Harmonized US National Health and Nutrition Examination Survey 1988-2018 for high throughput exposome-health discovery

Abstract

The National Health and Nutrition Examination Survey (NHANES) provides data on the health and environmental exposure of the non-institutionalized US population. Such data have considerable potential to understand how the environment and behaviors impact human health. These data are also currently leveraged to answer public health questions such as prevalence of disease. However, these data need to first be processed before new insights can be derived through large-scale analyses. NHANES data are stored across hundreds of files with multiple inconsistencies. Correcting such inconsistencies takes systematic cross examination and considerable efforts but is required for accurately and reproducibly characterizing the associations between the exposome and diseases. Thus, we developed a set of curated and unified datasets and accompanied code by merging 614 separate files and harmonizing unrestricted data across NHANES III (1988-1994) and Continuous (1999-2018), totaling 134,310 participants and 4,740 variables. The variables convey 1) demographic information, 2) dietary consumption, 3) physical examination results, 4) occupation, 5) questionnaire items (e.g., physical activity, general health status, medical conditions), 6) medications, 7) mortality status linked from the National Death Index, 8) survey weights, 9) environmental exposure biomarker measurements, and 10) chemical comments that indicate which measurements are below or above the lower limit of detection. We also provide a data dictionary listing the variables and their descriptions to help researchers browse the data. We also provide R markdown files to show example codes on calculating summary statistics and running regression models to help accelerate high-throughput analysis and secular trends of the exposome.

Ratio of Red Blood Cell Distribution Width to Albumin Level and Risk of Mortality

“…The data included demographic information, physical examination results, questionnaire items, and mortality status linked to the National Death Index. In this cohort, we also used data from a publicly available data dictionary, 27 and participants aged 18 years or older with complete data on serum albumin concentration, RDW, and death were included and analyzed. The final sample from NHANES included 50 622 (aged 19-85 years) individuals (eFigure 1 in Supplement 1 ).…”

Random survival forest for predicting the combined effects of multiple physiological risk factors on all-cause mortality

“…NHANES is a cross-sectional study to characterize the health of the non-institutionalized, civilian US population. For this study, we used the continuous 1999–2014 NHANES data on physiological factor measurements and demographics and merged these data with the National Death Index (age > = 18) to ascertain mortality information collected through December 31, 2015 23 . We excluded participants who did not have data on mortality status (N = 37,046) and those who were not followed up (N = 13), yielding a final sample of 45,032 with 28 physiological factors and mortality information.…”

High Throughput Transcriptomics to Understand Chemical Drivers of Aggressive Breast Cancer Subtypes

“…For this analysis, we used our curated NHANES dataset, which contains information on chemical biomarker concentrations of the 21 assessed chemicals in up to 57786 women recruited from 1999-2018. 31 Linkage between chemicals used in vitro and their corresponding exposure biomarkers in NHANES are shown in Supplemental Table 2. Chemical biomarker concentrations were converted to molarity units and then compared to the benchmark dose concentrations identified through the benchmark dose analyses of the RNA-seq data using boxplots.…”