Dataset Information

A framework for assessing neuropsychiatric phenotypes by using smartphone-based location data.

ABSTRACT: The use of smartphone-based location data to quantify behavior longitudinally and passively is rapidly gaining traction in neuropsychiatric research. However, a standardized and validated preprocessing framework for deriving behavioral phenotypes from smartphone-based location data is currently lacking. Here, we present a preprocessing framework consisting of methods that are validated in the context of geospatial data. This framework aims to generate context-enriched location data by identifying stationary, non-stationary, and recurrent stationary states in movement patterns. Subsequently, this context-enriched data is used to derive a series of behavioral phenotypes that are related to movement. By using smartphone-based location data collected from 245 subjects, including patients with schizophrenia, we show that the proposed framework is effective and accurate in generating context-enriched location data. This data was subsequently used to derive behavioral readouts that were sensitive in detecting behavioral nuances related to schizophrenia and aging, such as the time spent at home and the number of unique places visited. Overall, our results indicate that the proposed framework reliably preprocesses raw smartphone-based location data in such a manner that relevant behavioral phenotypes of interest can be derived.

SUBMITTER: Jongs N

PROVIDER: S-EPMC7329884 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A framework for assessing neuropsychiatric phenotypes by using smartphone-based location data.

Jongs Niels N Jagesar Raj R van Haren Neeltje E M NEM Penninx Brenda W J H BWJH Reus Lianne L Visser Pieter J PJ van der Wee Nic J A NJA Koning Ina M IM Arango Celso C Sommer Iris E C IEC Eijkemans Marinus J C MJC Vorstman Jacob A JA Kas Martien J MJ

Translational psychiatry 20200701 1

The use of smartphone-based location data to quantify behavior longitudinally and passively is rapidly gaining traction in neuropsychiatric research. However, a standardized and validated preprocessing framework for deriving behavioral phenotypes from smartphone-based location data is currently lacking. Here, we present a preprocessing framework consisting of methods that are validated in the context of geospatial data. This framework aims to generate context-enriched location data by identifyin ...[more]

PMID: 32612118

Similar Datasets

Project description:BackgroundEnvironmental exposures are commonly estimated using spatial methods, with most epidemiological studies relying on home addresses. Passively collected smartphone location data, like Google Location History (GLH) data, may present an opportunity to integrate existing long-term time-activity data.ObjectivesWe aimed to evaluate the potential use of GLH data for capturing long-term retrospective time-activity data for environmental health research.MethodsWe included 378 individuals who participated in previous Global Positioning System (GPS) studies within the Washington State Twin Registry. GLH data consists of location information that has been routinely collected since 2010 when location sharing was enabled within android operating systems or Google apps. We created instructions for participants to download their GLH data and provide it through secure data transfer. We summarized the GLH data provided, compared it to available GPS data, and conducted an exposure assessment for nitrogen dioxide (NO2) air pollution.ResultsOf 378 individuals contacted, we received GLH data from 61 individuals (16.1%) and 53 (14.0%) indicated interest but did not have historical GLH data available. The provided GLH data spanned 2010-2021 and included 34 million locations, capturing 66,677 participant days. The median number of days with GLH data per participant was 752, capturing 442 unique locations. When we compared GLH data to 2-wk GPS data (∼1.8 million points), 95% of GPS time-activity points were within 100m of GLH locations. We observed important differences between NO2 exposures assigned at home locations compared with GLH locations, highlighting the importance of GLH data to environmental exposure assessment.DiscussionWe believe collecting GLH data is a feasible and cost-effective method for capturing retrospective time-activity patterns for large populations that presents new opportunities for environmental epidemiology. Cohort studies should consider adding GLH data collection to capture historical time-activity patterns of participants, employing a "bring-your-own-location-data" citizen science approach. Privacy remains a concern that needs to be carefully managed when using GLH data. https://doi.org/10.1289/EHP10829.

Project description:BackgroundThere are a variety of bioinformatic pipelines and downstream analysis methods for analyzing 16S rRNA marker-gene surveys. However, appropriate assessment datasets and metrics are needed as there is limited guidance to decide between available analysis methods. Mixtures of environmental samples are useful for assessing analysis methods as one can evaluate methods based on calculated expected values using unmixed sample measurements and the mixture design. Previous studies have used mixtures of environmental samples to assess other sequencing methods such as RNAseq. But no studies have used mixtures of environmental to assess 16S rRNA sequencing.ResultsWe developed a framework for assessing 16S rRNA sequencing analysis methods which utilizes a novel two-sample titration mixture dataset and metrics to evaluate qualitative and quantitative characteristics of count tables. Our qualitative assessment evaluates feature presence/absence exploiting features only present in unmixed samples or titrations by testing if random sampling can account for their observed relative abundance. Our quantitative assessment evaluates feature relative and differential abundance by comparing observed and expected values. We demonstrated the framework by evaluating count tables generated with three commonly used bioinformatic pipelines: (i) DADA2 a sequence inference method, (ii) Mothur a de novo clustering method, and (iii) QIIME an open-reference clustering method. The qualitative assessment results indicated that the majority of Mothur and QIIME features only present in unmixed samples or titrations were accounted for by random sampling alone, but this was not the case for DADA2 features. Combined with count table sparsity (proportion of zero-valued cells in a count table), these results indicate DADA2 has a higher false-negative rate whereas Mothur and QIIME have higher false-positive rates. The quantitative assessment results indicated the observed relative abundance and differential abundance values were consistent with expected values for all three pipelines.ConclusionsWe developed a novel framework for assessing 16S rRNA marker-gene survey methods and demonstrated the framework by evaluating count tables generated with three bioinformatic pipelines. This framework is a valuable community resource for assessing 16S rRNA marker-gene survey bioinformatic methods and will help scientists identify appropriate analysis methods for their marker-gene surveys.

Dataset Information

A framework for assessing neuropsychiatric phenotypes by using smartphone-based location data.

Publications

A framework for assessing neuropsychiatric phenotypes by using smartphone-based location data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets