Bioinformatics and data science

Data scientists collaborate at a whiteboard

Using genomic data to guide clinical and public health responses

The work in bioinformatics, which involves analyzing and interpreting the vast amount of sequencing data, is central to improving patient care and informing public health decisions

National surveillance programs

The NSPHL laboratory participates in three primary national surveillance programs. PulseNet and the GenomeTrakr networks utilize whole genome sequencing (WGS) of foodborne infectious agents. These networks are central to reviewing foodborne illness cases and identifying the bacteria responsible for making people sick. The third program relates to antimicrobial resistance.

PulseNet is a national laboratory network, coordinated by the CDC and the Association of Public Health Laboratories (APHL), that connects human foodborne illness cases to detect outbreaks. Labs in the network use WGS to identify the specific type of bacteria and share this data nationally to detect clusters of illness.

PulseNet USA

The GenomeTrakr network, led by the FDA, is the first distributed network of laboratories to utilize WGS for pathogen identification from food and environmental sources. This network consists of public health, university, and other laboratories that collect and share genomic and geographical data, which is housed in public databases at the National Center for Biotechnology Information (NCBI).

GenomeTrakr

CDC’s Antimicrobial Resistance Laboratory: NSPHL sequences all pathogenic isolates from Nevada that are submitted to this surveillance network focused on controlling the emergence of antimicrobial resistance.

Antimicrobial Resistance Laboratory

NSPHL shares genomic and geographical data from foodborne pathogens with scientists across the country through these platforms.

Additional programs

The NSPHL actively participates in additional national and international work that puts the laboratory and its scientists on the front line of protecting the health of Nevadans.

The Global Initiative on Sharing All Influenza Data (GISAID) is a worldwide science initiative that provides an open-access, and secure, repository for researchers to share viral sequencing and genomic data of influenza viruses and the SARS-CoV-2 coronavirus in real-time.

GISAID

NSPHL participates in the CaliciNet Surveillance Network, coordinated by the CDC, to better understand national norovirus outbreaks and allow the CDC to develop interventions that prevent the spread of Norovirus.

CaliciNet

Through the Epidemiology Laboratory Capacity (ELC) grant, using the PulseNet and ARLN regions, CDC’s Office of Advanced Molecular Detection (AMD) has established regional bioinformatics resources and training leads. Training leads provide support and training for laboratories across the region to build their sequencing capacity.

Each region has designated bioinformatics regional resource and training leads. In some cases, the same laboratory may serve as the bioinformatics regional resource and training lead.

Our team

Jonathan Chastain, D.O.

Assistant Professor, Medicine/Clinical Informaticist, Medicaid Partnership

jchastain@med.unr.edu

David Hess, Ph.D.

Research Associate Professor, Nevada State Public Health Lab

(775) 682-6240

dhess@med.unr.edu