May 30, 2008

PhenX Newsletter - Information and Updates
Issue 2. May 30, 2008

About PhenX

The project is called "PhenX" (pronounced like "phoenix") for Phenotypes and eXposures. Led by RTI International, and funded by the National Human Genome Research Institute (NHGRI), the goal of PhenX is to establish a set of standard measures for use in genome-wide association studies (GWAS) and other large-scale genomic research efforts. The PhenX Steering Committee (SC), led by SC Chair, Dr. Jonathan Haines, and Vice-Chair, Dr. William R. Harlan, is providing leadership in the selection of domains and domain experts and overall guidance to the project.

For more information about PhenX, visit www.phenxtoolkit.org.

Highlights

PhenX to Launch Demographics Measures Survey

Reaching out to the scientific community, RTI International will launch a survey from the PhenX website to get feedback on the first set of proposed measures. The Demographics Measures Survey is expected to go live at the end of June. To sign up to be notified whenever a PhenX Survey goes live, please go to www.phenxtoolkit.org. Or visit the PhenX website in July to take the survey. Survey responses will be collected for 30 days and be considered when building consensus on a set of measures for inclusion in the PhenX Toolkit. If researchers incorporate measures from the PhenX Toolkit into their studies, then it may be possible to combine complementary studies and maximize the benefits of their research. The proposed demographics measures were chosen by the Demographics Working Group (WG). For more information about who is involved, please go to www.phenxtoolkit.org.

The Demographics Measures Survey is the first in a series of surveys that will present proposed measures to the scientific community. In each survey, researchers will have an opportunity to rate the usefulness and the priority of the measures, make suggestions to include other measures, and comment on the protocols and procedures for each of the proposed measures. Survey responses will be anonymous. The feedback from the surveys will be used to refine both the selection of measures and the measurement protocols prior to inclusion in the PhenX Toolkit.

Working Groups

Demographics

The Demographics WG was the first WG to be established and is helping to pave the way for future WGs. Composed of seven experts, the WG is chaired by Dr. Myles Cockburn, an epidemiologist at the University of Southern California. Each WG also has a member of the PhenX SC who serves as liaison, and the SC liaison to the Demographics WG is Dr. Peter Kraft (see featured SC members below). Other WG members include academic and government researchers and scientists. The WG had their first teleconference on March 11, 2008, and an in-person meeting on April 9, 2008, in Washington, DC; the WG deliberated again by phone on May 21, 2008.

During these meetings, the WG discussed a variety of demographics measures used in large health studies (e.g., Census and National Health Interview Survey [NHIS] and GWAS (e.g., Genetic Association Information Network [GAIN]). The WG is proposing 14 domain elements (see below). Further deliberations are currently under way to select 25 measures to be included in a PhenX Survey expected to launch at the end of June.

Proposed Domain Elements - Demographics

Time/Age
Income
Ancestry
Years in the U.S.
Race/Ethnicity
Language
Sex/Gender
Current Employment Status
Location
Social Position
Current Marital Status
Household Roster
Education
Health Care

Anthropometrics

The Anthropometrics WG has nine-members; is chaired by Dr. Michele Forman, University of Texas; and includes experts in anthropometry, epidemiology, and genomics research. The SC liaison to the Anthropometrics WG is Dr. Michelle Williams (see featured SC members below). The WG held their first conference call on March 11, 2008, and their in-person meeting on May 2, 2008, in Washington, DC.

During their deliberations, the WG examined various anthropometric measures found in the database of Genotype and Phenotype (dbGaP; e.g., Framingham), and large health studies (e.g., National Health and Nutrition Examination Survey [NHANES]). The WG is considering 15 domain elements (see below) and multiple anthropometrics measures. Further deliberations are needed before presenting the proposed measures to the research community. A PhenX Survey presenting the proposed anthropometrics measures is expected to launch in late July.

Height
Head Circumference
Knee Height/Lower Leg Length
Neck Circumference
Sitting Height/Trunk
Body Composition
Arm Span
Body Frame
Weight/Weight History
Bone Age/Skeletal Age
Waist Circumference
Sagittal Abdominal Diameter
Hip Circumference
Dominance
Mid-upper Arm Circumference

Featuring Steering Committee Members

Within each newsletter, we will highlight two members of the SC. Here, we present Drs. Peter Kraft and Michelle Williams, who in addition to lending their expertise and guidance to the SC, are currently serving as SC liaisons to the Demographics and Anthropometrics WGs, respectively.

Michelle Williams, ScD. Professor of Epidemiology at the University of Washington School of Public Health and Community Medicine.

Dr. Williams is also Co-Director of the Center for Perinatal Studies at Swedish Medical Center, a multidisciplinary research program involving clinical scholars, basic scientists, and epidemiologists. Her research program focuses on integrating genomic sciences and epidemiological research methods to identify risk factors, diagnostic markers, treatments, and prevention targets for disorders that contribute to maternal and infant mortality. Her current activities include research and teaching collaborations with epidemiologists in Peru, Ecuador, Vietnam, Thailand, Ethiopia, Zimbabwe, and the Republic of Georgia. She has over 180 original research publications.

Peter Kraft, PhD. Assistant Professor of Epidemiology at Harvard University School of Public Health.

Dr. Kraft's research concentrates on statistical methodology for genetic association studies, with particular emphasis on genome-wide association studies (GWAS) and gene-environment interaction. He has published on cost-saving multi-stage designs for GWAS and integrating gene-environment and gene-gene interaction into the analysis of GWAS. He collaborates with researchers at the National Cancer Institute and the Harvard School of Public health on the Cancer Genetic Markers of Susceptibility project-parallel scans for loci influencing breast and prostate cancer risk-and PanScan, a screen for pancreatic cancer susceptibility loci. He is a member of the statistics working group for the international Breast and Prostate Cancer Cohort Consortium, which is investigating the joint contribution of environmental exposures and variation in particular pathways using a large, prospectively ascertained sample. He also collaborates with researchers at the Harvard School of Public Health and Brigham and Women's Hospital on studies of colorectal cancer, diabetes, heart disease, and kidney stone formation.

Steering Committee Members

Jonathan Haines, PhD, Chair, Vanderbilt University, Center for Human Genetics Research
Dr. Haines' work includes localization and identification of genes involved in common and genetically complex human disease, with a primary focus on neurological and eye disease, including studies of Alzheimer's Disease, multiple sclerosis, autism, amyotrophic lateral sclerosis, age-related macular degeneration, and adult-onset glaucoma.
William R. Harlan, MD, Vice Chair,National Library of Medicine Consultant
Dr. Harlan is currently a consultant with the National Library of Medicine's ClinicalTrials.gov. He advises on clinical study registration and results reporting. For 35 years he was professor of medicine at VCU, Duke, UAB, and University of Michigan. He then retired and went to the National Heart, Lung and Blood Institute (NHLBI) to work on a research portfolio of clinical trials and observational studies. He also served as the Associate Director for Disease Prevention at the NIH.
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
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
More...

Research Team Members

Carol M. Hamilton, PhD, PhenX Principal Investigator, RTI International
Diane Wagener, PhD, PhenX co-Investigator, RTI International
Richard Kwok, 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