March 22, 2012

PhenX Newsletter - Information and Updates Issue 18. March 22, 2012


The PhenX (Phenotypes and eXposures) Toolkit ( is a catalogue of well-established, standard measures of phenotypes and exposures recommended for research studies with human subjects. The PhenX Toolkit includes 21 research domains (fields of research) and 295 measures; an additional 43 measures were added to the Toolkit, in support of Substance Abuse and Addiction research, on February 24, 2012. The Toolkit is funded by the National Human Genome Research Institute (NHGRI) through a cooperative agreement with RTI International. Additional support was provided by the Office of Behavioral and Social Sciences Research (OBSSR) and the National Institute on Drug Abuse (NIDA).

The Toolkit includes detailed protocols to ensure that the data collected are comparable across studies. Investigators who come to the Toolkit when designing or expanding a study can be confident that PhenX measures are high quality, having been validated in previous studies. This is particularly helpful for investigators who want to expand their study’s data collection beyond the primary research focus. We encourage you to provide feedback when you use the Toolkit, so we can ensure that the Toolkit meets the needs of the scientific community.


PhenX Toolkit Update

On February 24, 2012, Version 5.0 of the PhenX Toolkit was released. This release included the following updates and enhancements to the Toolkit site:
  • Substance Abuse and Addiction (SAA) Core collection (data)
  • Substance Abuse and Addiction (SAA) Specialty Area collections (data).
  • 21 domains update - Logical Observation Identifiers Names and Codes (LOINC) were developed for the 295 measures / 21 domains and are included in the "Standards" section of Toolkit protocols.
  • Resource update - Newsletters, News and Views, Press Releases (resource)

Top Domains and Top Measures

Top domains and measures are those found most often in the reports generated from user “My Toolkits.” They are listed on the home page of the PhenX Toolkit: These are calculated based on the number of times they are present in reports generated from user Toolkits, cumulatively. The measures and domains with the highest inclusion in reports are those listed as Top Measures and Top Domains. These lists are recalculated and updated with each new release. Toolkit release notes and dates can be found at the following link:

Top 5 domains in the PhenX Toolkit

February 24, 2012

  • Demographics
  • Nutrition and Dietary Supplements
  • Anthropometrics
  • Oral Health
  • Alcohol, Tobacco and Other Substances

Top 20 measures in the PhenX Toolkit

February 24, 2012

  1.  Current Age   11.  Height
  2.  Breastfeeding   12.  Annual Family Income
  3.  Hand Dominance   13.  Race
  4.  Alcohol - 30 Day Quantity and Frequency   14.  Weight
  5.  Body Image   15.  Family History of Heart Attack
  6.  Breast or Bottle Feeding Patterns   16.  Lipid Profile
  7.  Gender   17.  Alcohol - Lifetime Use
  8.  Birthplace   18.  Waist Circumference
  9.  Arm Span   19.  Cancer Screenings
  10.  Birth Weight   20.  Abdominal Aortic Aneurysm

Substance Abuse and Addiction (SAA)

The SAA project released 43 new measures into the PhenX Toolkit on February 24th, bringing the total number of Toolkit measures to 338. The measures were chosen by working groups of domain experts using a consensus-based approach. The measures were vetted through community outreach, and reviewed and approved by the PhenX Substance Abuse and Addiction Scientific Panel (SSP) and the PhenX Steering Committee (SC).

The new SAA measures are organized into a two-tiered "Core" Collection and six "Specialty" Collections. Measures in the Core Collection are broadly relevant to substance abuse and addiction research, such as measures related to demographics and history of tobacco, alcohol, and substance use. Measures in the Specialty Collections are relevant to specific SAA areas, such as self-reported craving, externalizing problems, and substance abuse treatment quality. The Core collection includes PhenX measures from the 21 research domains, as well as some measures from the Specialty collections. A list of the six Specialty collections is provided in the Newsletter dated June 29, 2011. Seven new measures were also added to Supplemental Information. This work was funded by NIDA in collaboration with NHGRI. NIDA is encouraging investigators to include some common protocols (see NIH Guide Notice) in their study design. It is envisioned that the series of SAA Core and Specialty Collection protocols will promote collaboration and cross-study analysis among NIDA funded researchers.

Steering Committee (SC)

The PhenX Steering Committee (SC) held a conference call on January 21, 2012 to formally review and approve the chosen Toolkit measures for the six SAA specialty areas and the two-tiered Core Collection. They also discussed possible future directions for PhenX.

Substance Abuse and Addiction Scientific Panel (SSP)

The PhenX Substance Abuse and Addiction Scientific Panel (SSP) met for their final teleconference on January 13, 2012. Having previously reviewed the measures proposed by the SAA Working Groups (WGs) for the six Specialty Collections and the draft contents of the Core Collection, the SSP provided their final approval of the SAA Specialty and Core Collections.

The SSP adopted a two-tiered Core Collection to provide a comprehensive set of important and broadly relevant protocols while considering the time required to administer them. "Core: Tier 1" includes 19 measures that can be administered in a short timeframe (approximately 10 minutes). The eight measures in "Core: Tier 2" require a greater time commitment. The Core Collection includes SAA Specialty Collection measures, existing Domain measures, and three additional high-priority measures recommended by the SSP to assess body mass index, HIV testing, and behavioral health disorders. The body mass index measure was derived from the Height and Weight measures in the Antropometrics Domain.  For the measures on HIV testing and behavioral health disorders, selected items were chosen from two measures in the Substance Use-related Co-morbidities and Health-related Outcomes Collection.


PhenX RISING (Real world, Implementation, SharingING) is comprised of seven groups of investigators funded by National Human Genome Research Institute (NHGRI) and the Office of Behavioral and Social Sciences Research (OBSSR) to incorporate PhenX measures into existing population-based genomic studies.

PhenX RISING is just over half-way through its one-year timeline. During recent monthly conference calls the groups have outlined a manuscript to describe the overall methods for adopting PhenX measures into their projects, discussed potential cross-study collaborations, and made plans to submit abstracts to upcoming conferences. The PhenX RISING project will wrap up this summer with an in-person meeting in Washington DC. At this meeting, the seven groups will present their findings and make their final recommendations for improving the functionality of the PhenX Toolkit.

The seven studies that have been funded under PhenX RISING (NOT-HG-11-009) are:

  • Ecologic Stressors, Post-Traumatic Stress Disorder, and Drug Use in Detroit
    University of Michigan, Ann Arbor, Allison Aiello, PhD
    National Institute on Drug Abuse
  • Human Translational Applications Core
    University of California, Los Angeles, Robert Bilder, PhD
    National Institute of Mental Health
  • Creating a Pediatric Imaging-Genomics Data Resource
    University of California, San Diego, Terry Jernigan, PhD
    National Institute on Drug Abuse
  • Genome-Wide Study of Cataract and Low HDL in Personalized Medicine Research Project
    Essentia Institute of Rural Health, Duluth, Minn., Catherine McCarty, PhD
    National Human Genome Research Institute
  • Genome-Wide Association Scan to Identify Risk Genes for Type 2 Diabetes in Asian Indians
    University of Oklahoma, Oklahoma City, Dharambir Sanghera, PhD
    National Institute of Diabetes and Digestive and Kidney Diseases
  • Self-Regulation Failure: Identifying and Modifying a Risk Phenotype
    Duke University, Durham, NC, Timothy Strauman, PhD, and Ahmad Hariri, PhD
    National Institute on Drug Abuse
  • Determinants of Healthy Longevity in China
    Duke University, Durham, NC, Yi Zeng, PhD
    National Institute on Aging

Featured PhenX Contributors

In this newsletter, we highlight the eight Principal Investigators who have been funded under PhenX RISING: Dr. Robert Bilder, Dr. Allison Aiello, Dr. Ahmad Hariri, Dr. Terry Jernigan, Dr. Catherine McCarty, Dr. Dharambir Sanghera, Dr. Timothy Strauman and Dr. Yi Zeng.

Robert Bilder, PhDRobert Bilder, PhD
Professor of Psychiatry and Psychology, University of California, Los Angeles Semel Institute for Neuroscience & Human Behavior

Dr. Bilder received a bachelors degree from Columbia College of Columbia University in Biology and Psychology (1978), and a Ph.D. in Psychology from City College, City University of New York, where he specialized in human neuropsychology (1984). He did his Internship in the Division of Neuropsychology, New York State Neurological Institute, Columbia-Presbyterian Medical Center (1982). Before joining UCLA in 2002, Dr. Bilder held a series of faculty appointments at Columbia University College of Physicians & Surgeons and the Albert Einstein College of Medicine. He served as Chief of Neuropsychology at Zucker Hillside Hospital of North Shore Long Island Jewish Medical Center from 1988 to 2002, and was Associate Director for Human Research at the Center for Advanced Brain Imaging at the Nathan Kline Institute for Psychiatric Research from 1996 to 2002. Dr. Bilder has been awarded diplomate status by the American Board of Clinical Neuropsychology. Dr. Bilder is a Clinical Neuropsychologist who has been actively engaged for over 20 years in research on the neuroanatomic and neuropsychological bases of major mental illnesses. He has received many awards for his research contributions, served on diverse federal and international advisory boards, provided editorial service to many scholarly journals, and received multiple grants from the NIH, private foundations, and industry. His work has been presented in more than 100 publications and 300 scientific presentations.

Dr. Bilder’s current research focuses on transdisciplinary and translational research. He directs the Consortium for Neuropsychiatric Phenomics (CNP) which aims to understand neuropsychological phenotypes on a genome-wide scale through a combination of human research, basic research, and informatics strategies (the CNP is one of nine NIH Roadmap interdisciplinary research consortia across all biomedicine; see Dr. Bilder also directs the Tennenbaum Center for the Biology of Creativity; is Co-Director of an NIMH-sponsored Center for Intervention Development and Applied Research focusing on translational research to enhance cognitive control; and is Co-Director of a new NCRR-sponsored Integrative Phenotyping Center for Neuropsychiatry at UCLA. Dr. Bilder also directs the Medical Psychology Assessment Center (a training clinic for neuropsychological and psychodiagnostic assessment) and the UCLA-Semel Institute Postdoctoral Training Program in Neuropsychology.

Allison Aiello, PhDAllison Aiello, PhD
University of Michigan, Ann Arbor

Dr. Aiello is a tenured Associate Professor of Epidemiology at the University of Michigan-School of Public Health in the Department of Epidemiology and faculty member in the Center for Social Epidemiology and Population Health. She received her PhD in Epidemiology from Columbia University-Mailman School of Public Health where she held a National Institute of Allergy and Infectious Diseases training fellowship and was the recipient of the Ana C. Gelman award for outstanding achievement and promise in the field of epidemiology for her dissertation work. Before beginning her PhD work, Dr. Aiello was an Emerging Infectious Diseases Fellow at the Centers for Disease Control and Prevention (CDC). Dr. Aiello earned her Masters of Science in Environmental Health Sciences and Engineering at the University of North Carolina- School of Public Health, Chapel Hill. From 2003-2005, Dr. Aiello was a Robert Wood Johnson Foundation Health and Society Scholar at the University of Michigan School of Public Health. In 2010, Dr. Aiello was a Yerby Visiting Associate Professor of Epidemiology at Harvard School of Public Health. Her research investigates psychosocial, socioeconomic and race/ethnic disparities in health, the relationship between infection and chronic diseases, and prevention of infection in the community setting. She has identified relationships between psychosocial determinants and immune response to infection and helped uncover social disparities in the burden of infection and immune response to cytomegalovirus in the US population. Currently, Dr. Aiello is the PI of an NIH funded large representative prospective cohort study of the Detroit population where she is examining social, biological, and genetic, determinants of mental health outcomes.

Ahmad Hariri, PhDAhmad Hariri, PhD
Professor, Psychology and Neuroscience, Duke University

Dr. Hariri is Professor of Psychology & Neuroscience and Investigator in the Institute for Genome Sciences & Policy at Duke University. Prior to joining the faculty at Duke Dr. Hariri served as the director of the Developmental Imaging Genetics Program at the University of Pittsburgh. Dr. Hariri received both a BS and MS from the University of Maryland where he studied evolutionary biology. In 2000, he completed his PhD in Neuroscience at UCLA working with Dr. Susan Bookheimer. He joined the faculty at University of Pittsburgh in 2003 after working as a research fellow in the laboratory of Dr. Danny Weinberger at the NIMH.

Dr. Hariri's research is focused on using modern molecular genetics and neuroimaging methods to identify specific biological pathways that help shape individual differences in temperament and personality, as well as related risk for neuropsychiatric disease. His program of research also employs pharmacological challenge fMRI paradigms and multimodal PET/fMRI neuroimaging to identify specific molecular mechanisms through which individual differences in behaviorally-relevant brain function emerges. The long-term goals of Dr. Hariri's research program are to identify neurobiological pathways mediating variability in complex behaviors and related risk for neuropsychiatric disease that will allow for the development of more effective, individually tailored disease treatment and, ultimately, prevention.

Findings from Dr. Hariri's program of research have been published in Science, Nature, Nature Neuroscience, Journal of Neuroscience, Archives of General Psychiatry, Biological Psychiatry, Trend in Cognitive Sciences and the Annual Review of Neuroscience. In August 2009, Dr. Hariri's contributions to the science of individual differences was recognized by the American Psychological Association who presented him with the Distinguished Scientific Award for Early Career Contribution to Psychology.

Terry L. Jernigan, PhDTerry L. Jernigan, PhD
Professor of Cognitive Science, Psychiatry, and Radiology,
Director, University of California, San Diego Center for Human Development

Dr. Jernigan is a clinical and experimental neuropsychologist. She received a PhD from UCLA and interned and conducted post-doctoral research at Stanford and the Palo Alto VA Medical Center before joining the faculty at UCSD in 1984. Since the late 1970’s she has used brain imaging to study brain development and aging, neurodevelopmental disorders in children, neuropsychiatric and substance use disorders in adults, and neurodegenerative disorders, including brain effects of HIV. In 2008, she was appointed Director, UCSD Center for Human Development, where she joined others conducting research focused on social-emotional, cognitive, and brain development in children. She is a lead investigator of the large American Recovery & Reinvestment Act (ARRA) funded project called PING, for Pediatric Imaging, Neurocognition, and Genetics, involving collaborators at 9 other sites throughout the U.S. This project aims to relate common genetic variation to variability in brain architectures, to the time course of brain maturation, and ultimately to behavioral phenotypic variability, in children and adolescents. Recently, as part of collaborative work in a National Science Foundation Science of Learning Center (Temporal Dynamics of Learning Center) she has studied adaptive, computer-mediated tutoring systems and the role of emotional and motivational factors in learner responses to such systems. She is Principal Investigator or Co-investigator on several research projects funded by the National Institutes of Health, the National Science Foundation, and the Lundbeck Foundation, and she is author of more than 150 peer-reviewed publications.

Catherine A. McCarthy, PhD, MPH, RDCatherine A. McCarty, PhD, MPH, RD
Essentia Institute of Rural Health, Principal Research Scientist

Dr. McCarty was born and raised in Duluth. She received her BS and MPH degrees in nutrition from the University of Minnesota and her PhD in Epidemiology from the University of Pittsburgh. After completing her PhD, she was the Head of the Epidemiology Research Unit in the Department of Ophthalmology at the University of Melbourne, Australia for eight years. During that time, she directed a population-based study of eye disease in Victoria, Australia and collaborated on similar projects in Hyderabad and Chennai, India. Dr. McCarty returned to the US in 2001 as a Senior Research Scientist at Marshfield Clinic Research Foundation where she was the Principal Investigator for the Personalized Medicine Research Project, a population-based biobank with more than 20,000 adult participants and 20 active research projects. Dr. McCarty's awards include the Gwen Sebold research award at Marshfield Clinic, Alumni of the Year from her undergraduate college at the University of Minnesota and Silver Fellow of the Association for Research in Vision and Ophthalmology. She has published more than 300 peer-reviewed manuscripts, earned more than $9 million in research grants, been invited to give many scientific talks, and mentored many students. She is on the VA Genomic Medicine Program Advisory Committee and has served as a consultant to several organizations seeking to start biobanks.

Dharambir K. Sanghera, PhD, FAHADharambir K. Sanghera, PhD, FAHA
Associate Professor, Department of Pediatrics/Genetics
University of Oklahoma Health Sciences Center

Dr. Sanghera’s research specializes in the study of molecular and genetic epidemiological aspects of common complex diseases, including type 2 diabetes (T2D), coronary heart disease (CHD), and metabolic syndrome. Her laboratory is focused on efforts to understand the interplay between environmental and genetic factors involved in T2D and CHD pathogenesis using a population of Punjabi origin from Northern India and the US Asian Indians who are first generation immigrants. She has been the Principal Investigator (PI) and Co-investigator on many NIH funded research projects. Currently she is PI on a NIDDK funded grant to perform genome-wide scan to find genes for T2D in Asian Indians. She is an International Fellow of the American Heart Association (FAHA), serve on the Council on Atherosclerosis Thrombosis and Vascular Biology and Council of Basic Cardiovascular Sciences of American Heart Association. She also is South Central Affiliate of the American Heart Association since 2009. She serves on the panel of membership committee of the International Genetic Epidemiology Society and is an elected fellow of Society of Biology, UK. She has served as a reviewer for the American Diabetes Association, NIH/NIGM study section and NIH/NIDDK’s Special Emphasis Review panel ZDK1GRB-7(03), NIDDK/KNOD study section, NIDDK/ Charted Committees Section DDK-B, and NIDDK/ ZDK1 GRB-2 (M3) study section. She reviewed grant proposals from "Diabetes UK" and the "Medical Research Council" in the UK. She is a frequent reviewer for a number of journals focused on genetics of diabetes and cardiovascular diseases. She is on the editorial boards of Cholesterol in 2009, International Journal of Diabetes Mellitus, Journal of Biomedicine and Biotechnology, Journal of Diabetes & Metabolism, World Journal of Medical Genetics, and Global Heart.

Timothy Strauman, PhDTimothy Strauman, PhD
Professor Psychology & Neuroscience, Arts & Sciences, Duke University

Dr. Strauman is Professor of Psychology and Neuroscience and Professor of Psychiatry and Behavioral Sciences at Duke University. Dr. Strauman is a clinical and social psychologist with research interests in translating theories of the social-cognitive processes underlying self-regulation into treatments and preventive interventions for psychological disorders. His recent research includes development of Self-System Therapy, a translational psychotherapy for depression based on regulatory focus theory; examining the role of self-regulatory dysfunction in the emergence of gender differences in depression; studies of the neural correlates of self-regulatory cognition in healthy and depressed individuals; and longitudinal studies of how children acquire individual differences in regulatory focus and the implications of those differences for behavioral disorders. Dr. Strauman is a Fellow of the Beck Institute for Cognitive Therapy and Van Ameringen Fellow of the Academy of Cognitive Therapy as well as a Fellow of the Association for Psychological Sciences and the Society for Experimental Social Psychology.

Yi Zeng, PhDYi Zeng, PhD
Center for Study of Aging and Human Development and Geriatric Division/Dept of Medicine of Medical School, and Institute of Population Research and Dept. of Sociology, Duke University

Dr. Zeng is a Professor at the Center for Study of Aging and Human Development and Geriatric Division/Department of Medicine of Medical School, and Institute of Population Research and Dept. of Sociology, Duke University. He is also a Professor at the China Center for Economic Research, National School of Development at Peking University in China, and Distinguished Research Scholar of the Max Planck Institute for Demographic Research (MPIDR) in Germany, and a foreign member of the Royal Netherlands Academy of Arts and Sciences. He received his doctoral degree from Brussels Free University in May 1986 while his Ph.D research was conducted at Netherlands Interdisciplinary Demographic Research in 1984-1986. He conducted post-doctoral study at Princeton University in 1986-87. As of September 15, 2011, he has had 114 professional articles written in English published in academic journals or as book chapters in the United States and Europe; among them, 77 articles were published in anonymously peer-reviewed academic journals. He has had 104 professional articles written in Chinese and published in China; among them, 80 articles were published in national Chinese academic journals. He has published twenty-three academic books, including eight books written in English (three published by Springer Publisher and one by the University of Wisconsin Press), and one book written in both Chinese and English.

Yi Zeng has been awarded eleven national academic prizes and three international academic prizes, such as the Dorothy Thomas Prize of the Population Association of America, the Harold D. Lasswell Prize in Policy Science awarded by the international journal Policy Sciences and Kluwer Academic Publishers, the national prizes for advancement of science and technology awarded by the State Sciences and Technology Commission of China and the State Education Commission, the highest academic honor of Peking University: "Prize for Outstanding Contributions in Sciences," and the "Chinese Population Prize (Science and Technology)", jointly awarded by nine ministries and seven national non-governmental associations in China.

Steering Committee Members

Jonathan Haines, PhD, Chair   Vanderbilt University, Center for Human Genetics Research
William R. Harlan, MD, Vice Chair   Retired, National Institutes of Health
Terri H. Beaty, PhD   Johns Hopkins School of Public Health
Lindsay A. Farrer, PhD   Boston University
Mary L. Marazita, PhD   University of Pittsburgh, Center for Craniofacial and Dental Genetics
Jose M. Ordovas, PhD   Tufts University, Human Nutrition Research Center on Aging
Carlos Neves Pato, M.D., Ph.D.   University of Southern California, Zilkha Neurogenetic Institute
Erin Ramos, PhD, MPH   National Human Genome Research Institute
Margaret R. Spitz, MD, MPH   University of Texas, MD Anderson Cancer Center
Diane Wagener, PhD   RTI International
Michelle Williams, ScD   University of Washington School of Public Health and Community Medicine

SAA Scientific Panel Members

Kenneth Sher, PhD, Chair   University of Missouri
Arpana Agrawal, PhD   Washington University in St. Louis
Erik Augustson, PhD   National Cancer Institute
Warren Bickel, PhD   Virginia Tech Carilion Research Institute
James Bjork, PhD   National Institute on Drug Abuse
Kevin Conway, PhD   National Institute on Drug Abuse
Lindsay Farrer, PhD, SC Liaison   Boston University
Andrea Hussong, PhD   University of North Carolina at Chapel Hill
Marcia Scott, PhD   National Institute on Alcohol Abuse and Alcoholism
Paul Wakim, PhD   National Institute on Drug Abuse

Research Team Members

Carol M. Hamilton, PhD   PhenX Principal Investigator, RTI International
Lisa C. Strader, MPH   PhenX Co-Investigator, RTI International
Jane Hammond, PhD   PhenX Investigator, RTI International
Dana Hancock, PhD
  PhenX Investigator, RTI International
Tabitha Hendershot   PhenX Investigator, RTI International
Wayne Huggins, PhD   PhenX Investigator, RTI International
Deborah Maiese, MPA   Consensus Coordinator, RTI International
Joe Pratt, MPM   PhenX Project Manager, RTI International
Erin Ramos, PhD, MPH   Project Scientist, NHGRI
Heather Junkins, MS   Scientific Program Analyst, NHGRI
Teri Manolio, MD, PhD   Director, Office of Population Genomics;
  Senior Advisor to the Director, NHGRI, for Population Genomics


  • On November 29, 2011 Version 4.6 of the PhenX Toolkit was released:
  • PhenX will present at the following meetings in 2012:
    • Society for Research on Nicotine and Tobacco – Houston, TX – March 13-16, 2012
    • Society for Pediatric and Perinatal Epidemiologic Research (SPER) – Minneapolis, MN - June 25-27 (tentative).
    • Society for Epidemiologic Research (SER) (Nedra) – June 27-30, Minneapolis. Abstract submitted February 1 (tentative).
    • American Society of Human Genetics (ASHG), 2012 Annual Meeting - San Francisco, CA - November 6-10, 2012 (tentative).

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