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The PhenX Toolkit: get the most from your measures.

The potential for genome-wide association studies to relate phenotypes to specific genetic variation is greatly increased when data can be combined or compared across multiple studies. To facilitate replication and validation across studies, RTI International (Research Triangle Park, North Carolina) and the National Human Genome Research Institute (Bethesda, Maryland) are collaborating on the consensus measures for Phenotypes and eXposures (PhenX) project. The goal of PhenX is to identify 15 high-priority, well-established, and broadly applicable measures for each of 21 research domains. PhenX measures are selected by working groups of domain experts using a consensus process that includes input from the scientific community. The selected measures are then made freely available to the scientific community via the PhenX Toolkit. Thus, the PhenX Toolkit provides the research community with a core set of high-quality, well-established, low-burden measures intended for use in large-scale genomic studies. PhenX measures will have the most impact when included at the experimental design stage. The PhenX Toolkit also includes links to standards and resources in an effort to facilitate data harmonization to legacy data. Broad acceptance and use of PhenX measures will promote cross-study comparisons to increase statistical power for identifying and replicating variants associated with complex diseases and with gene-gene and gene-environment interactions.

Pubmed ID: 21749974 RIS Download

Mesh terms: Computational Biology | Genome, Human | Genome-Wide Association Study | Genomics | Genotype | Humans | Information Dissemination | Internet | Phenotype | Polymorphism, Genetic | Reference Standards

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This is a list of tools and resources that we have found mentioned in this publication.


PROMIS

Patient Reported Outcomes Measurement Information System (PROMIS) is a system of highly reliable, precise measures of patientreported health status for physical, mental, and social wellbeing. PROMIS tools measure what patients are able to do and how they feel by asking questions. PROMIS'' measures can be used as primary or secondary endpoints in clinical studies of the effectiveness of treatment, and PROMIS tools can be used across a wide variety of chronic diseases and conditions and in the general population. PROMIS instruments use modern measurement theory to assess patientreported health status for physical, mental, and social wellbeing to reliably and validly measure patientreported outcomes (PROs) for clinical research and practice. PROMIS instruments measure concepts such as pain, fatigue, physical function, depression, anxiety and social function. PROMIS has constructed item banks (a collection of questions measuring the same thing that can be administered in short forms or adaptively through computerized adaptive testing). Short forms require 410 items; computerized adaptive testing require 37 items for more precise scores. * PROMIS measures are available for children and adults. * Most PROMIS instruments are available through Assessment Center, which can be administered online or through an offline computer. You can also download instruments from the Assessment Center for paperbased administration or entry of information into other data collection platforms. The data collected in PROMIS provides clinicians and researchers with important patientreported information about the effect of therapy that cannot be found in traditional clinical measures. When used with traditional clinical measures of health, PROMIS tools allow clinicians to better understand how various treatments might affect what patients are able to do and the symptoms they experience. Not only can the reports be used to design treatment plans, but also can be used by patients and physicians to improve improving communication and manage chronic disease. The PROMIS initiative is carried out by a network of twelve NIHfunded primary research sites and coordinating centers working collaboratively to develop a series of dynamic tools to reliably and validly measure patientreported outcomes (PROs). Primary research sites are responsible for: * completing independent research project(s) * developing and shaping the PROMIS item banks in cooperation with other PROMIS research sites and coordinating centers * collecting data and conducting analyses to support the validity of PROMIS instruments Public Use Data: Researchers are invited to submit applications for specific analysis projects to the PROMIS Statistical Center (PSC), for review and approval. Available Datasets * Wave I Public Use Dataset * User specified extract (possible, for a fee)

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NCBI

A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.

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PhenX Toolkit

The Toolkit provides standard measures related to complex diseases, phenotypic traits and environmental exposures. Use of PhenX measures facilitates combining data from a variety of studies, and makes it easy for investigators to expand a study design beyond the primary research focus. New Substance Abuse and Addiction measures are now available. Toolkit Users can: * Search or Browse the Toolkit to review and select PhenX measures * Generate Data Collection Worksheets and Data Dictionaries for Selected Measures In 2007, the National Human Genome Research Institute (NHGRI) along with the Office of Behavioral and Social Sciences Research (OBSSR) launched a project to identify high priority, generally low burden, standard measures for use in genome wide association studies and other large scale research efforts. This project, PhenX (consensus measures for Phenotypes and eXposures) used a consensus process to identify 15 high priority measures for each of 21 broad research domains. The PhenX Toolkit presents the measures and protocols free of charge to the scientific community in a web-based resource (https://www.phenxtoolkit.org/). The Toolkit provides a brief description of each measure, the purpose and rationale for its inclusion, the standard protocols for collecting the data, and references; it also describe the requirements (e.g., training, personnel, equipment, any applicable licensing fees) for data collection. Widespread adoption of PhenX measures will promote scientific collaboration, accelerate validation studies, and lead to new insights and identification of shared underlying mechanisms in health and disease. There are a total of 338 measures in the PhenX Toolkit. Top 5 Measures 1. Current Age 2. Breastfeeding 3. Hand Dominance 4. Breast or Bottle Feeding Patterns 5. Gender Top 5 Domains 1. Demographics 2. Nutrition and Dietary Supplements 3. Anthropometrics 4. Oral Health 5. Alcohol, Tobacco and Other Substances

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National Library of Medicine

NLM collects, organizes, and makes available biomedical science information to scientists, health professionals, and the public. The Library's Web-based databases, including PubMed/Medline and MedlinePlus, are used extensively around the world. NLM conducts and supports research in biomedical communications; creates information resources for molecular biology, biotechnology, toxicology, and environmental health; and provides grant and contract support for training, medical library resources, and biomedical informatics and communications research. Celebrating its 175th anniversary in 2011, the National Library of Medicine (NLM), in Bethesda, Maryland, is a part of the National Institutes of Health, U.S. Department of Health and Human Services (HHS). Since its founding in 1836 as the library of the U.S. Army Surgeon General, NLM has played a pivotal role in translating biomedical research into practice. It is the world's largest biomedical library and the developer of electronic information services that deliver trillions of bytes of data to millions of users every day. Scientists, health professionals, and the public in the United States and around the globe search the Library's online information resources more than 1 billion times each year. The Library is open to all and has many services and resources for scientists, health professionals, historians, and the general public. NLM has over 17 million books, journals, manuscripts, audiovisuals, and other forms of medical information on its shelves, making it the largest health-science library in the world. In today's increasingly digital world, NLM carries out its mission of enabling biomedical research, supporting health care and public health, and promoting healthy behavior by: * Acquiring, organizing, and preserving the world's scholarly biomedical literature; * Providing access to biomedical and health information across the country in partnership with the 5,800-member National Network of Libraries of Medicine (NN/LM); * Serving as a leading global resource for building, curating and providing sophisticated access to molecular biology and genomic information, including those from the Human Genome Project and NIH Common Fund; * Creating high-quality information services relevant to toxicology and environmental health, health services research, and public health; * Conducting research and development on biomedical communications systems, methods, technologies, and networks and information dissemination and utilization among health professionals, patients, and the general public; * Funding advanced biomedical informatics research and serving as the primary supporter of pre- and post-doctoral research training in biomedical informatics at 18 U.S. universities.

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