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University of California-Berkeley

Superfund Research Program

Data Science and Laboratory Core

Project Leader: Alan E. Hubbard
Co-Investigators: David L. Sedlak, Andres Cardenas (Stanford University)
Grant Number: P42ES004705
Funding Period: 2017-2022
View this project in the NIH Research Portfolio Online Reporting Tools (RePORT)

Project-Specific Links

Project Summary (2017-2022)

The University of California (UC) Berkeley SRP Center investigators are working to understand potential health risks posed by complex exposure scenarios present at hazardous waste sites, using a novel ’seeing the whole picture’ exposomic approach. Several projects are using cutting-edge analytical chemistry, sequencing and other approaches to produce high-dimensional "omic" data with thousands of parallel measurements on a specific endpoint. These data are analyzed to identify biological processes that are perturbed in complex environmental exposure scenarios. Several projects rely on a carefully maintained biorepository of mammalian cell lines and biospecimens from human populations exposed to arsenic, benzene, formaldehyde, trichloroethene, and benzo(a)pyrene.

The Data Science and Laboratory Core supports the data science, analytical chemistry, and biospecimen processing and storage needs of the UC Berkeley SRP Center and is critical to the success of the program. Specifically, the data science component supports the acquisition, storage, analysis, and sharing of large, complex datasets through the development of tools, infrastructure, and expertise. It develops data-driven, machine-learning methods to find patterns in high-dimensional data sets in order to understand biological perturbations and potential health risks associated with exposures. As these methods require a lot of computing power, existing powerful Linux servers are adapted to host and analyze the data. The Data Science and Laboratory Core leaders work with the Berkeley Research Computing group to develop ways to annotate and share the data and analysis protocols with the project leaders and ultimately the greater scientific community. The Laboratory component supports the processing, storage, and management of human biospecimens and cell lines, leveraging years of expertise in this area. The team innovatively connects with the Community Engagement Core (CEC) to advise on the development of study protocols and to analyze arsenic, nitrate, chromium, pesticides, and chlorinated hydrocarbons in water samples, for the pilot Domestic Well Intervention Study of the CEC. By leveraging expertise from the research projects, the Laboratory component enables the CEC and the UC Berkeley SRP Center to respond to community issues and needs, and pursue interventions to improve drinking water quality for affected communities.

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