to facilitate the inclusion of a Core Collection and three Specialty Collections of MHR measures in the Toolkit. Dr. Gregory K. Farber, director of the Office of Technology Development and Coordination at NIMH, is the project scientist. Co-chairs of the Eating Disorders WG were Dr. James D. Lock and Dr. James E. Mitchell. Mental Health Research
Core Tier 1 measures are relevant and essential to all areas of MHR and are recommended for use by all NIMH-funded investigators performing human subjects research. Core Tier 2 measures are relevant to many areas of MHR but are more specialized, require a greater time commitment, and are complementary to Core Tier 1 measures.

Core Tier 1 (10 measures)
Core Tier 2 (11 measures)
Eating Disorders Specialty Collection (10 measures)
Post-traumatic Stress Disorders (PTSD) Specialty Collection (10 measures)
Suicide Specialty Collection (7 measures)

PhenX Steering Committee In-Person Meeting—Oct. 19-20, 2015

The PhenX Steering Committee (SC) met in-person in Bethesda, MD. During the two-day meeting, the SC provided guidance on emerging issues related to proposed measures for the Toolkit, the inclusion of additional relevant measures to domain pages on the Toolkit, Expert Review Panel (ERP) processes and procedures, and annotations for specific conditions. The SC finalized the scope of the next Working Group, Pregnancy and Pediatrics, and selected domains to be reviewed by the next three ERPs. The next three ERPs to be assembled are:

  • ERP 5 – Cancer, and Infectious Diseases and Immunity
  • ERP 6 – Skin, Bone, Muscle and Joint
  • ERP 7 – Respiratory and Cardiovascular

In addition, the SC received updates from the current ERPs, the Obesity Working Group, and the three Administrative Supplements: Tobacco Regulatory Research, Mental Health Research, and Sickle Cell Disease Research. Representatives from caDSR (Cancer Data Standards Registry and Repository) and Trans-NIH CDE (Common Data Element) also attended and presented on the ongoing work of these initiatives as well as their collaboration efforts with PhenX.

PhenX Expert Review Panel 1 Completes Review Oct. 1, 2015

The first PhenX Expert Review Panel (ERP 1) completed a thorough review of the measures in the Anthropometrics, Diabetes, Nutrition and Dietary Supplements, and Physical Activity and Physical Fitness domains. Changes to these domains were released in early October.

These experts met for several months to review the measures. They identified protocols that did not need modification, that needed to be replaced, updated, and any new measures to be added. The new “Process and Review” section provides a summary of the ERP changes on each protocol page.

A total of 57 measures and Supplemental Information were reviewed across the four domains. All ERP recommendations were approved by the Steering Committee at its April in-person meeting. This ERP successfully paved the way for future ERPs to conduct a review process of PhenX measures.

The four domains released by ERP 1 are linked below:

Anthropometrics (16 measures)
Diabetes (15 measures)
Nutrition and Dietary Supplements (12 measures)
Physical Activity and Physical Fitness (14 measures)

PhenX on the Move—ASHG and More

PhenX presented the following at the 2015 Conference for the American Society of Human Genetics:   PhenX Featured Measure button


  • Dr. Jonathan Haines of Case Western Reserve University and Dr. Carol Hamilton of RTI International moderated an invited session, "Human Phenotypes for Researchers, Clinicians and Patients, ” on Oct. 7, 2015. Dr. Abel Kho (Northwestern University), Dr. Cathy McCarty (Essentia Institute for Rural Health), Dr. Heidi Rehm (Harvard Medical School) and James O'Leary (Genetic Alliance) were on the panel of speakers.
  • PhenX Investigator Wayne Huggins presented a poster, "The PhenX Toolkit: A Genomic Resource for Collaborative and Translational Biomedical Research," on Oct. 9, 2015.
  • The PhenX Toolkit Team presented information on the PhenX Toolkit at a booth in the ASHG exhibit hall.

Other recent PhenX presentations include the following:  

Dr. Hamilton presented “Linking Disease Model Phenotypes to Human Conditions” at a symposium hosted by the National Institutes of Health (NIH), in Rockville, MD, on Sept. 10, 2015.

PhenX Project Scientist Erin Ramos presented a webinar, “NIH Common Data Elements (CDEs),” hosted by the NIH on Sept. 8, 2015.

Dr. Ramos; Dr. Ellen Werner, Project Scientist of the PhenX Measures for SCD Research project; and PhenX Team members presented an all-day session, “PhenX-Sickle Cell Disease: Consensus Measures for Research,” at the NHLBI’s Annual Sickle Cell Disease Clinical Research Meetings in Bethesda, MD, on Aug. 20, 2015.

Dr. Ramos, Dr. Hamilton, and Katherine Lambertson of the Genetic Alliance presented a webinar, “PhenX Measures for Rare Genetic Conditions: Introducing an Annotation Tool and Crowdsourcing Approach,” for the Genetic Alliance on July 8, 2015. Sharon Terry, CEO of the Genetic Alliance, arranged the webinar.

Explore the PhenX Toolkit

PhenX Protocols Ready for Web-Based Data Collection as REDCap Instrument Zip Files

PhenX Featured Measure button


PhenX protocols are now available as "Instrument Zip" files from REDCap™ External Libraries in the PhenX Toolkit, providing the ability for Web-based data collection. You can download PhenX protocols from PhenX “My Toolkit” and upload them directly into REDCap using the “Upload” option under “Online Designer.”

REDCap is a secure Web application for building and managing online surveys and databases. It can be used to collect virtually any type of data but is specifically designed to support data capture for research studies. The application allows users to quickly and securely build and manage online surveys and databases.

PhenX Toolkit Home Page—New Look!


PhenX Featured Measure button

The Annotation Tool: A Crowdsourcing Approach

The Annotation Tool has been added to the PhenX Toolkit under the Resources tab, making it easy to share expertise assessing conditions and diseases by annotating PhenX measures. Through collaboration with the Rare Genetic Conditions WG and the Genetic Alliance, PhenX introduced the Annotation Tool via a webinar on July 8, 2015. Using a crowdsourcing approach, the goal is to use annotations to provide additional information and support to investigators and clinicians who need to recognize or assess rare conditions. Measures in the Substance Abuse and Addiction Research and the Mental Health Research collections were recently added to the Tool. By annotating PhenX measures, you will help the biomedical community use PhenX measures to assess conditions and promote the use of common measures.
Top Domains and Top Measures

The Top 5 Domains and Top 5 Measures for October 2015 are listed below. The top domains and measures are listed on the Toolkit Use Statistics 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. Environmental Exposures
  5. Cardiovascular
Top 5 Measures in the PhenX Toolkit
  1. Current Age
  2. Gender
  3. Ethnicity
  4. Race
  5. Weight
Featured: Sickle Cell Disease Research and Scientific Panel (SRSP)

SRSP Project Scientist

Ellen M. Werner, PhD, MA

Dr. Werner is the project scientist on the PhenX-Sickle Cell Disease Research supplement, funded by the National Heart, Lung, and Blood Institute (NHLBI). She is a program director in the Blood Epidemiology and Clinical Therapeutics Branch at NHLBI, National Institutes of Health (NIH). Dr. Werner joined the NIH in August 2000 as a program director in training and career development programs. Since then, she has established new research programs in clinical, epidemiologic, and patient-reported outcomes research. She is the science officer on the Adult Sickle Cell Quality of Life Measurement Information System (ASCQ-Me) and on the Patient-Reported Outcomes Measurement Information System (PROMIS). Dr. Werner holds the Investigational New Drug application with the Food and Drug Administration for hydroxyurea in the BABY HUG studies on pediatric sickle cell anemia. She is the lead workgroup coordinator for Healthy People 2020 Blood Disorders and Blood Safety. Before coming to the NIH, Dr. Werner was a senior health scientist at the Institute for Survey Research at Temple University and at several survey research organizations. She has a master’s degree in educational administration and a doctorate in public health education with a concentration in epidemiology.

SRSP Co-Chairs

Kathryn L. Hassell, MD

Dr. Hassell is a professor of medicine in the Hematology Division at the University of Colorado, Denver. She directs the Colorado Sickle Cell Treatment and Research Center and supervises the Hemoglobinopathies Newborn Screening Follow-Up program for the states of Colorado and Wyoming. Dr. Hassell provides inpatient and outpatient care to adults with SCD at the University of Colorado Hospital. She is a site principal investigator for multicenter clinical trials for adults with SCD and has provided national leadership on study steering and executive committees and data/safety monitoring boards. Dr. Hassell has participated in multiple national clinical research, health services, and disease management guideline development projects sponsored by the NIH, the Health Resources and Services Administration, and the Centers for Disease Control and Prevention. She also completed a four-year, part-time, Intergovernmental Personnel Act assignment with the NHLBI.

James R. Eckman, MD

Dr. Eckman is emeritus professor of the Department of Hematology and Medical Oncology and held appointments as professor of medicine and adjunct professor of pediatrics in medical genetics at Emory University School of Medicine. He was committed to establishing a sickle cell program at Grady Memorial Hospital and after intensive state lobbying for funding in 1984, became medical director of the world's first 24-hour comprehensive acute care sickle cell center.

He has broad research experience in basic science, translational research, clinical research and clinical trials related to disorders of hemoglobin, including studies of red cell metabolism; sickle erythrocyte endothelial interactions; mechanisms of renal complication in sickle cell disease; coagulation activation with sickle complications; psychological and social complications from sickle cell disease; drug and chemotherapy of sickle complications; pain assessment and management; and bone marrow transplantation in sickle cell disease. Dr. Eckman's other interest is in public health services for individuals with genetic diseases. He has championed newborn screening for sickle cell disease on a local and national level. It was through his efforts that Georgia instituted universal mandatory sickle cell screening for newborns in October of 1998. He serves as a member of several local and national committees and acts as an advocate to continue awareness and support of these programs.

Research Team Members
RTI International National Human Genome Research Institute
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).