November 7, 2008

PhenX Newsletter - Information and Updates
Issue 6. November 7, 2008

Overview

The project PhenX, for Phenotypes and eXposures, is funded by National Institutes of Health's, National Human Genome Research Institute. The goal of the project is to select 15 measures for up to 20 research domains that will be recommended for use in genome-wide association studies (GWAS) and other large-scale genomic studies. The active input from researchers is critically important for this consensus effort. We seek input from the research community through web-based surveys. Your expertise and insight will be extremely valuable while developing an effective consensus process.

Highlights

Call for Survey Response on Alcohol, Tobacco, and Other Substances Measures

RTI International is currently seeking comments on measuring quantity and frequency of consumption, age of initiation and offset of use, and other alcohol, tobacco, and substance use measures. Feedback is being gathered via an anonymous web-based survey. The initial comment period for this survey is November 3rd through December 1st and may be accessed at http://www.phenx.org/surveys. The survey features two sections. The first section allows you to provide your feedback on proposed measures such as Lifetime use, 30-day consumption: quantity and frequency, Age of initiation of use, and also welcomes suggestions for additional measures and/or alternative protocols. In the second section of the survey, you can prioritize measures to be included in the Toolkit. Your expertise and insight will be extremely valuable to developing consensus on a set of measures.

These measures are being proposed by the PhenX Alcohol, Tobacco and Other Substances Working Group chaired by Deborah Hasin, with representatives from academia and government. Your input will help the PhenX Working Group prioritize the 15 measures that will be recommended for genome wide research studies.

Posters to be presented at ASHG Conference

Two posters representing the PhenX consensus project will be presented at the 2008 American Society for Human Genetics (ASHG) conference. One poster provides an Overview of PhenX processes and the Toolkit. The second poster focuses on the Demographics Domain and highlights the measures that will be included in the PhenX Toolkit. The conference will be held in Philadelphia, PA from November 11 – 15. Presenters are the PhenX PI, Carol Hamilton, and the PhenX Co-Investigator and Steering Committee member, Diane Wagener.

Steering Committee

On September 22-23, 2008, the PhenX Steering Committee (SC) held its third in-person meeting in Washington DC. All twelve members of the SC attended, along with six liaisons from NIH Institutes and Centers (ICs). Discussions during the two-day meeting covered a wide range of topics, including updates from the Chairs of the four active Working Groups (WGs): Demographics, Anthropometrics, Alcohol, Tobacco and Other Substances (ATOS) and Cardiovascular (CV). The Demographics and Anthropometrics WGs had already collected and considered input from the web-based surveys on their preliminary measures. The Demographics WG Chair (Myles Cockburn) presented the final 15 measures for inclusion in the Toolkit, and the SC voiced their approval. In the absence of the Anthropometrics WG Chair (Michelle Forman), the SC Liaison, Michelle Williams, discussed some of the issues that the WG faces as they narrow down the measures to the final 15. The ATOS Chair (Deborah Hasin) reported that the WG was on track and was in the process of finalizing the measures that would be included in the survey. Finally, as work begins on the first disease-based domain, the SC and Cardiovascular WG Chair (Tom Pearson) discussed ways to refine the scope of that domain.

A highlight of the meeting was getting the first glimpse of the Toolkit. The development team presented an interactive prototype for the Toolkit to illustrate the functionality and show how researchers will use the Toolkit. Some features include:

Browse and Search functions will help the user view and select measures
A 'shopping cart' will include selected measures and protocols
Custom reports will include detailed protocols and information about the selected measures

The SC deliberated about the scope of the upcoming domains and refined the list of 20 domains. The upcoming domains and the SC Liaison to each WG are as follows:

WORKING GROUP/DOMAIN	SC LIAISON
Nutrition and Dietary Supplements	Jose Ordovas
Cancer	Margaret Spitz
Exposures	Diane Wagener
Oral Health	Mary Marazita
Reproduction	Michelle Williams
Lung Function	Terry Beaty
Diabetes	Bill Harlan
Neurological	Lindsay Farrer
Psychiatric	Carlos Pato
Physical Activity and Physical Fitness	Jose Ordovas
Ocular	Jonathan Haines
Psychosocial	Carlos Pato

Featuring Steering Committee Members

We have highlighted the newest member of the Steering Committee (SC) in this newsletter. Here, we present Dr. Carlos Neves Pato.

Carlos Neves Pato, M.D., Ph.D.

Dr. Carlos Pato has an ongoing interest in the genetics of complex phenotypes such as psychotic disorders, schizophrenia and bipolar disorder, as well as obsessive-compulsive disorder. Trying to understand the genetics of these complex diseases has been extremely difficult, given inherent genetic variability and variability in the disorders themselves. Dr. Pato’s other interests include pioneering techniques for using microarray gene expression studies to pursue potential diagnostic and screening tests for these mental-health disorders and looking at whole-genome linkage studies and family-based association studies to better understand the genetics of schizophrenia and bipolar disorder. Dr. Pato has had over 70 publications.

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
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

Announcements

The Anthropometrics Survey was closed on September 8, 2008
The Steering Committee had an in-person meeting on September 22-23, 2008
The Cardiovascular WG had an Introductory call on October 1, 2008
The Nutrition and Dietary Supplements WG had an Introductory call on November 3, 2008