Whole Genome Sequencing: A Tutorial and Hands-on Workshop to Help Understand Its Application to Food Safety

The Institute for Food Safety and Health (IFSH) is a one-of-a-kind applied food research institute solving key issues in food safety, food defense and nutrition

Institute for Food Safety and Health

<H2 CLASS="MsoNormal">An IFSH Symposium &amp; Workshop, May 6-7, 2019</H2>
Whole Genome Sequencing: A Tutorial and Hands-on Workshop to Help Understand Its Application to Food Safety
Agenda May 6th: Seminar and high-level overview
9:00 – 10:00 Introduction to sequencing, food safety, and this course – Eric Stevens
10:00 – 10:45 Overview of analyzing sequence data – Eric Stevens
10:45 – 11:00 Break
11:00 – 11:45 Understanding molecular evolution and phylogenetics – Eric Stevens
11:45 – 12:15 FDA’s GenomeTrakr – Eric Stevens
12:15 – 1:15 Lunch
1:15 – 2:15 FDA’s CDC’s PulseNet and FDA’s CORE – Matt Wise and Jenny Beal
2:00 – 2:45 Pathogen Detection Website at NCBI – Bill Klimke
2:45 – 3:30 WGS in Regulatory Decision Making – Leslie Hintz
3:30 – 3:45 Break
3:45 – 4:30 Future of sequencing, data sharing, and food safety – Eric Stevens
4:30 – 5:00 Questions and Answers - Panel
5:30 - 7:30 Reception at Eddie Merlot's
 
Agenda May 7th: Workshop at Moffett Center
The workshop is designed for a maximum number of 30 participants. The registration for the workshop will be closed as the first 30 people are registered. If you are interested in attending a similar workshop, and you cannot register due to registration limitation, please send your information to Dr. Behzad Imanian at <A HREF="mailto:bimanian@iit.edu" TARGET="_blank" REL="nofollow noopener noreferrer">bimanian@iit.edu</A> He will keep a waiting list, and if any of the first 30 registrants cancels their attendance, you may have the chance for getting in the workshop.
The workshop attendees are required to bring a good quality laptop (preferably not older than 5 years) with admin privileges. Further details will be forthcoming.
8:00 – 9:00 Morning Coffee and Continental Breakfast
9:00 – 10:00 Hands-On Exercises Using NCBI and Pathogen Detection Website - Bill Klimke
10:00 – 11:00 Basic requirements for analyzing/understanding sequence data – Peter Cook
11:00 – 11:15 Break
11: 15 – 12:15 Introduction to a Bioinformatic Computing Environment – Peter Cook
12:15 – 1:15 Lunch
1:15 – 1:45 Hands-On Analysis: Introduction, Raw Read Analysis, and Read Cleaning – Peter Cook, Eric Stevens, Bill Klimke
1:45 – 2:45 Hands-On Analysis: Genome Assembly – Peter Cook, Eric Stevens, Bill Klimke
1:45 – 2:45 (concurrent) DTU/ Molecular Epidemiology Website, SeqSero Website
2:45 – 3:15 Hands-On Analysis: Tree Generation – Peter Cook, Eric Stevens, Bill Klimke
2:45 – 3:15 (concurrent) Galaxy
3:15 – 3:30 Break
3:30 – 4:00 Hands-On Analysis: Tree Visualization and Interpretation - Peter Cook, Eric Stevens, Bill Klimke
3:30 – 4:00 (concurrent) Galaxy
4:00 – 4:30 Hands-On Analysis: Antimicrobial Resistance Gene Identification – Bill Klimke, Peter Cook, Eric Stevens
4:30 – 5:00 Additional Time for Exercises
4:30 – 5:00 Closing Questions and Answers
 
Synopsis: Whole-Genome Sequencing (WGS) is revolutionizing our understanding of the bacterial genome and is increasingly being used to improve food safety. WGS has been used as part of foodborne outbreak investigations, both domestically and globally, to trace the source of outbreaks. Furthermore, we are just beginning to utilize the full power of improved DNA and RNA sequencing technologies to understand microbial communities and their impact on the farm-to-fork continuum to better improve the quality and safety of food and public health. However, sequencing analysis is more complex than previous methodologies and requires advanced training in molecular techniques, data analysis, and data interpretation. This workshop will provide participants an overview of the various DNA and RNA sequencing technologies and allow for a hands-on demonstration of the various data analysis options – and the science behind them. Furthermore, FDA personnel will offer sessions on data interpretation so that participants can better understand how WGS is used as part of the regulatory decision-making process for foodborne outbreaks. FDA personnel will also provide session on how the application of WGS on foodborne pathogens can be used as part of a preventative control strategy and will be increasingly used to make safer food. Additionally, participants will have the opportunity to request (in advance) specific sessions on topics related to WGS and food safety of their choosing, allowing for a more directed learning experience. 
 
Who should attend: This symposium is for food safety professionals from industry, academia and government in food processing, food safety, quality assurance, regulatory functions, public health administration, and those involved in developing or using pathogen detection equipment and methods.
Symposium Location: The symposium will be hosted at the Chicago Marriott Southwest Hotel in Burr Ridge, Illinois. 
Workshop Location: The workshop will be held at IIT Moffett Campus (6502 South Archer Road) in Bedford Park, Illinois. 
Sponsorship: Please contact Armand Paradis at aparadi2@iit.edu for information about sponsorship opportunities. 
For more information about the Whole Genome Sequencing Symposium, including information related to sponsoring this event, see the Flyer and Sponsorship Prospectus.  
Conference Hotel: <A HREF="https://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=IFSH%20May%20Meeting%5Echisw%60insinsr%60179.00%60USD%60false%602%605/5/19%605/8/19%604/15/19&app=resvlink&stop_mobi=yes" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">Chicago Marriott Southwest at Burr Ridge</A>  1200 Burr Ridge Parkway, Burr Ridge, IL 60527
IFSH May Meeting
<UL>
<LI>Start date: 5/5/19</LI>
<LI>End date: 5/8/19</LI>
<LI>Last day to book: 4/15/19</LI>
</UL>
Marriott hotel(s) offering your special group rate:
<UL>
<LI>  Chicago Marriott Southwest at Burr Ridge  for 179.00 USD  per night</LI>
</UL>
<A HREF="http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=IFSH%20May%20Meeting%5Echisw%60insinsr%60179.00%60USD%60false%602%605/5/19%605/8/19%604/15/19&app=resvlink&stop_mobi=yes" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">Book your group rate for IFSH May Meeting </A>
 
Hotel: Rooms can also be reserved at Crowne Plaza 300 S. Frontage Road, Burr Ridge, IL 60527.  Go to <A HREF="http://www.cpchicagosw.com" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">www.cpchicagosw.com</A>  Enter your Corporate ID# 10205220  or call 630-325-2900 and mention the rate code IL8SE
 
Scientific Program Contact: Behzad Imanian | <A HREF="mailto:bimanian@iit.edu" TARGET="_blank" REL="nofollow noopener noreferrer">bimanian@iit.edu</A>
Logistics Contact: Cindy Koschetz | <A HREF="ckoschet@iit.edu%20" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">ckoschet@iit.edu </A>
 
 
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I hereby grant to Illinois Institute of Technology, Institute for Food Safety and Health (IFSH), and those acting under its permission or upon its authority, the free right and permission to use photographic reproductions or likenesses of me (which may include use in, but is not limited to, print publications or Web sites) taken these days 6-7 in May 2019 for the purpose of publicly advancing the university.
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