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PhenX Newsletter - Information and Updates Issue 27. April 13, 2017

Highlights

PhenX to dbGaP Variable Mapping Update



PhenX has collaborated with the National Center for Biotechnology Information (NCBI) database of Genotypes and Phenotypes (dbGaP) to use PhenX measures to identify dbGaP studies for cross-study analysis. For new study submissions to dbGaP, PhenX provides a Data Dictionary compatible with the dbGaP data submission packet, where the "Variable Source" is pre-filled with "PhenX." For existing studies in dbGaP, PhenX is linking dbGaP studies by mapping PhenX variables to dbGaP variables as "comparable" or "related."

PhenX-dbGaP variable mapping results can be accessed in both PhenX and dbGaP. In the PhenX Toolkit, these mappings can be found in the "Variable" section in the protocol page, or via "dbGaP Variable Mapping" under the "Search" menu. In dbGaP, the mappings can be found in "dbGaP Advanced Search" (faceted browsing) under "Common Data Elements" in the "Variable" tab. Additionally, the mappings can be found in dbGaP in the "Search" box by selecting the "PhenX" field. This development enables both PhenX and dbGaP users to identify potential dbGaP studies for cross-study analysis


Mental Health Research Early Psychosis Measures - Released January 19, 2017

The PhenX Toolkit released two Early Psychosis specialty collections in the PhenX Measures for Mental Health Research (MHR) Collection, funded by the National Institute of Mental Health (NIMH). Dr. Gregory K. Farber, director of the Office of Technology Development and Coordination at NIMH, is the project scientist. Led by Drs. Lisa Dixon and Dost Öngür, co-chairs, the Early Psychosis Working Group (WG) selected 26 new measures, which were approved by the PhenX Steering Committee.

The Early Psychosis Clinical Services Specialty Collection presents 19 standardized measures of diagnosis, symptoms, functioning, treatment interventions, and recovery outcomes. The Early Psychosis Translational Research Specialty Collection presents eight specific approaches for anatomical imaging and cognitive assessment. Two measures (Family History of Mental Illness and Premorbid Adjustment and Psychosis) are included in both specialty collections.

On January 25, 2017, NIMH posted a "Notice Announcing the Availability of Common Data Elements for Research Related to Early Psychosis," strongly encouraging NIMH grantees and applicants to incorporate the measures into research protocols. "By encouraging the use of this set of data elements," the notice states, "NIMH is trying to promote these into the category of common data elements widely used by a research field."

The MHR Collection also includes specialty collections for Suicide, Post-traumatic Stress Psychopathology (including PTSD), and Eating Disorders and a core collection of PhenX measures recommended for use by all mental health researchers. For more information about the project's implications for investigators in the mental health research community, see NIMH's Notice Announcing Data Harmonization for NIMH Human Subject Research via the PhenX Toolkit.


Pregnancy Measures - Released January 31, 2017

The Pregnancy Working Group (WG), chaired by Dr. Siobhan Dolan of Albert Einstein College of Medicine, recommended a set of Pregnancy measures for inclusion in the PhenX Toolkit. These measures were reviewed and approved by the PhenX Steering Committee and released in the Toolkit on January 31, 2017. The Pregnancy Domain has 14 measures and 1 protocol in Supplemental Information. At the WG's suggestion, the domain page has a link to "Additional Relevant Measures," providing access to the large number of pregnancy-related measures already in the Toolkit. A poster highlighting the Pregnancy measures was presented at the National Institute of Environmental Health Sciences (NIEHS) Environmental Health Sciences Fest in December 2016 in Raleigh, NC (see "PhenX on the Move" below).


Update of Reproductive Health Measures - Released April 11, 2017

Changes to the Reproductive Health domain in the PhenX Toolkit were released on April 11, 2017, culminating a thorough review by the Reproductive Health Expert Review Panel (ERP), led by Dr. Andrea Dunaif of Northwestern University.

The ERP reviewed 15 measures in the Reproductive Health domain and two measures in Supplemental Information. All ERP recommendations were approved by the Steering Committee at its February 2017 in-person meeting.

In the PhenX Toolkit, the "Process and Review" section of each protocol provides a summary of any ERP changes. Protocols that have been updated, replaced, or retired are available on the Archived Measures and Protocols page.


PhenX Protocols Available in the cancer Data Standards Registry and Repository Form Builder

PhenX protocols will be available soon in Form Builder at the cancer Data Standards Registry and Repository (caDSR), providing the ability for Web-based data collection. You can search and download PhenX protocols and incorporate them into your data collection protocols.

caDSR is a metadata registry in the form of data elements, forms, models, and components of these items maintained and administered by the National Cancer Institute (NCI). Form Builder at caDSR is a registry of data collection forms for cancer studies and other types of studies. This development extends the availability of PhenX protocol to the cancer research field and establishes a base for standardizing the questions on the PhenX measures.


PhenX Steering Committee In-Person Meeting - February 21-22, 2017

The PhenX Steering Committee (SC) met in person in Chevy Chase, MD. The SC heard speakers from the database of Genotypes and Phenotypes (dbGaP), the National Institutes of Health (NIH) Sexual and Gender Minority Research Office (SGMRO), and the Clinical Genome Resource (ClinGen).

The SC received updates on the Pregnancy and Geriatric Working Groups and from three Expert Review Panels (ERPs) reviewing Respiratory, Neurology/Psychosocial/Psychiatric, and Reproductive Health measures in the Toolkit. The SC approved the ERP's recommendations for the Reproductive Health domain. Representatives of the Mental Health Research and Tobacco Regulatory Research administrative supplements presented updates and items for discussion.

The PhenX Team presented information on recent conferences, presentations and publications in process. The SC discussed potential new collaborations and new Toolkit content moving forward.


PhenX on the Move

Resources like the PhenX Toolkit are increasingly important in data archiving for environmental health sciences research, according to two panelists at the National Institute of Environmental Health Sciences (NIEHS) 50th anniversary Environmental Health Sciences FEST in Durham, NC, December 5-8, 2016. Dr. Fred Wright, Director of the Bioinformatics Program at North Carolina State University, and fellow panelist Dr. Susan Pinney, Deputy Director of the University of Cincinnati's Center for Environmental Genetics, commented on the PhenX Toolkit in a panel discussion December 6 titled "Perspectives on Data across the Research Lifecycle." Mike Phillips provided more details on the Toolkit on December 7 with a poster presentation, "The PhenX Toolkit: Standard Phenotype and eXposure Measures for Pregnancy Research."

Dr. Helen Pan gave a webinar, "Linking Data in dbGaP Using PhenX Measures," to the Clinical Common Data Elements Task Force (CDETF) for the National Library of Medicine (NLM), National Institutes of Health (NIH) March 28, 2017.

Dr. Helen Pan gave a podium presentation, "Linking Data in dbGaP Using PhenX Measures," at the American Medical Informatics Association's 2017 Joint Summits on Translational Science in San Francisco, CA, March 27, 2017.

Mike Phillips presented a poster, "The PhenX Toolkit: A Resource for Standard Phenotype and eXposure Measures for Pregnancy and Environmental research," at the Society of Toxicology's 56th Annual Meeting and ToxExpo on March 13, 2017, in Baltimore, MD.

PhenX Tobacco Regulatory Research Project Scientist Dr. Kay Wanke presented a poster, "Tobacco Regulatory Research Measures in the PhenX Toolkit," at the Society for Research on Nicotine & Tobacco Annual Meeting on March 10, 2017, in Florence, Italy.

Drs. Carol M. Hamilton and Helen Pan gave a webinar, "The PhenX Toolkit: Standard Measures for Collaborative Research," to the TOPMed Phenotype Harmonization Committee on March 2, 2017.

Drs. Carol M. Hamilton and Helen Pan gave a webinar for the Clinical and Translational Science Awards (CTSA) Informatics Domain Task Force meeting on February 3, 2017.

Dr. Hamilton gave a webinar to the Clinical Common Data Elements Task Force (CDETF) for the National Library of Medicine (NLM), National Institutes of Health (NIH) on November 4, 2016.


Explore the PhenX Toolkit

Top Domains and Top Measures

The Top 5 Domains and Top 5 Measures as of March 2017 are listed below. The top domains and measures are listed on the Toolkit Use Statistics Page and are recalculated and updated with each new release.

Top 5 Domains in the PhenX Toolkit Top 5 Measures in the PhenX Toolkit
1. Demographics 1. Current Age
2. Anthropometrics 2. Gender
3. Alcohol, Tobacco and Other Substances 3. Ethnicity
4. Environmental Exposures 4. Race
5. Cardiovascular 5. Cigarette Smoking Status

Featured:
Mental Health Research Early Psychosis Co-Leads
Lisa Dixon, MD, MPH

Dr. Dixon is a Professor of Psychiatry at the Columbia University Medical Center, where she directs the Division of Behavioral Health Services and Policy Research and the Center for Practice Innovations (CPI) at the New York State Psychiatric Institute. Dr. Dixon is an internationally recognized health services researcher with more than 25 years of continuous research funding from the National Institute of Mental Health, the U.S. Department of Veterans Affairs, and foundations. As the director of CPI, she oversees activities for the New York State Office of Mental Health in implementing evidence-based practices in behavioral health programs throughout the state. She leads OnTrackNY, a statewide initiative designed to improve outcomes and reduce disability for individuals experiencing their first episode of psychosis. Dr. Dixon's grants have focused on improving the quality of care for individuals with serious mental disorders, with emphasis on services that include families, reducing the negative impact of co-occurring addictions and medical problems, and improving treatment engagement and adherence. Dr. Dixon's work has joined individuals engaged in self-help and outpatient psychiatric care, as well as clinicians and policy makers, in collaborative research endeavors. Dr. Dixon assumed the role of editor-in-chief of the journal Psychiatric Services in January 2017. She has published more than 250 articles in peer-reviewed journals and has received many awards, including the 2009 American Psychiatric Association Health Services Senior Scholar Award and the Wayne Fenton Award for Exceptional Clinical Care.


Dost Öngür, MD, MPH

Dr. Öngür obtained his MD/PhD degree in 2000 from Washington University in St. Louis and completed his psychiatric residency training at the MGH/McLean Adult Psychiatry program. He is the chief of the Psychotic Disorders Division, responsible for all clinical services serving patients with psychotic disorders, including a first-episode psychosis subspecialty program. In addition to his clinical work, he receives funding from the National Institute of Mental Health for clinical and brain imaging research in patients with schizophrenia and bipolar disorder. He is an associate professor of psychiatry at Harvard Medical School and the author of more than 130 articles on research into the neurobiology of bipolar disorder and schizophrenia. He has won awards from the Harvard Medical School for his teaching and mentoring, and he is the associate editor of JAMA Psychiatry.


Pregnancy Working Group Chair
Siobhan Dolan, MD, MPH

Dr. Dolan is professor and vice chair for research in the Department of Obstetrics and Gynecology (Ob/Gyn) and Women's Health at Albert Einstein College of Medicine and Montefiore Medical Center. A graduate of Brown University and Harvard Medical School, she trained in Ob/Gyn at Yale New Haven Hospital and then completed a fellowship in clinical genetics at Albert Einstein College of Medicine and a master's degree in public health at Columbia University.

In addition to her clinical work in the Division of Reproductive and Medical Genetics, Dr. Dolan is involved in research on the genetics and epidemiology of preterm birth, as well as the use of group prenatal care to prevent preterm birth. In addition to her clinical work, she serves as a medical advisor to the March of Dimes.


Reproductive Health Expert Review Panel Leader
Andrea Dunaif, MD

Dr. Dunaif is the Charles F. Kettering Professor of Endocrinology and Metabolism at the Feinberg School of Medicine, Northwestern University. She is the director of the National Institutes of Health-supported Northwestern University Specialized Center of Research on Sex Differences. Formerly, she was chief of the Division of Endocrinology, Metabolism and Molecular Medicine at the Feinberg School of Medicine for 10 years. Before joining Northwestern in 2001, Dr. Dunaif held faculty appointments at the Mount Sinai School of Medicine, Pennsylvania State University College of Medicine, and Harvard Medical School. Dr. Dunaif is an internationally recognized expert in endocrinology and women's health. Her research on polycystic ovary syndrome (PCOS) has shown that it is a leading risk factor for type 2 diabetes mellitus. Further, this research has revolutionized the treatment of PCOS with insulin-sensitizing drugs.

Most recently, Dr. Dunaif led an international team that successfully mapped novel susceptibility genes for PCOS. Dr. Dunaif has more than 135 original scientific publications and has edited four books. She has received numerous awards and honors including the Endocrine Society's highest award for clinical research, the Clinical Investigator Award, and a Doctor Honoris Causa from the University of Athens Medical School. She has been elected to the American Society for Clinical Investigation and the Association of American Physicians. She is a past president of the Endocrine Society, a former associate editor of the Journal of Clinical Endocrinology and Metabolism and Obesity, and a past chair of the National Institutes of Health Integrative and Clinical Endocrinology and Reproduction Study Section.

Research Team Members

RTI International National Human Genome Research Institute
Carol M. Hamilton, PhD Principal Investigator Erin Ramos, PhD, MPH Project Scientist
Tabitha Hendershot Co-Investigator Teri Manolio, MD, PhD Director, Division of Genomic Medicine
Amanda Riley, PMP Project Manager Margaret Ginoza Scientific Program Analyst
Deborah Maiese, MPA Consensus Coordinator National Institute of Mental Health
Rebecca Boyles, MSPH Investigator Greg Farber, PhD Project Scientist
Wayne Huggins Investigator National Heart, Lung and Blood Institute
Michael Phillips, MS Investigator Ellen Werner, PhD Project Scientist
Helen Pan, PhD Toolkit Lead National Institute of Drug Abuse
Pat West Communications Lead Kevin Conway, PhD Project Scientist
Tobacco Regulatory Research Program
Kay Wanke, PhD Project Scientist

Previous PhenX Newsletters         Phenx Steering Committee



Funding
PhenX is supported by Genomic Resource for PhenX Toolkit (U41), funded by the National Institutes of Health (NIH) National Human Genome Research Institute (NHGRI), with co-funding by the National Institute on Drug Abuse (NIDA). Supplemental funding was provided by the Tobacco Regulatory Science Program (TRSP), the Food and Drug Administration (FDA), the National Institute of Mental Health (NIMH) and the National Heart, Lung, and Blood Institute (NHLBI).
  
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