GenomeTrakr Meeting

The US Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition (CFSAN) in collaboration with the Association of Public Health Laboratories (APHL) will convene the 2024 GenomeTrakr Meeting from October 16–17, 2024 in College Park, MD. This will be an in-person meeting.

The meeting will bring together public health and university laboratories who contribute to the FDA's GenomeTrakr network. Meeting participants will hear updates from FDA and GenomeTrakr collaborators, network with their peers, discuss best practices and common challenges, and learn about how their data is used to detect and speed up the response to foodborne outbreak investigations.

​Additional Trainings and Events

There is no registration fee for these training events, but advanced registration is required. APHL will provide shuttle service from the hotel at UMD to the training events, which are held at the FDA campus in College Park, MD.

Please note: Space is limited in these training events. Registering for a training is not a guaranteed spot. You will be notified if you have been accepted into a particular training event by NLT September 1. Please note that non-US citizens will be required to complete security forms prior to attending training on FDA's campus.

Illumina MiSeq Wet Lab Workshop and Data Analysis

October 15, 2024 | 8:00 am – 5:00 pm ET — Wet Lab
October 16, 2024 | 8:00 am – 12:00 pm ET — Wet Lab
October 18, 2024 | 8:00 am – 5:00 pm ET — Introduction to WGS Data Analysis (Separate Registration)

Join us for a workshop designed specifically for GenomeTrakr participants, focusing on the laboratory procedures for Next Generation Sequencing (NGS) utilizing the Illumina MiSeq instrument. NGS technology revolutionizes our ability to explore the complete genomic content of target organisms, making it an invaluable tool for characterizing bacterial isolates during foodborne outbreak investigations.

During the workshop, you will have the opportunity to gain hands-on training in the wet laboratory portion, where you will learn and perform essential skills such as DNA quality control (QC), library preparation using the Nextera DNA Prep kit, loading samples onto the MiSeq instrument and evaluating the MiSeq run for optimal sequencing outcomes.

The introductory data analysis sessions will provide training on sequence and assembly quality control, NCBI data submission and basic whole genome sequencing (WGS) data analysis. 

Register

Introduction to WGS Data Analysis

October 18, 2024 | 8:00 am – 5:00 pm ET

Join us for a comprehensive training session on the analysis of Whole Genome Sequence (WGS) data for foodborne pathogen surveillance. This in-person training is open to 20 participants who are new users to WGS data analysis. During this training, we will provide an introduction to the GalaxyTrakr environment and suite of WGS-based analysis tools and guide you through the utilization of the NCBI Pathogen Detection Browser. Participants will gain a solid foundation in WGS data analysis, including basic QC, genome assembly, serotyping, genotyping for AMR and virulence, clustering, and phylogenetic inference.

Sample Agenda:

• Sequencing Run Quality Metrics
• Data Analysis and Interpretation
• Introduction to GalaxyTrakr
• GalaxyTrakr Tools and Workflow
• QA/QC Workflow
• Assemblies
• Tools: AMRFinderPlus, SeqSero, ECTyper, ConFindr
• CFSAN SNP Pipeline and Visualization of Phylogenetic Trees
• GalaxyTrakr Best Practices
• NCBI Pathogen Detection Browser
  

Metadata Cleanup Challenge

October 16, 2024 | 9:00–11:00 am ET

The Metadata Cleanup Challenge agenda will be announced at a later date.

Oxford Nanopore Technologies (ONT) Wet Lab and Data Analysis Training

October 15, 2024 | 8:00 am – 5:00 pm ET – Wet Lab
October 18, 2024 | 8:00 am – 5:00 pm ET – Data Analysis

A wet lab and data analysis training event on ONT technologies will be held in conjunction with this year's GenomeTrakr meeting. This training is only open to laboratorians participating in the LFFM ONT project track. FDA will connect with those who should attend this training. 

​General Meeting Information​

Travel

The Meeting will commence at 1:30 pm ET on Wednesday, October 16 and adjourn at 3:00 pm ET on Thursday, October 17. Please plan on taking flights that depart after 5:00 pm ET on October 17. Participants are strongly encouraged to attend all sessions and avoid early departures. 

Fun​​​ding

FDA-funded grantees are expected to use their Cooperative Agreement funds to support registration, travel, lodging and other per diem expenses associated with participating in this meeting. 

​Consent to ​Use Photographic Images

Registration and attendance at or participation at this meeting constitutes an agreement by the registrant to FDA’s and APHL’s use and distribution (both now and in the future) of the registrant’s or attendee’s image or voice, without compensation, in photographs, videotapes, electronic reproductions and audiotapes of such events and activities.

Hot​el

APHL has negotiated a block of rooms at $189.00 per/night. This is below the federal per diem rate. Reservations are available on a first come, first served basis and are valid until Monday, September 16, 2024 or until the block is filled. Call-in and online reservation information is below. Mention "2024 GenomeTrakr Meeting" when making your reservations.  This block may fill up quickly so be sure to make your reservation early. APHL has secured several rooms at the discounted block rate on October 17 for those unable to depart after the meeting's end. 

If you have questions about the program, please contact Amy Bryant at foodsafety@aphl.org​ or 240.485.2791. 

If you have questions or problems regarding registration, please contact Lauren Writer at lauren.writer@aphl.org or 240.638.2015. ​