whole genome sequencing for food safety initiative€¦ · massively parallel signature sequencing...
TRANSCRIPT
WHOLE GENOME SEQUENCING FOR FOOD SAFETY INITIATIVE
Obstacles, Opportunities and an Outlook
Behzad Imanian: Project Leader, IFSH WGS Initiative
WGS is not a perfect tool
It is new
Whole ≠ Complete
Genome ≠ Organism
Data intensive
Hard to analyze
Hard to interpret
It is expensive
It takes too long
WGS is the new ‘gold standard’
‘Genotype’ vs ‘Phenotype’
Genome ≈ Organism
Data intensive More informative
Broad view
Better resolution
Reproducible
More applications
Becoming faster, cheaper
Advancing fast
Adopted and applied widely
WGS: data up; costs down
http://www.ncbi.nlm.nih.gov/genbank/statistics/
https://www.genome.gov/27565109/the-cost-of-sequencing-a-human-genome/
2015-2016
2014
WGS
Massively parallel signature sequencing (MPSS)
Polony sequencing
454 pyrosequencing
Illumina (Solexa) sequencing
Ion Torrent semiconductor sequencing
DNA nanoball sequencing
Heliscope single molecule sequencing
Single molecule real time (SMRT) sequencing (PacBio)
Nanopore DNA sequencing
(Oxford Nanopore Tech)
Tunneling currents DNA sequencing
Sequencing with mass spectrometry
Microfluidic Sanger sequencing
Main article: Sanger sequencing
Microscopy-based techniques
RNAP sequencing
In vitro virus high-throughput sequencing
Developed In Development
Courtesy of Wikipedia
IFSH WGS Project
Proposal and a preliminary charter (March/April 2015)
Start date: (Oct 01 2015)
Objectives: - Collaboration with food companies
- Research and laboratory services
- Pathogens and GenomeTrakr
IFSH WGS ‘Consortium’
IFSH/Industry ‘Steering Committee’ Several members of industry
Several members of IFSH officials/scientists
‘Steering Committee’ Conference call, (July 2015)
Advising instead of Steering
Concerns about WGS data interpretation
Obstacles: legal repercussions
IFSH WGS Initiative
A new Industry Advisory Committee (July 2016)
15 companies invited, 14 accepted
Advisory Committee Conference Call (August 2016)
Interpretation of WGS data
Concerns about regulatory policies
Concerns about traceability, privacy, metadata
IFSH WGS Initiative: What’s done so far?
Infrastructure Laboratory
IFSH WGS Initiative: What’s done so far?
Infrastructure Laboratory
Equipment
IFSH WGS Initiative: What’s done so far?
Infrastructure Laboratory
Equipment
HPC
Data transfer
IFSH WGS Initiative: What’s done so far?
Outreach IFSH WGS Symposium for Food Safety
Industry Advisory Committee
Collaborations IFSH/FDA Scientists (Moffett Campus)
IIT Scientists (Main Campus)
External Scientists
Consulting and Analytical Companies
IFSH WGS Initiative: What’s being done?
Charter Has been revised (September 2016)
Spoilage, allergenic and toxin producing microorganisms
Collaboration with industry, academia and consulting/analytical companies
Extra staff A postdoctoral fellow (November 2016)
Students (January 2017)
IFSH WGS Initiative: What’s being done?
Cost estimates Are being done (October 2016)
Business plan Is being developed (October 2016)
A note: We are not a for-profit organization! Collaboration
Competition
IFSH WGS Initiative: Services
WGS sequencing Genomic
Pathogens (all FDA-defined zones)
Spoilage
Allergenic substance and toxin producing bacteria
Viruses (January 2017?)
Metagenomic 16S
Shotgun
Environmental samples
Transcriptomic (March 2017?)
RNA-seq
IFSH WGS Initiative: Services
Data analysis & bioinformatics Filtering data (read trimming and contaminant removal)
Genome assembly
Whole genome annotation
SNP analysis
Phylogenetic analysis (SNP, gene, multi-genes, genome wide, source tracking …)
Specific analysis (pathogenicity, antibiotic or heat/cold resistance …)
IFSH WGS Initiative: Workflow
Sample submission (directly or through 3rd party)
Re-labelling
DNA extraction
Library preparation Sequencing (MiSeq)bacterial isolates
IFSH WGS system
DNA
Strain confirmation
Quantification
Metadata
Metadata minimum requirements
bioproject ID
Sample type (clinical, environmental, food, etc.)
If clinical specific host host disease
Collection
collector, year, source
Location
country State
Obstacles
WGS regulatory policies Not legislated yet Not spoken of officially Not fully communicated
Confusion
Privacy and liability concerns Metadata Traceability of isolates Matches with past and present outbreaks ….
Not enough dialogues
Realities
WGS is providing superior power to Identify
Differentiate
Track sources
Monitor environments
Government has embraced WGS and is promoting it
Despite reservations, industry is interested
We are in a transitional period
Opportunities
Dialogues
Collaborations
Better policies
Faster implementation of WGS & its growing apps
Preventing outbreaks, recalls, loss of money
Preventing suffering and loss of and life
WGS Initiative: An outlook and our plans
Infrastructure Local database (IFSH WGS data) Third party submission of isolates? An extra HPC Other high throughput sequencing equipment
Training Wet lab, data submission & analysis
Promoting the dialogues between the government & industry
Expand collaborations with Industry Academia Analytical/consulting companies Government
Acknowledgements
Kristin M. Schill
Richard E. McDonald, Mary Lou Tortorello, Glen Black
Wei Zhang, Armand Paradis, Alvin Lee, Jason Wan, Robert Brackett
Cindy Koschetz, Haley Tomlinson, Barbara Neuman, Andrew Ehn, Ellen Spiewak, David Griesemer, KaipingDeng, Yingshu He
Jean-Francois Pombert
The Industry Advisory Committee
Eric Brown, Marc Allard, Ruth Timme, Hugh Rand, Errol strain and the rest of the WGS team in College Park
George Atkinson, Tim Jackson, Mickey Parish, Chris Braden, Palmer Orlandi, Peter Gerner-Smidt
Our fantastic speakers
Consulting/Analytical Companies who have reached us and our sponsors
FDA/IFSH/IIT Others