Using PhenX measures to identify opportunities for cross-study analysis

Pan, Huaqin; Tryka, K. A.; Vreeman, Daniel J.; Huggins, Wayne; Phillips, M.; Mehta, Jayashri P.; Phillips, Jacqueline H.; McDonald, Clement J.; Junkins, Heather; Ramos, Erin M.; Hamilton, Carol M.

doi:10.1002/humu.22074

Cited by 28 publications

(22 citation statements)

References 18 publications

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“…Documentation supporting the use of the MIxS standard for the human microbiome community and improved user interfaces for tools that allow annotation and deposition of standards--compliant data could resolve a major bottleneck in current studies (Yilmaz et al, 2011). Similarly, the PhenX project, which identifies a common set of phenotype variables that are useful across many studies (Pan et al, 2012), provides a model for how microbiome metadata could be annotated. Adherence to the PhenX standard and to obtaining BioSample identifiers that are stable across multiple analyses of the same specimen will be especially useful for complex multi’omic studies (Barrett et al, 2012), as well as for systematic meta--analysis of datasets where statistical power is limited due to small population sizes in individual studies.…”

Section: Assaying and Understanding The Microbiomementioning

confidence: 99%

Advancing the Microbiome Research Community

Huttenhower

Knight

Brown

et al. 2014

Cell

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Section: Assaying and Understanding The Microbiomementioning

confidence: 99%

Advancing the Microbiome Research Community

Huttenhower

Knight

Brown

et al. 2014

Cell

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“…The PhenX Real world Implementation and Sharing (RISING) consortium is a significant step forward in the practical application of PhenX measures (49). PhenX publications have been largely focused on implementation of PhenX measures (35, 50-53), including a recent publication on the commonality of findings in different addictive disorders across measures of addiction (54). …”

Section: Introductionmentioning

confidence: 99%

Addictions Neuroclinical Assessment: A Neuroscience-Based Framework for Addictive Disorders

Kwako

Momenan

Litten

et al. 2016

Biological Psychiatry

304

278

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This paper proposes a heuristic framework for an Addictions Neuroclinical Assessment (ANA) that incorporates key functional domains derived from the neurocircuitry of addiction. We review how addictive disorders (AD) are presently diagnosed, and the need for new neuroclinical measures to differentiate patients who meet clinical criteria for addiction to the same agent while differing in etiology, prognosis and treatment response. The need for a better understanding of the mechanisms provoking and maintaining addiction, as evidenced by the limitations of current treatments and within-diagnosis clinical heterogeneity, is articulated. In addition, recent changes in the nosology of AD, challenges to current classification systems, and prior attempts to subtype individuals with AD are described. Complementary initiatives, including the Research Domain Criteria (RDoC) project, which have established frameworks for the neuroscience of psychiatric disorders, are discussed. Three domains, executive function, incentive salience, and negative emotionality, tied to different phases in the cycle of addiction, form the core functional elements of AD. Measurement of these domains in epidemiologic, genetic, clinical, and treatment studies will provide the underpinnings for an understanding of cross-population and temporal variation in addictions, shared mechanisms in addictive disorders, impact of changing environmental influences, and gene identification. Finally, we show that it is practical to implement such a deep neuroclinical assessment using a combination of neuroimaging and performance measures. Neuroclinical assessment is key to reconceptualizing the nosology of AD on the basis of process and etiology, an advance that can lead to improved prevention and treatment.

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“…Despite the numerous benefits of the use of standard measures and protocols, the propensity for each researcher to incorporate a set of uniquely defined variables into their study remains, 40 limiting the ability to meta-analyze data across studies. The PhenX Toolkit stands well poised to champion progress in this regard, and there is evidence that PhenX measures are increasingly recognized across the scientific community.…”

Section: Commentmentioning

confidence: 99%

“…This approach enables ready identification of investigations using common variables, which will allow for cross-study analysis. 40 …”

Section: Commentmentioning

confidence: 99%

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Research standardization tools: pregnancy measures in the PhenX Toolkit

Malinowski

Ananth

Catalano

et al. 2017

American Journal of Obstetrics and Gynecology

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Only through concerted and well-executed research endeavors can we gain the requisite knowledge to advance pregnancy care and positively impact maternal and newborn health. Yet the heterogeneity inherent in individual studies limits our ability to compare and synthesize study results, thus impeding the capacity to draw meaningful conclusions that can be trusted to inform clinical care. The PhenX Toolkit (http://www.phenxtoolkit.org), supported since 2007 by the National Institutes of Health, is a web-based catalog of standardized protocols for measuring phenotypes and exposures relevant for clinical research. In 2016, a working group of pregnancy experts recommended 15 measures for the PhenX Toolkit that are highly relevant to pregnancy research. The working group followed the established PhenX consensus process to recommend protocols that are broadly validated, well-established, nonproprietary, and have a relatively low burden for investigators and participants. The working group considered input from the pregnancy experts and the broader research community and included measures addressing mode of conception, gestational age, fetal growth assessment, prenatal care, mode of delivery, gestational diabetes, behavioral and mental health, and environmental exposure biomarkers. These pregnancy measures complement the existing measures for other established domains in the PhenX Toolkit, including reproductive health, anthropometrics, demographic characteristics, and alcohol, tobacco, and other substances. The preceding domains influence a woman's health during pregnancy. For each measure, the PhenX Toolkit includes data dictionaries and data collection worksheets that facilitate incorporation of the protocol into new or existing studies. The measures within the pregnancy domain offer a valuable resource to investigators and clinicians and are well poised to facilitate collaborative pregnancy research with the goal to improve patient care. To achieve this aim, investigators whose work includes the perinatal population are encouraged to utilize the PhenX Toolkit in the design and implementation of their studies, thus potentially reducing heterogeneity in data measures across studies. Such an effort will enhance the overall impact of individual studies and increasing the ability to draw more meaningful conclusions that can then be translated into clinical practice.

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Using PhenX measures to identify opportunities for cross-study analysis

Cited by 28 publications

References 18 publications

Advancing the Microbiome Research Community

Advancing the Microbiome Research Community

Addictions Neuroclinical Assessment: A Neuroscience-Based Framework for Addictive Disorders

Research standardization tools: pregnancy measures in the PhenX Toolkit

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