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

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. O_TBL View this table: org.highwire.dtl.DTLVardef@9f5eb0org.highwire.dtl.DTLVardef@1019e2aorg.highwire.dtl.DTLVardef@136df18org.highwire.dtl.DTLVardef@170baecorg.highwire.dtl.DTLVardef@8cd_HPS_FORMAT_FIGEXP M_TBL C_TBL Background & SummaryThe Centers for Disease Control and Prevention (CDC) designed the National Health and Nutrition Examination Survey (NHANES) to monitor the health and nutritional status of adults and children in the US1. Beginning in 1960s, the NHANES program has included a series of surveys to ascertain health, nutritional, and environmental measurements in nationally representative samples. NHANES III was conducted in 1988-1994, consisting of a total of 39,695 persons aged 2 months and older, and was separated into two phases, Phase 1 (1988-1991) and Phase 2 (1991-1994). Continuous NHANES is a series of surveys conducted every two years since 1999, consisting of approximately 10,000 participants for every two-year study period to culminate to a total of 134,310 participants2. The data were ascertained through home interviews and health examinations. The interviews included self-reported questionnaires on demographics, socioeconomic status, health history, dietary intake, and occupation2. The health examination was conducted in mobile exam centers (MEC) staffed by a highly trained medical team2. The examination consists of clinical and physiological measurements of health metrics. In addition, the physical examination includes laboratory tests to quantify biomarkers of environmental chemical exposures in serum or urine. Overall, NHANES houses a wealth of data to be used to understand the health of the nation, but the potential to study secular changes in associations, such as in cancer mortality, over a wide range of time have not been evaluated.