Smoking cessation, harm reduction, and biomarkers protocols in the PhenX Toolkit: Tools for standardized data collection.

The use of standard protocols in studies supports consistent data collection, improves data quality, and facilitates cross-study analyses. Funded by the National Institutes of Health, the PhenX (consensus measures for otypes and eposures) Toolkit is a catalog of recommended measurement protocols that address a wide range of research topics and are suitable for inclusion in a variety of study designs. In 2020, a PhenX Working Group of smoking cessation experts followed a well-established consensus process to identify and recommend measurement protocols suitable for inclusion in smoking cessation and smoking harm reduction studies.

The PhenX Toolkit: Recommended Measurement Protocols for Social Determinants of Health Research.

Health disparities are driven by unequal conditions in the environments in which people are born, live, learn, work, play, worship, and age, commonly termed the Social Determinants of Health (SDoH). The availability of recommended measurement protocols for SDoH will enable investigators to consistently collect data for SDoH constructs. The PhenX (consensus measures for Phenotypes and eXposures) Toolkit is a web-based catalog of recommended measurement protocols for use in research studies with human participants.

T-CLEARE: A Pilot Community-Driven Tissue-Clearing Protocol Repository.

Selecting and implementing a tissue-clearing protocol is challenging. Established more than 100 years ago, tissue clearing is still a rapidly evolving field of research. There are currently many published protocols to choose from, and each performs better or worse across a range of key evaluation factors (e.

The PhenX Toolkit: Measurement Protocols for Assessment of Social Determinants of Health.

Introduction: Social determinants are structures and conditions in the biological, physical, built, and social environments that affect health, social and physical functioning, health risk, quality of life, and health outcomes. The adoption of recommended, standard measurement protocols for social determinants of health will advance the science of minority health and health disparities research and provide standard social determinants of health protocols for inclusion in all studies with human participants.

Methods: A PhenX (consensus measures for Phenotypes and eXposures) Working Group of social determinants of health experts was convened from October 2018 to May 2020 and followed a well-established consensus process to identify and recommend social determinants of health measurement protocols.

The PhenX Toolkit: standard measurement resources for cancer outcomes and survivorship research.

This brief report introduces the Cancer Outcomes and Survivorship domain in the PhenX Toolkit (consensus measures for Phenotypes and eXposures), which includes 15 validated measurement protocols for cancer survivorship research that were recommended for inclusion in this publicly available resource. Developed with input from the scientific community, the domain provides researchers with well-established measurement protocols for evaluating physical and psychological effects, financial toxicity, and patient experiences with cancer care. The PhenX Toolkit, funded by the National Human Genome Research Institute since 2007, is an online resource that provides high-quality standard measurement protocols for a wide range of research areas (eg, smoking cessation, harm reduction and biomarkers, and social determinants of health).

Identifying Datasets for Cross-Study Analysis in dbGaP using PhenX.

Identifying relevant studies and harmonizing datasets are major hurdles for data reuse. Common Data Elements (CDEs) can help identify comparable study datasets and reduce the burden of retrospective data harmonization, but they have not been required, historically. The collaborative team at PhenX and dbGaP developed an approach to use PhenX variables as a set of CDEs to link phenotypic data and identify comparable studies in dbGaP.

Correlation Analysis of Variables From the Atherosclerosis Risk in Communities Study.

The need to test chemicals in a timely and cost-effective manner has driven the development of new alternative methods (NAMs) that utilize in silico and approaches for toxicity prediction. There is a wealth of existing data from human studies that can aid in understanding the ability of NAMs to support chemical safety assessment. This study aims to streamline the integration of data from existing human cohorts by programmatically identifying related variables within each study.

Standard metadata for 3D microscopy.

Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining provide unprecedented opportunities to investigate brain structure and function. These experiments' images make it possible to catalog brain cell types and define their location, morphology, and connectivity in a native context, leading to a better understanding of normal development and disease etiology. Consistent annotation of metadata is needed to provide the context necessary to understand, reuse, and integrate these data.

Linking complex disease and exposure data-insights from an environmental and occupational health study.

The disparate measurement protocols used to collect study data are an intrinsic barrier to combining information from environmental health studies. Using standardized measurement protocols and data standards for environmental exposures addresses this gap by improving data collection quality and consistency. To assess the prevalence of environmental exposures in National Institutes of Health (NIH) public data repositories and resources and to assess the commonality of the data elements, we analyzed clinical measures and exposure assays by comparing the Caribbean Consortium for Research in Environmental and Occupational Health study with selected NIH environmental health resources and studies.

Tools for standardized data collection: Speech, Language, and Hearing measurement protocols in the PhenX Toolkit.

The PhenX Toolkit (https://www.phenxtoolkit.org/) is an online catalog of recommended measurement protocols to facilitate cross-study analyses for biomedical research.

Using the PhenX Toolkit to Select Standard Measurement Protocols for Your Research Study.

The goals of PhenX (consensus measures for Phenotypes and eXposures) are to promote the use of standard measurement protocols and to help investigators identify opportunities for collaborative research and cross-study analysis, thus increasing the impact of individual studies. The PhenX Toolkit (https://www.phenxtoolkit.

Genomic medicine implementation protocols in the PhenX Toolkit: tools for standardized data collection.

Purpose: The PhenX Toolkit ( www.phenxtoolkit.org ), an online catalog of recommended measurement protocols, facilitates cross-study analyses for research with human participants.

The PhenX Toolkit: Establishing Standard Measures for COVID-19 Research.

The PhenX (consensus measures for Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org/) is a publicly available, web-based catalog of recommended, well-established measurement protocols of phenotypes and exposures.

An Assessment of Environmental Health Measures in the Deepwater Horizon Research Consortia.

Research consortia play a key role in our understanding of how environmental exposures influence health and wellbeing, especially in the case of catastrophic events such as the Deepwater Horizon oil spill. A common challenge that prevents the optimal use of these data is the difficulty of harmonizing data regarding the environmental exposures and health effects across the studies within and among consortia. A review of the measures used by members of the Deepwater Horizon Research Consortia highlights the challenges associated with balancing timely implementation of a study to support disaster relief with optimizing the long-term value of the data.

The China tuberculosis clinical trials consortium network: a model for international TB clinical trials capacity building.

Background: With the second largest tuberculosis (TB) burden globally, China is committed to actively engage in international TB clinical trials to contribute to global TB research. However, lack of research capacity among local sites has been identified as a barrier.

Main Text: The China Tuberculosis Clinical Trials Consortium (CTCTC) was initiated by Beijing Chest Hospital with investment from the US National Institutes of Health and technical support from Family Health International 360 in 2013, as a nationwide collaborative clinical trial network to strengthen selected clinical site research capacity and attract TB clinical trials.

Common Data Elements for National Institute of Mental Health-Funded Translational Early Psychosis Research.

The National Institutes of Health has established the PhenX Toolkit as a web-based resource containing consensus measures freely available to the research community. The National Institute of Mental Health (NIMH) has introduced the Mental Health Research Core Collection as part of the PhenX Toolkit and recently convened the PhenX Early Psychosis Working Group to generate the PhenX Early Psychosis Specialty Collection. The Working Group consisted of two complementary panels for clinical and translational research.

Over- and under-treatment of TB patients in Eastern China: an analysis based on health insurance claims data.

Objective: Poor compliance with existing guidelines for tuberculosis (TB) care and treatment is an issue of concern in China. We assessed health service use by TB patients over the entire treatment process and compared it to the recommended guidelines.

Methods: We collected insurance claims data in three counties of one province of Eastern China.

The Children's Respiratory and Environmental Workgroup (CREW) birth cohort consortium: design, methods, and study population.

Background: Single birth cohort studies have been the basis for many discoveries about early life risk factors for childhood asthma but are limited in scope by sample size and characteristics of the local environment and population. The Children's Respiratory and Environmental Workgroup (CREW) was established to integrate multiple established asthma birth cohorts and to investigate asthma phenotypes and associated causal pathways (endotypes), focusing on how they are influenced by interactions between genetics, lifestyle, and environmental exposures during the prenatal period and early childhood.

Methods And Results: CREW is funded by the NIH Environmental influences on Child Health Outcomes (ECHO) program, and consists of 12 individual cohorts and three additional scientific centers.

Recommendations and Challenges of the Clinical Services Panel of the PhenX Early Psychosis Working Group.

Coordinated specialty care (CSC) is a promising multielement treatment for the care of individuals experiencing the onset of schizophrenia. The community mental health block grant program has increased federal support for CSC programs. In order to maximize the number of sites capable of science-to-service or service-to-science translation, the National Institute of Mental Health funded a supplement to the PhenX toolkit consisting of measures for early psychosis.

Building capacity for advances in tuberculosis research; proceedings of the third RePORT international meeting.

RePORT International is a global network of research sites in India, Brazil, Indonesia, South Africa, China, and the Philippines dedicated to collaborative tuberculosis research in the context of HIV. A standardized research protocol (the Common Protocol) guides the enrollment of participants with active pulmonary tuberculosis and contacts into observational cohorts. The establishment of harmonized clinical data and bio-repositories will allow cutting-edge, large-scale advances in the understanding of tuberculosis, including identification of novel biomarkers for progression to active tuberculosis and relapse after treatment.