dbgap2x: an R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP).

SUMMARY: Based on the Genomic Data Sharing Policy issued in August 2007, the National Institutes of Health (NIH) has supported several repositories such as the database of Genotypes and Phenotypes (dbGaP). dbGaP is an online repository that provides access to large-scale genetic and phenotypic datasets with more than 1000 studies. However, navigating the website and understanding the relationship between the studies are not easy tasks. Moreover, the decryption of the files is a complex procedure. In this study we propose the dbgap2x R package that covers a broad range of functions for searching dbGaP studies, exploring the characteristics of a study and easily decrypting the files from dbGaP. AVAILABILITY AND IMPLEMENTATION: dbgap2x is an R package with the code available at https://github.com/gversmee/dbgap2x. A containerized version including the package, a Jupyter server and with a Notebook example is available at https://hub.docker.com/r/gversmee/dbgap2x. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indoor Temperatures in the 2018 Heat Wave in Quebec, Canada: Exploratory Study Using Ecobee Smart Thermostats.

BACKGROUND: Climate change, driven by human activity, is rapidly changing our environment and posing an increased risk to human health. Local governments must adapt their cities and prepare for increased periods of extreme heat and ensure that marginalized populations do not suffer detrimental health outcomes. Heat warnings traditionally rely on outdoor temperature data which may not reflect indoor temperatures experienced by individuals. Smart thermostats could be a novel and highly scalable data source for heat wave monitoring. OBJECTIVE: The objective of this study was to explore whether smart thermostats can be used to measure indoor temperature during a heat wave and identify houses experiencing indoor temperatures above 26°C. METHODS: We used secondary data-indoor temperature data recorded by ecobee smart thermostats during the Quebec heat waves of 2018 that claimed 66 lives, outdoor temperature data from Environment Canada weather stations, and indoor temperature data from 768 Quebec households. We performed descriptive statistical analyses to compare indoor temperatures differences between air conditioned and non-air conditioned houses in Montreal, Gatineau, and surrounding areas from June 1 to August 31, 2018. RESULTS: There were significant differences in indoor temperature between houses with and without air conditioning on both heat wave and non-heat wave days (P<.001). Households without air conditioning consistently recorded daily temperatures above common indoor temperature standards. High indoor temperatures persisted for an average of 4 hours per day in non-air conditioned houses. CONCLUSIONS: Our findings were consistent with current literature on building warming and heat retention during heat waves, which contribute to increased risk of heat-related illnesses. Indoor temperatures can be captured continuously using smart thermostats across a large population. When integrated with local heat health action plans, these data could be used to strengthen existing heat alert response systems and enhance emergency medical service responses.

Usability of Smart Home Thermostat to Evaluate the Impact of Weekdays and Seasons on Sleep Patterns and Indoor Stay: Observational Study.

BACKGROUND: Sleep behavior and time spent at home are important determinants of human health. Research on sleep patterns has traditionally relied on self-reported data. Not only does this methodology suffer from bias but the population-level data collection is also time-consuming. Advances in smart home technology and the Internet of Things have the potential to overcome these challenges in behavioral monitoring. OBJECTIVE: The objective of this study is to demonstrate the use of smart home thermostat data to evaluate household sleep patterns and the time spent at home and how these behaviors are influenced by different weekdays and seasonal variations. METHODS: From the 2018 ecobee Donate your Data data set, 481 North American households were selected based on having at least 300 days of data available, equipped with ≥6 sensors, and having a maximum of 4 occupants. Daily sleep cycles were identified based on sensor activation and used to quantify sleep time, wake-up time, sleep duration, and time spent at home. Each household's record was divided into different subsets based on seasonal, weekday, and seasonal weekday scales. RESULTS: Our results demonstrate that sleep parameters (sleep time, wake-up time, and sleep duration) were significantly influenced by the weekdays. The sleep time on Fridays and Saturdays is greater than that on Mondays, Wednesdays, and Thursdays (n=450; P<.001; odds ratio [OR] 1.8, 95% CI 1.5-3). There is significant sleep duration difference between Fridays and Saturdays and the rest of the week (n=450; P<.001; OR 1.8, 95% CI 1.4-2). Consequently, the wake-up time is significantly changing between weekends and weekdays (n=450; P<.001; OR 5.6, 95% CI 4.3-6.3). The results also indicate that households spent more time at home on Sundays than on the other weekdays (n=445; P<.001; OR 2.06, 95% CI 1.64-2.5). Although no significant association is found between sleep parameters and seasonal variation, the time spent at home in the winter is significantly greater than that in summer (n=455; P<.001; OR 1.6, 95% CI 1.3-2.3). These results are in accordance with existing literature. CONCLUSIONS: This is the first study to use smart home thermostat data to monitor sleep parameters and time spent at home and their dependence on weekday, seasonal, and seasonal weekday variations at the population level. These results provide evidence of the potential of using Internet of Things data to help public health officials understand variations in sleep indicators caused by global events (eg, pandemics and climate change).

Identifying the Socioeconomic, Demographic, and Political Determinants of Social Mobility and Their Effects on COVID-19 Cases and Deaths: Evidence From US Counties.

Background: The spread of COVID-19 at the local level is significantly impacted by population mobility. The U.S. has had extremely high per capita COVID-19 case and death rates. Efficient nonpharmaceutical interventions to control the spread of COVID-19 depend on our understanding of the determinants of public mobility. Objective: This study used publicly available Google data and machine learning to investigate population mobility across a sample of US counties. Statistical analysis was used to examine the socioeconomic, demographic, and political determinants of mobility and the corresponding patterns of per capita COVID-19 case and death rates. Methods: Daily Google population mobility data for 1085 US counties from March 1 to December 31, 2020, were clustered based on differences in mobility patterns using K-means clustering methods. Social mobility indicators (retail, grocery and pharmacy, workplace, and residence) were compared across clusters. Statistical differences in socioeconomic, demographic, and political variables between clusters were explored to identify determinants of mobility. Clusters were matched with daily per capita COVID-19 cases and deaths. Results: Our results grouped US counties into 4 Google mobility clusters. Clusters with more population mobility had a higher percentage of the population aged 65 years and over, a greater population share of Whites with less than high school and college education, a larger percentage of the population with less than a college education, a lower percentage of the population using public transit to work, and a smaller share of voters who voted for Clinton during the 2016 presidential election. Furthermore, clusters with greater population mobility experienced a sharp increase in per capita COVID-19 case and death rates from November to December 2020. Conclusions: Republican-leaning counties that are characterized by certain demographic characteristics had higher increases in social mobility and ultimately experienced a more significant incidence of COVID-19 during the latter part of 2020.

Multi-PheWAS intersection approach to identify sex differences across comorbidities in 59 140 pediatric patients with autism spectrum disorder.

OBJECTIVE: To identify differences related to sex and define autism spectrum disorder (ASD) comorbidities female-enriched through a comprehensive multi-PheWAS intersection approach on big, real-world data. Although sex difference is a consistent and recognized feature of ASD, additional clinical correlates could help to identify potential disease subgroups, based on sex and age. MATERIALS AND METHODS: We performed a systematic comorbidity analysis on 1860 groups of comorbidities exploring all spectrum of known disease, in 59 140 individuals (11 440 females) with ASD from 4 age groups. We explored ASD sex differences in 2 independent real-world datasets, across all potential comorbidities by comparing (1) females with ASD vs males with ASD and (2) females with ASD vs females without ASD. RESULTS: We identified 27 different comorbidities that appeared significantly more frequently in females with ASD. The comorbidities were mostly neurological (eg, epilepsy, odds ratio [OR] > 1.8, 3-18 years of age), congenital (eg, chromosomal anomalies, OR > 2, 3-18 years of age), and mental disorders (eg, intellectual disability, OR > 1.7, 6-18 years of age). Novel comorbidities included endocrine metabolic diseases (eg, failure to thrive, OR = 2.5, ages 0-2), digestive disorders (gastroesophageal reflux disease: OR = 1.7, 6-11 years of age; and constipation: OR > 1.6, 3-11 years of age), and sense organs (strabismus: OR > 1.8, 3-18 years of age). DISCUSSION: A multi-PheWAS intersection approach on real-world data as presented in this study uniquely contributes to the growing body of research regarding sex-based comorbidity analysis in ASD population. CONCLUSIONS: Our findings provide insights into female-enriched ASD comorbidities that are potentially important in diagnosis, as well as the identification of distinct comorbidity patterns influencing anticipatory treatment or referrals. The code is publicly available (https://github.com/hms-dbmi/sexDifferenceInASD).

Understanding User Behavior Through the Use of Unsupervised Anomaly Detection: Proof of Concept Using Internet of Things Smart Home Thermostat Data for Improving Public Health Surveillance.

BACKGROUND: One of the main concerns of public health surveillance is to preserve the physical and mental health of older adults while supporting their independence and privacy. On the other hand, to better assist those individuals with essential health care services in the event of an emergency, their regular activities should be monitored. Internet of Things (IoT) sensors may be employed to track the sequence of activities of individuals via ambient sensors, providing real-time insights on daily activity patterns and easy access to the data through the connected ecosystem. Previous surveys to identify the regular activity patterns of older adults were deficient in the limited number of participants, short period of activity tracking, and high reliance on predefined normal activity. OBJECTIVE: The objective of this study was to overcome the aforementioned challenges by performing a pilot study to evaluate the utilization of large-scale data from smart home thermostats that collect the motion status of individuals for every 5-minute interval over a long period of time. METHODS: From a large-scale dataset, we selected a group of 30 households who met the inclusion criteria (having at least 8 sensors, being connected to the system for at least 355 days in 2018, and having up to 4 occupants). The indoor activity patterns were captured through motion sensors. We used the unsupervised, time-based, deep neural-network architecture long short-term memory-variational autoencoder to identify the regular activity pattern for each household on 2 time scales: annual and weekday. The results were validated using 2019 records. The area under the curve as well as loss in 2018 were compatible with the 2019 schedule. Daily abnormal behaviors were identified based on deviation from the regular activity model. RESULTS: The utilization of this approach not only enabled us to identify the regular activity pattern for each household but also provided other insights by assessing sleep behavior using the sleep time and wake-up time. We could also compare the average time individuals spent at home for the different days of the week. From our study sample, there was a significant difference in the time individuals spent indoors during the weekend versus on weekdays. CONCLUSIONS: This approach could enhance individual health monitoring as well as public health surveillance. It provides a potentially nonobtrusive tool to assist public health officials and governments in policy development and emergency personnel in the event of an emergency by measuring indoor behavior while preserving privacy and using existing commercially available thermostat equipment.