July 21, 2009

PhenX Newsletter - Information and Updates Issue 9. July 21, 2009




The project PhenX, consensus measures for Phenotypes and eXposures, is funded by the National Institutes of Health, National Human Genome Research Institute. The goal of the project is to select 15 high-priority measures for 20 research domains that are recommended for use in genome-wide association studies (GWAS) and other large-scale genomic studies. Active input from the scientific community is critically important to the process so we solicit feedback through web-based surveys and through the use of the PhenX Toolkit. Your expertise and insight are extremely valuable in the process to achieve effective consensus.




PhenX Toolkit


The PhenX toolkit (https://www.phenxtoolkit.org) continues to evolve to serve the needs of its users and currently includes the following features:
  • Toolkit Guidance for following good scientific practices when conducting studies
  • Browse and Search Capabilities to identify PhenX measures that are appropriate for your research study
  • User Registration for providing login capabilities to facilitate saving your cart and interact with other users in the future
  • Frequently Asked Questions (FAQs) to present a quick resource to commonly asked questions
  • Glossary to inform users of commonly used terms for the PhenX project
  • Data Dictionary to provide a logical model and relationship diagram of the data in the PhenX Toolkit




Nutrition and Dietary Supplements:

RTI International is currently seeking comments on the Nutrition and Dietary Supplements measures to be included in the PhenX Toolkit. Feedback is being gathered via an anonymous web-based survey. The initial comment period for this survey is July 6th through July 27th and may be accessed at http://www.phenx.org/surveys. The survey features two sections; the first section allows you to provide feedback on the proposed measures and the second section allows you to prioritize the measures to be included in the Toolkit. Measures include items such as:

  • Total Dietary Intake
  • Dietary Supplements
  • Breastfeeding
  • Selenium
  • Vitamin D

Measures of individual food groups like Dairy and Fiber as well as others are also included. We welcome your suggestions for additional measures and/or alternative protocols to those the Working Group (WG) has selected. These measures are being proposed by the PhenX Nutrition and Dietary Supplements WG, chaired by Dr. Patrick Stover (See Biosketch below), which includes representatives from academia and government. Your insights are important to develop consensus on the measures that will be recommended for the Toolkit.

Environmental Exposures:

The Environmental Exposures WG released its web-based survey on July 15, 2009. The survey is available to the research community until August 5, 2009. These measures are being proposed by the PhenX Environmental Exposures WG, chaired by Dr. Lynn Goldman (See Biosketch below). The WG includes representatives from academia and government. Your input is critical in helping the WG to prioritize the measures that will be recommended for the Toolkit.

  • Characteristics of current residence - interviewer administered
  • Characteristics of current residence - technician observations
  • Water source
  • Residence history
  • Current occupation
  • Longest held job
  • Personal protective equipment and exposures at work
  • Exposure at work and in daily life
  • Occupational exposures brought into the home
  • Occupational history
  • Exposures from hobbies
  • Current environmental tobacco smoke exposure
  • Previous environmental tobacco smoke exposure
  • Environmental tobacco smoke - cotinine in serum, urine, or saliva
  • Lifetime farm exposure
  • Sibship/birth order
  • Day care attendance
  • History of being breastfed
  • Air contaminants in the home environment
  • Phthalate exposures in the home
  • Blood sample - lead
  • Dust sample - vacuum bag
  • Water sample - nitrates
  • Time activity and location
  • Ultraviolet light exposure


Steering Committee


On June 4-5, 2009 the PhenX Steering Committee (SC) held its fifth in-person meeting in Washington DC. The meeting included updates from the four WGs that are actively working towards survey or the Toolkit: Nutrition and Dietary Supplements, Oral Health, Cardiovascular and Environmental Exposures.

The Nutrition and Dietary Supplements WG Chair, Dr. Patrick Stover, and the Environmental Exposures WG SC Liaison, Dr. Diane Wagener, reported on the respective proposed measures for survey. The Oral Health WG Co-chair, Dr. James Beck, discussed a list of preliminary measures planned for survey. The Cardiovascular WG Chair, Dr. Tom Pearson, presented the results of the Cardiovascular survey as well as the proposed measures for the Toolkit.

Updates were provided on other WGs that are in the initial stages of the consensus process (Ocular, Cancer, and Reproductive Health WGs). The SC Liaison for the Lung Function WG, Dr. Terri Beaty, reported on the scope and sought approval to change the WG name to Respiratory, which was approved.

Dr. Yonette Thomas from National Institute on Drug Abuse presented on the content for a proposed Social Environment domain. The SC also discussed adding a Speech and Hearing domain. The SC will further explore pursuing these domains.


Working Group Meetings



On June 17, 2009, the Cancer WG gathered for an in-person meeting with the goal of identifying a set of measures and protocols. Dr. Christine Ambrosone and Dr. Neil Caporaso are the WG Co-Chairs. Dr. Ambrosone is the Chair of the Department of Cancer Prevention and Control at Roswell Park Cancer Institute. Dr Caporaso is the Chief of the Pharmacogenetics Section, Genetic Epidemiology Branch at the National Cancer Institute. The SC liaison, Dr. Margaret Spitz, is the Chair of the Department of Epidemiology at the University of Texas M.D. Anderson Cancer Center. The WG consists of five additional cancer experts. During this meeting the WG discussed measures and protocols regarding family history of cancer, cancer risk factors such as diet, physical activity, tobacco use, cancer screening among other elements. The WG is in the process of preparing these measures and protocols for release in a survey to obtain feedback from the scientific community.


The Ocular WG is comprised of eight members whose expertise broadly encompasses the field of ophthalmology. The WG is chaired by Dr. Janey Wiggs from the Massachusetts Eye and Ear Infirmary. The SC liaison is Dr. Jonathan Haines from the Vanderbilt University Medical School. On June 9, 2009, the WG gathered for an in-person meeting. During this meeting, the WG members presented information on several key topics and identified potential measures that addressed elements within the ocular domain. The WG plans to present the proposed measures and measurement protocols in fall 2009 in a web-based survey available on the PhenX portal. The current list of measures includes:

  • Use of glasses and contact lenses
  • Refractive error
  • Eye patching
  • Low vision/blindness
  • Dry eye
  • Migraine
  • Nutrition supplements
  • UV light exposure
  • Visual acuity
  • Biometry
  • Intraocular pressure
  • Central corneal thickness
  • Corneal topography
  • Retinal digital photography
  • Visual field
  • Use of eye drops
  • Lens grading
  • Color blindness
  • Systematic medications
  • Optic neuritis
  • Personal and Family history of eye disease
  • History of laser and ocular surgery

Reproductive Health:

On June 3, the Reproductive Health WG met in-person in Washington, DC. The WG consists of seven members and is chaired by Dr. Carol Hogue, Professor of Maternal and Child Health and Epidemiology/Chair of the Women's and Children's Center at Emory University. Dr. Michelle Williams, from the University of Washington, is the SC liaison. During this meeting the WG discussed measures and protocols regarding pregnancy history, sexual history, treatments and procedures for both males and females, among other elements. The WG is in the process of preparing these measures and protocols for release in a survey to obtain feedback from the scientific community.


On June 18, 2009, the Respiratory WG gathered for an in-person meeting with the goal of identifying a set of measures and protocols to cover the broad range of respiratory issues. The WG Chair, Dr. Edwin (Ed) Silverman, is an Associate Professor of Medicine at Harvard Medical School and an Associate Physician at Brigham and Women’s Hospital. The SC liaison, Terri Beaty, is a professor in the Department of Epidemiology at John Hopkins University School of Pubic health. The WG consists of six respiratory experts. Measures currently being considered include:

  • Respiratory Symptoms
  • Early Childhood Respiratory Illnesses/Vaccinations, Hospitalizations
  • Respiratory Disease History
  • Pulmonary Function Test
  • Biomarkers from Biological Samples
  • Quality of Life
  • Imaging
  • Family History
  • Medical Care Received
  • Other Physiological Measurements


Featured Working Group Chairs


In each newsletter, we highlight two Working Group chairs. Here, we present Dr. Patrick Stover and Dr. Lynn Goldman.


Patrick J. Stover, PhD (Nutrition and Dietary Supplements WG Chair)
Professor and Director of the Division of Nutritional Sciences at Cornell University and the Director of the United Nations Food and Nutrition Programme for Human and Social Development

Dr. Stover is Professor and Director of the Division of Nutritional Sciences at Cornell University and Director of the United Nations Food and Nutrition Programme for Human and Social Development. The Stover laboratory investigates the biochemical, genetic, and epigenetic mechanisms that underlie the relationships between folic acid and human pathologies, including neural tube defects and other developmental anomalies, cardiovascular disease, and cancer. Dr. Stover’s specific interests include the regulation of folate-mediated one-carbon metabolism and cellular methylation reactions, molecular basis of the fetal origins hypothesis, development of mouse models to elucidate mechanisms of folate-related pathologies, and translational control of gene expression.

Dr. Stover received his BS in chemistry from Saint Joseph's University and his PhD degree in biochemistry and molecular biophysics from the Medical College of Virginia. He conducted his postdoctoral research at the University of California at Berkeley in Nutritional Sciences.

Dr. Stover received the Presidential Early Career Award for Scientists and Engineers from President William Jefferson Clinton. He received the ERL Stokstad Award in Nutritional Biochemistry from the American Society for Nutritional Sciences, and has been selected as an Outstanding Educator four times by Cornell Merrill Presidential Scholars. He is a member of the Food and Nutrition Board of the Institute of Medicine, recently served on the Board's Nutrigenomics Workshop Planning Group. He serves on the editorial board for the Annual Review of Nutrition, the American Journal of Clinical Nutrition and the Journal of Biological Chemistry.


Lynn Goldman, MD, MPH (Environmental Exposures WG Chair)
Professor of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University - Environmental Exposures WG Chair

Lynn R. Goldman, a pediatrician and an epidemiologist, is a professor of Environmental Health Sciences at the Johns Hopkins University Bloomberg School of Public Health. Her areas of focus are children’s environmental health research, public health preparedness, and environmental health policy. She has joint appointments in the Departments of Health Policy and Management and Epidemiology and in Emergency Medicine at the Johns Hopkins School of Medicine.

From 1993-1998, Dr. Goldman served as Assistant Administrator for the Environmental Protection Agency’s Office of Prevention, Pesticides and Toxic Substances (OPPTS). In that position she was responsible for the nation's pesticide, toxic substances, and pollution prevention laws, and was responsible for managing a number of complex regulatory and science issues. Her achievements included expanding the Toxics Release Inventory, reauthorizing the nation’s pesticides laws (Food Quality Protection Act of 1996), and development of a framework for the regulation of biotechnology chemical and pesticide products. She led consensual processes that developed frameworks for testing of high-volume industrial chemicals and for identification of chemicals that disrupt endocrine systems.

Between 1985 and 1993 Dr. Goldman served at the California Department of Health Services, most recently as head of the Division of Environmental and Occupational Disease Control. She led public health efforts to respond to emergencies such as earthquakes and unintentional releases of pesticides in communities. She conducted public health investigations on pesticides, childhood lead poisoning, and other environmental hazards.

Dr. Goldman has a BS from UC Berkeley, an MPH from the Johns Hopkins University School of Public Health, an MD from UC San Francisco, and pediatric training at Children’s Hospital, Oakland, California. She has served on numerous boards and expert committees, including the Committee on Environmental Health of the American Academy of Pediatrics and the Centers for Disease Control and Prevention’s Lead Poisoning Prevention Advisory Committee. Dr. Goldman is a member of the Institute of Medicine, Vice Chair of the Institute of Medicine Roundtable on Environmental Health Sciences, a member of the National Academy of Sciences Standing Committee on Risk Analysis Issues and Reviews, and serves as Chair of the Institute of Medicine’s Committee on Secondhand Smoke Exposure and Acute Coronary Events.


Steering Committee Members


Jonathan Haines, PhD, Chair     Vanderbilt University, Center for Human Genetics Research
William R. Harlan, MD, Vice Chair     National Library of Medicine Consultant
Terri H. Beaty, PhD     Johns Hopkins School of Public Health
Lindsay A. Farrer, PhD     Boston University
Peter Kraft, PhD     Harvard School of Public Health
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


Research Team Members


Carol M. Hamilton, PhD     PhenX Principal Investigator, RTI International
Lisa C. Strader, MPH     PhenX Co-Investigator, RTI International
Richard Kwok, PhD     PhenX Investigator, RTI International
Jane Hammond, 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
Teri Manolio, MD, PhD     Director, Office of Population Genomics;
  Senior Advisor to the Director, NHGRI, for Population Genomics
Heather Junkins, MS     Scientific Program Analyst, NHGRI


Upcoming In-Person Meetings


  • September 9, 2009: Psychiatric
  • September 10-11, 2009: Steering Committee


Link to Previous PhenX Newsletters




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