2023 GenomeTrakr Miseq and WGS Data Analysis Training

​​We are pleased to announce a series of training events in collaboration with FDA/CFSAN, APHL and the Joint Institute for Food Safety and Applied Nutrition (JIFSAN). These training events will be held in conjunction with the upcoming 2023 GenomeTrakr Meeting. The training events aim to provide educational opportunities for participants interested in various aspects of genomics and food safety. Individual registration is required for each session.​​​ Shuttle service from Hotel at UMD will be provided for hotel guests.​​​Laboratory Training: Illumina MiSeq Workflow and Data Analysis for Whole Genome SequencingDates and times​​: ​October 23, 2023 | 8:30 am – 5:00 pm ET — Wet LabOctober 24, 2023 | 8:30 am – 12:00 pm ET — Wet LabOctober 26, 2023 | 9:00 am – 5:00 pm ET — Introduction to WGS Data Analysis Location: JIFSAN, FDA​​​ About the Training​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 session will provide training on sequence and assembly quality control, NCBI data submission​​​ and basic WGS data analysis. ​ ​​​Apply to Participate ObjectivesUpon completion of this training program, participants will have the ability to:Describe the laboratory procedures involved in sample preparation and MiSeq run setup. This includes understanding DNA quality control (QC), library preparation using the GenomeTrakr DNAPrep protocol, completing relevant worksheets, setting up MiSeq runs, and evaluating run data.Develop skills to troubleshoot errors and suboptimal runs on the MiSeq instrument, ensuring optimal sequencing outcomes.Demonstrate proficiency in maintaining and caring for the MiSeq equipment, ensuring its longevity and reliable performance in the laboratory.Utilize the knowledge and skills acquired during the workshop to independently perform Next Generation Sequencing (NGS) on the MiSeq instrument in your home laboratory.Exhibit a comprehensive understanding of Illumina sequencing technology.Analyze and interpret quality control metrics of raw NGS data.Demonstrate the ability to upload NGS data to BaseSpace, a cloud-based platform for secure storage, analysis, and sharing of sequencing data.Describe the quality control analysis of genome assemblies, ensuring accurate and reliable reconstruction of draft genomes.Utilize genotyping tools to characterize serotypes, virulence factors, resistance determinants, and plasmids, enabling comprehensive genomic characterization of bacterial isolates.Demonstrate the process of submitting metadata to the GenomeTrakr Metadata Validation System (GMVS) and directly submitting sequence data to NCBI, facilitating the integration of genomic data into public databases for public health and regulatory applications.​​​Learn More​​ If you have questions about the program, please contact Rhodel Bradshaw at foodsafety@aphl.org  or 240.485.3828. If you have questions or problems regarding registration, please contact Terry Reamer at terry.reamer@aphl.org or 240.485.2776.  ​