The Technology Core will support all four Research Projects by providing a broad range of next-generation sequencing and data analysis capabilities. Core functions are divided into sequencing, primary data analysis, and comparative analysis. Sequencing strategies will include whole genome and targeted sequencing, transcriptome profiling by RNA-seq, rRNA profiling, and metagenomic and metatranscriptomic sequencing. Six different sequencing instrument platforms will be used including lllumina MiSeq and HiSeq, lon Torrent, ABI 3730x1, 454 FLX+, and Pacific Biosciences RSH. Sample tracking is managed throughout the process and extensive quality assessment is performed to maximize the yield of usable information. Ongoing evaluation of new methods will enable implementation of new approaches for library construction and sequencing, increase efficiency and lower costs. Automated pipelines are in place to handle most assembly, variant detection, and annotation tasks. Data analysis methods will be improved throughout the project to increase automation, improve results by incorporating new analytical methods, and provide more readily shared software, Comparative analysis will leverage PanOCT to identify shared and strain/clade-specific genome features. New methods will be developed for metatranscriptome analysis that enable quantitative comparisons between samples with and without reference genomes or metagenomes. The results of the Core will provide Research Projects with analyzed data that is suitable for further integrative analysis and interpretation. The Technology Core will work closely with the Data Management, Analysis and Resource Dissemination (DMARD) Core to ensure prompt submission of sequence data, clones, and software tools to the appropriate public repositories.

Public Health Relevance

The Technology Core provides high-throughput DNA and RNA sequencing in support of diverse projects related to infectious disease pathogens and host interactions. Sequence assembly, gene annotation, and analysis to compare genomes will provide datasets to the Research Projects for interpretation of experiments related to genetic variation, evolution, and genome function.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Program--Cooperative Agreements (U19)
Project #
1U19AI110819-01
Application #
8711785
Study Section
Special Emphasis Panel (ZAI1-EC-M (J1))
Project Start
Project End
Budget Start
2014-04-04
Budget End
2015-03-31
Support Year
1
Fiscal Year
2014
Total Cost
$1,239,523
Indirect Cost
$580,202
Name
J. Craig Venter Institute, Inc.
Department
Type
DUNS #
076364392
City
Rockville
State
MD
Country
United States
Zip Code
20850
Shao, Lulu; Fischer, David D; Kandasamy, Sukumar et al. (2016) Comparative In Vitro and In Vivo Studies of Porcine Rotavirus G9P[13] and Human Rotavirus Wa G1P[8]. J Virol 90:142-51
Rojas, Laura J; Wright, Meredith S; De La Cadena, Elsa et al. (2016) Initial Assessment of the Molecular Epidemiology of blaNDM-1 in Colombia. Antimicrob Agents Chemother 60:4346-50
Chavda, Kalyan D; Chen, Liang; Fouts, Derrick E et al. (2016) Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms. MBio 7:
Rosas-Salazar, Christian; Shilts, Meghan H; Tovchigrechko, Andrey et al. (2016) Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy. J Infect Dis 214:1924-1928
Nelson, Martha I; Stucker, Karla M; Schobel, Seth A et al. (2016) Introduction, Evolution, and Dissemination of Influenza A Viruses in Exhibition Swine in the United States during 2009 to 2013. J Virol 90:10963-10971
Schobel, Seth A; Stucker, Karla M; Moore, Martin L et al. (2016) Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene. Sci Rep 6:26311
Shilts, Meghan H; Rosas-Salazar, Christian; Tovchigrechko, Andrey et al. (2016) Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery. Microb Ecol 71:233-42
Chen, Rubing; Puri, Vinita; Fedorova, Nadia et al. (2016) Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus. J Virol 90:10600-10611
Rosas-Salazar, Christian; Shilts, Meghan H; Tovchigrechko, Andrey et al. (2016) Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk. Am J Respir Crit Care Med 193:1180-3
Nelson, Martha I; Wentworth, David E; Das, Suman R et al. (2016) Evolutionary Dynamics of Influenza A Viruses in US Exhibition Swine. J Infect Dis 213:173-82

Showing the most recent 10 out of 20 publications