October 15, 2010

PhenX Newsletter - Information and Updates Issue 14. October 15, 2010




The PhenX project, 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. PhenX measures for 17 research domains are currently in the Toolkit; measures for the remaining 4 research domains will be in the Toolkit by the end of calendar 2010. The PhenX team is working hard to raise awareness and promote use of the Toolkit. 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 October 8 2010, Version 3.7 of the PhenX Toolkit was released. Below are the release notes:
  • Speech & Hearing Measures added to the Toolkit
  • Social Environments Measures added to the Toolkit
  • Neurology - Migraine Measure added to the Toolkit
  • Browse Tree - Improvements made to the add to/delete from Cart options within the browse tree
  • Cart - "Users who chose this measure also chose these measures" feature added (displays measures with links and options to also add those displayed to Cart)
  • Browse measures in Conceptual Groups - The Conceptual Groups include measures that cut across Research Domains and provide users with an alternate way to browse the Toolkit

Please visit the Toolkit to find the available measures.


Top 20 measures in the PhenX Toolkit


  1.  Current Age   11.  Substances - Lifetime Abuse and Dependence
  2.  Gender   12.  Height
  3.  Ethnicity   13.  Alcohol - Lifetime Abuse and Dependence
  4.  Race   14.  Myocardial Infarction
  5.  Tobacco - Smoking Status   15.  Current Educational Attainment
  6.  Alcohol - 30-Day Quantity and Frequency   16.  Annual Family Income
  7.  Weight   17.  Birthplace of Grandparents
  8.  Alcohol - Lifetime Use   18.  Current Employment Status
  9.  Lipid Profile   19.  Blood Pressure (Adult/Primary)
  10.  Birthplace   20.  Maximum Adult Weight


Get the most from your measures!


As PhenX reaches out to the larger research community we plan to attend several conferences, including the American Society of Human Genetics (ASHG), the American Public Health Association (APHA), and the American Medical Informatics Association (AMIA) annual meetings.

ASHG- Nov 2-6, Washington DC, Booth #525
At the annual meeting of the ASHG we have the opportunity to present the Toolkit to a large group of scientists and trainees. Helen Pan and Wayne Huggins will each present a poster, PhenX Toolkit: Facilitating the use of common measures in genomics research and PhenX Measures: Enhancing Research Studies of Gene-Environment Interactions, respectively.

PhenX will present a booth that will facilitate sharing the Toolkit via scheduled presentations and ad hoc demonstrations. Helen Pan, Wayne Huggins, Destiney Nettles and the PhenX PI, Carol M. Hamilton will support the booth activities.

APHA - Nov 6-10, Denver, CO, Booth #1720
The APHA Annual Meeting & Exposition presents an opportunity for PhenX staff members to interact with public health professionals. PhenX will be highlighted in the RTI booth with Diane Wagener and Mike Philips giving presentations (including demonstrations of the Toolkit) on the following days:

  • Monday, November 8: 10:00 am and 2:00 pm
  • Tuesday, November 9: 10:00 am and 1:00 pm

There will also be a session at APHA on Tuesday, November 9, Public health implications of the use of standard epidemiologic measures: The PhenX Toolkit. The session organizers are Erin Ramos and Diane Wagener. The schedule is as follows:

  • 2:30 pm:
    Overview of challenges and opportunities of GWAS as it relates to epidemiology and public health
    Erin Ramos, PhD, MPH

  • 2:45 pm
    Methodologic approaches researchers have used to overcome challenges and address opportunities associated with GWAS
    Siiri Bennett, MD and Neil Caporaso, MD

  • 3:00 pm
    Analysis of GWAS: Opportunities and Obstacles
    Sara Lindstrom, PhD and Peter Kraft, PhD

  • 3:15 pm
    Population Architecture using Genomics and Epidemiology (PAGE) — from SNPs to GWAS and Beyond
    Dana Crawford, PhD, Gerardo Heiss, MD, PhD, Charles Kooperberg, PhD, Loic Le Marchand, MD, PhD, Tara Matise, PhD, José Luis Ambite, PhD, Steven Buyske, PhD, Shelley Cole, PhD, Christopher Haiman, ScD, Teri Manolio, MD, PhD, Kari North, PhD, Ulrike (Riki) Peters, PhD, MPH, Marylyn Ritchie, PhD, Lucia Hindorff, PhD, MPH, Jonathan Haines, PhD and . The PAGE Study

  • 3:30 pm
    Public health implications of the use of standard epidemiologic measures: The PhenX Toolkit
    Diane Wagner, PhD, Richard K. Kwok, PhD, Dean Jackman, PMP, Michal Zmuda, Wayne Huggins, PhD, Amanda Flynn, Ying Qin, MS, Vesselina Bakalov, MS, Helen Pan, PhD, Destiney Nettles, Joseph Pratt, MPM, Deborah Maiese, MPA, Lisa C. Strader, MPH and Carol M. Hamilton, PhD

  • Panel Discussion

AMIA - Nov 13-17, Washington DC, Booth # 313
The AMIA Annual Symposium provides an opportunity for the PhenX Booth staff to interact with the Biomedical informatics community. We will provide demonstrations and information to interested parties.


Community Outreach


The final six domains have gone to community outreach. The table below lists the Working Groups (WGs), the WG chair(s) and the outreach dates. All measures will be in the Toolkit by the end of calendar 2010.
WG Name Chair Outreach Dates
Gastrointestinal Dr. David Whitcomb September 28 - October 12
Infectious Diseases and Immunity Dr. Richard Kaslow September 16 - September 29
Psychosocial Dr. Bernice Pescosolido September 8 - September 22
Skin, Bone, Muscle and Joint (SBMJ) Dr. Douglas Kiel September 21 - October 1
Social Environments Dr. Barbara Entwisle September 2 - September 15
Speech and Hearing Drs. Mabel Rice and Cynthia Morton August 13 - August 27


Featured Working Group Chairs


In each newsletter, we highlight a Working Group chair. Here, we present the co-chairs of the Speech and Hearing WG, Dr. Cynthia Morton and Dr. Mabel Rice.


Cynthia Morton, Ph.D.
William Lambert Richardson Professor of Obstetrics, Gynecology and Reproductive Biology and Professor of Pathology at Harvard Medical School, and Director of the Biomedical Research Institute and Director of Cytogenetics at Brigham and Women’s Hospital
Dr. Morton received her Bachelor’s of Science degree from the College of William and Mary in Virginia and her Ph.D. in Human Genetics from the Medical College of Virginia in Richmond. She is certified by the American Board of Medical Genetics in Ph.D. Medical Genetics, Clinical Cytogenetics and Clinical Molecular Genetics. Her research interests are in molecular cytogenetics, hereditary deafness, genetics of uterine leiomyomata and human developmental disorders.
As Director of Cytogenetics, Dr. Morton oversees one of the largest full-service academic cytogenetics laboratories in the country. This laboratory has been at the forefront in implementing molecular methods in diagnostic testing for chromosome studies that cross the lifespan. These tests include preimplantation and prenatal diagnostics, perinatal and childhood studies in the evaluation of congenital and developmental disorders, infertility and pregnancy loss studies, and cytogenetics of leukemias, lymphomas and solid tumors. Her laboratory has been a major site for training laboratory geneticists in clinical cytogenetics.
Dr. Morton is a past member of the Board of Directors of the American Board of Medical Genetics where she served as Secretary, Treasurer and Chair of the Accreditation Committee. She was the Chair of the Molecular Genetic Pathology Policy and Exam Committees of the American Board of Medical Genetics and the American Board of Pathology. She served as Member and Chair of the Board of Scientific Counselors of the National Institute of Deafness and Other Communication Disorders, and Member and Chair of the Board of Regents of the National Library of Medicine. Dr. Morton is currently a member of the Counsel of Scientific Trustees of the Deafness Research Foundation, a member of the Board of Directors of the American Society of Human Genetics, and Editor of The American Journal of Human Genetics.


Mabel Rice, PhD
Fred & Virginia Merrill Distinguished Professor of Advanced Studies at the University of Kansas
Dr. Rice directs the Merrill Advanced Studies Center, the Child Language Doctoral Program, and the National Institute on Deafness and Other Communication Disorders (NIDCD)-funded Center for Biobehavioral Neurosciences of Communication Disorders. She has been a Scholar-in-Residence at MIT, Harvard, the University of Potsdam, German, and Curtin University in Perth, Australia, and a Japan Fellow in Tokyo. She serves on the Advisory Council of NIDCD, on the Communication Disorders Workgroup for American Psychiatric Association DSM-V, is a consultant for the Norwegian Institute of Public Health Longitudinal Study of Child Health Outcomes, and the Autism Speaks Treatment Advisory Board. She is a Fellow of American Association for the Advancement of Science (AAAS) and American Psychological Association (APA) and received American Speech-Language-Hearing Association (ASHA) Honors as well as the Alfred A. Kawana Council of Editors Award of ASHA. Her research interests focus on language acquisition and language impairments, morphosyntax (grammar markers of language impairment), genetics of language, reading, and speech impairments, language acquisition and impairments in twins, language impairments in children affected by HIV, and language impairments in children with autism. Her investigations are funded by awards from NIH. In collaboration with Shelley Smith and Javier Gayán in 2009 she reported a shared candidate gene for language impairments and reading impairments, KIAA0319. She enjoys and appreciates the support and contributions of scientific collaborators from Nebraska (Shelley Smith and Lesa Hoffman), Australia (Steve Zubrick and Kate Taylor), Spain (Javier Gayán), Johns Hopkins (Rebecca Landa), Tulane (Russ Van Dyke), University of Illinois (Ken Rich), Canada (Johanne Paradis and Martha Crago) and Norway (Synnve.Schjolberg) and the members of the Language Acquisition Studies lab at the University of Kansas.


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
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




  • On August 11, 2010 version 3.6 of the PhenX Toolkit was released: https://www.phenxtoolkit.org/index.php?pageLink=about.releasedetails&id=20
  • On July 30, 2010 version 3.5 of the PhenX Toolkit was released: https://www.phenxtoolkit.org/index.php?pageLink=about.releasedetails&id=19
  • PhenX presented at the following 2010 meeting:
    • Intelligent Systems for Molecular Biology (ISMB) Annual International Conference - Boston, MA July 11-13, 2010
    • International Association for Dental Research (IADR) General Session - Barcelona, Spain - July 14-17, 2010

  • PhenX will present at the following 2010 meetings:
    • American Society of Human Genetics (ASHG) Annual Meeting - Washington, DC - November 2-6, 2010
    • American Public Health Association (APHA) Annual Meeting - Denver, CO - November 6-10, 2010
    • American Medical Informatics Association (AMIA) Annual Symposium - Washington, DC - November 13-17, 2010


Link to Previous PhenX Newsletters




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