April 20, 2010

PhenX Newsletter - Information and Updates Issue 12. April 20, 2010




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, low burden, measures for 21 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 regarding proposed measures through a consensus building process meant to access subject matter experts and research professionals and through the use of the PhenX Toolkit. Your expertise and insight are extremely valuable in the process to achieve effective consensus.




PhenX Toolkit Update


On April 15, version 3.1 of the PhenX Toolkit was released. This release included the following:
  • Supplemental Information - All existing Supplemental Information relocated from PhenX Portal (www.phenx.org) to the PhenX Toolkit
  • Supplemental Information - Ocular Supplemental Information added to Toolkit
  • Smart Query Tool - Incorporates Supplemental Information into search results display
  • Improvements made to the Measure and Protocol display pages, including enhanced navigation to sections in protocols
  • News and outreach email subscription option added for site visitors
  • News and outreach email subscription option added as a profile setting for PhenX Toolkit registered uses

On February 26, version 3.0 of the PhenX Toolkit was released. The release included the following data and features:

  • Ocular - Ocular Measures available
  • Reproductive Health - Reproductive Health Measures available
  • Nutrition & Dietary Supplements Measure updates
  • Environmental Exposures Measure updates


  • Smart Query Tool
  • PhenX Toolkit Tutorial
  • Toolkit User Network

Please visit the Toolkit to review the available measures. Register on the Toolkit to gain access to additional features.

Smart Query Tool

The Smart Query Tool (SQT) is a new PhenX Toolkit feature that enables improved search capabilities. The SQT takes advantage of a logical framework, a PhenX Toolkit ontology that includes measure names and their aliases, name variants and keywords. The "Smart Search" option searches measure names, aliases, and keywords to get high-specificity (fewer) results, and the "Text Search" searches the full text of measures and protocols to get high-sensitivity (more, less specific) results. The SQT also searches Supplemental Information, providing access to reference documents relevant to the search.

Links to Collaborators

RTI is working collaboratively with the National Institutes of Health, including the National Library of Medicine, National Human Genome Research Institute, and the National Cancer Institute to ensure that PhenX is aligned with other NIH and international bioinformatics efforts. PhenX measures will be linked to measures that are included in the database of Genotypes and Phenotypes (dbGaP) and will extend to well-established standards such as Logical Observation Identifiers Names and Codes (LOINC), caBIG, and other related NHGRI programs such as the electronic Medical Records and Genomics Network (eMERGE). PhenX is also collaborating with the international Public Population Project in Genomics (P3G) to develop synergies between the PhenX Toolkit and the P3G DataSHaPER. Through these collaborations, researchers can identify opportunities to combine data from existing studies and potentially extend studies to include data and samples associated with biorepositories.

The PhenX Toolkit website currently links to the following related projects:

  • The PhenX web portal
  • caBIG - Cancer Data Standards Registry and Repository (caDSR) Common Data Element (CDE)
  • CDISC - Clinical Data Interchange Standards Consortium
  • dbGaP - The database of Genotype and Phenotype
  • eMERGE - electronic Medical Records and Genomics
  • Gen2Phen
  • GENEVA - Gene Environment Association Studies
  • HPO - Human Phenotype Ontology
  • LOINC - National Library Medicine Logical Observation Identifiers Names and Codes
  • P3G - Public Population Project in Genomics
  • PharmGKB - Pharmacogenomics Knowledge Base
  • PROMIS - Patient-Reported Outcomes Measurement Information System

The eMERGE and P3G websites currently link to the PhenX Toolkit. Work is in progress to add a Toolkit link to several additional websites.


Working Group (WG) Updates


Skin, Bone, Muscle and Joint (SBMJ)
The SBMJ WG, chaired by Dr. Douglas Kiel, met on March 10th in Washington DC for their in-person meeting. The WG members presented information on several key topics and identified potential measures that address elements within the SBMJ domain during the meeting. Dr. Lindsay Farrer is the Steering Committee (SC) liaison.

Social Environments
On April 9, 2010, the Social Environments WG gathered for an in-person meeting. During this meeting, the WG members presented information on several key topics and identified potential measures that address elements within the Social Environments domain. The Social Environments Working Group Chair is Dr. Barbara Entwisle, a Kenan Distinguished Professor of Sociology who serves as Director of the Carolina Population Center at the University of North Carolina at Chapel Hill. The SC liaison is Dr. Peter Kraft from Harvard University School of Public Health.

Speech and Hearing
The Speech and Hearing WG, co-chaired by Dr. Mabel Rice and Dr. Cynthia Morton, met on April 12th in Washington, D.C. for their in-person meeting. During this meeting, the WG members presented information on several key topics and identified potential measures that address elements within the speech and hearing domain. The SC liaison is Dr. Mary Marazita.

The Gastrointestinal WG held their introductory conference call on April 14th. The WG will hold an in-person meeting on May 14th in Washington, DC. The WG is chaired by Dr. David Whitcomb. Dr. William Harlan is the SC Liaison.

The Psychosocial WG will hold an in-person meeting in Washington, DC on May 11th. The WG is chaired by Dr. Bernice Pescosolido.


Current Outreach Efforts


In March and April, the Diabetes, Psychiatric and Neurology WGs presented their measures to the scientific community for review and comment. The WGs are now working through community feedback received and choosing their final measures. If you would like to provide feedback on one or all of the mentioned WG's proposed measures, send an e-mail to feedback@phenx.org.


Featured Working Group Chairs


In each newsletter, we highlight a Working Group chair. Here, we present Dr. Carol Hogue and Dr. Janey Wiggs.


Carol J. Rowland Hogue, Ph.D., M.P.H.
Dr. Hogue was appointed Professor of Epidemiology and Jules & Uldeen Terry Professor of Maternal and Child Health at the Rollins School of Public Health (RSPH) of Emory University in 1992. She holds joint appointments in the School of medicine Department of Pediatrics, Women's Studies Department of Emory College and the Department of Behavioral Sciences and Health Education of RSPH. Before returning to academia, she was at the federal Centers for Disease Control, Division of Reproductive Health, where she was chief of the Pregnancy Epidemiology Branch (1982-88) and then Director of the Division (1988-1992). Prior to her government service, she was on the Biometry faculty of Arkansas medical school (1977-82) and the Biostatistics faculty of UNC-CH School of Public Health (1974-77). Dr. Hogue served as President of the Society for Epidemiologic Research (1988-89), served on the Institute of Medicine Committee on Unintended Pregnancy (1993-1995), was Chair of the Regional Advisory Panel for the Americas of the World Health Organization Human Reproduction Programme (1997-99), President of the American College of Epidemiology (2002-4), Senior Fellow of the Emory Center for the Study of Law and Religion (2001-6), and received the MCH Coalition's National Effective Practice Award in 2002. Dr. Hogue has extensive experience in academic leadership. She was PI of a CDC-funded Cooperative Agreement to develop an MCH Epidemiology track in the RSPH Career MPH program, and has directed a HRSA-funded doctoral training program in MCH Epidemiology for 10 years. Under Dr. Hogue's leadership, Emory University was one of the first two academic health centers to receive an NICHD-sponsored T32 Reproductive, Perinatal, and Pediatric predoctoral training grant in 2005. Dr. Hogue has published extensively in the areas of long-term effects of induced abortion, epidemiology of stillbirths and preterm delivery–especially among African American women, improvement in reproductive health through improved general health, and causes of unintended pregnancy among U.S. adults. Recently she was PI of USDA- and CDC-funded intervention research projects to improve African American working women's health through physical activity and nutritional life changes. Her currently funded research projects include: Co-principal Investigator of the Emory/Battelle/Morehouse Study Center for the NIH-funded National Children's Study; and PI for the NIH-funded study of the scope and causes of stillbirth.


Janey L. Wiggs, MD, PhD
Dr. Wiggs is a physician scientist at the Massachusetts Eye and Ear Infirmary (MEEI) and Harvard Medical School (HMS). She currently holds the appointment of Associate Professor of Ophthalmology at Harvard Medical School and is the Associate Chief for Clinical Research in Ophthalmology at the Massachusetts Eye and Ear Infirmary. Dr. Wiggs received her BA and PhD degrees in biochemistry from the University of California at Berkeley and her MD degree from Harvard Medical School. She did post-doctoral training at MEEI under the direction of Dr. Ted Dryja. She also completed an ophthalmology residency at MEEI and fellowship training in glaucoma and in medical genetics, and is board certified in both ophthalmology and medical genetics.

Dr. Wiggs' research program is focused on the discovery and characterization of genetic factors that contribute to the blinding eye disease glaucoma, and is funded by the National Eye Institute (NEI) as well as other nonprofit foundations. She is the co-chair of the US-INDO joint working group (NEI) and is a member of the NEI eyeGENE consortium. Dr. Wiggs currently serves on the editorial boards of Investigative Ophthalmology & Visual Science (IOVS), Archives of Ophthalmology (Section Editor for Molecular Genetics), Molecular Vision and the Journal of Glaucoma. She is a member of the scientific advisory board for the Glaucoma Research Foundation and is a past member of the National Advisory Council of the NEI.


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
Peter Kraft, PhD     Harvard University 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
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


Upcoming In-Person Meetings


  • Psychosocial: May 11, 2010
  • Gastrointestinal: May 14, 2010





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