We anticipate a rich and rewarding experience for participants as ‘Genomics of Disease in Wildlife’ will be taught by a team of instructors skilled in NGS applications and will feature an array of special topics presented invited experts from CSU faculty and evening plenary speakers from other leading institutions in wildlife disease. The workshop curriculum will integrate segments on wildlife diseases such as those infecting iconic species of the North American West including wild felids, canids, elk, bison, and bighorn sheep; fauna that have experienced a precipitous decline in recent years such as amphibians, bats and primates; and the complex interactions between wildlife and domesticated species, livestock and companion animals in disease emergence and transmission.
Syllabus
The workshop will cover a typical workflow commonly used in NGS analyses starting with the initial raw sequence through the final stages of interpreting those key insights made possible only through the application of genomic tools in disease ecology, evolution and transmission. Each day of the workshop will cover an essential component of the NGS workflow.
Morning sessions will be a series of instructional lectures and demonstrations that will concisely present the purpose, justification and implementation of the specific workflow unit. Short and exciting ‘flash talks’ presented by CSU faculty and invited speakers will present some of their ongoing investigations using genomic tools in wildlife disease. The afternoon sessions will be computer-intensive labs in which attendees will perform ‘hands-on’ analyses with real-world genomic data for each workflow topic. Evening plenary lectures from invited external speakers will conclude each day’s activities.
Teaching tools will include exercises using ‘real-world’ NGS data from a range of pathogens and host species. Participants will learn the importance of integrating NGS data from both host and pathogen in order to better understand current epidemics such as chytridiomycosis in amphibians, retroviruses in wild felids, rabies in carnivores, white-nose in bats, morbilliviruses in marine mammals, diverse pathogens infecting wild ungulates world-wide and more.
For the duration of the course, each attendee will be provided with a MacBook Pro computer and peripheral equipment, and prepared genome datasets from several host species and associated pathogens. These datasets will be organized into various files and formats prior to the course, demonstrate key concepts, and be the foundation for computer exercises and teaching tools.
Schedule
Optional Pre-Workshop Clinic – Sunday June 4, 2023 (10 a.m. – 4 p.m.)
Optional Pre-Workshop: UNIX Command Line and Coding Clinic.
An optional pre-workshop clinic preceding the opening reception and activities on Sunday June 4, 2023. The crash course in basic coding skills will introduce conceptions of interacting with UNIX-based (Mac or Linux) platform, command line structure, navigating folders, and reading/writing files. The clinic will emphasize commands and terminology that will be used during GDW2021, and is designed for those with little or no experience in coding.
Day 1 – Sunday June 4, 2023*
Official Opening of GDW Workshop at 6 p.m.
Arrival, Registration and Opening Reception
The workshop begins in the evening of Sunday June 4, 2023 at the Smith Alumni Center. A welcome session will introduce faculty and an overview of the workshop. NGS workflow projects for teams will be introduced. An informal welcome reception follows with faculty, staff and participants.
*Participants will prepare a short 3-4 minute introduction of their background, projects and/or interests motivating their participation in the workshop. We will split the talks between Day 1 and Day 2.
Day 2 – Monday June 5, 2023*
Study design, optimizing NGS applications, types of data, sequence read QC/processing, and de novo assembly.
Lectures and computer labs will introduce the different types of NGS data and how to best use these data in the study of disease in wildlife. Topics will include the latest advances in NGS technologies, NGS definitions, assessment of sequence data quality, long and short reads, scaffolds, contigs, and genome assembly algorithms and de novo assembly.
*Participants will prepare a short 3-4 minute introduction of their background, projects and/or interests motivating their participation in the workshop. We will split the talks between Day 1 and Day 2
Day 3 – Tuesday June 6, 2023
Mapping genomes to a reference, genome alignments, and multiple sequence files
Lectures and computer labs will outline the critical steps essential to creating proper alignments of genomes or targeted portions of genomes of host and pathogen. Topics will include mapping reads and/or new genomes to a reference genome, using annotation files from a reference genome, and constructing and evaluating multiple sequence alignments.
Day 4 – Wednesday June 7, 2023
Comparative Genomics and Phylogenomics
Lectures and computer labs will introduce the concepts guiding the use of comparative genomic and phylogenomic analyses of host and pathogen and the utility of these methods in rapid assessment of critical factors characterizing pathogen outbreaks in the wild. Topics will include study design and sampling strategies, search algorithms, maximum likelihood and Bayesian methods, and interpretation of results.
Day 5 – Thursday June 8, 2023
Selection, Adaptation and Phylodynamics
Lectures and computer labs will introduce concepts and methods to detect signatures of selection within genes, gene systems. Topics will include neutral, positive and diversifying selection within genes and genomes, algorithms for scanning whole genomes, and an introduction to pathogen phylodynamics and metagenomics.
Day 6 – Friday June 9, 2023
Population and Landscape Genomics
Lectures and computer labs will address the types of information only possible through application of genomic tools in the study of population structure and diversity of both host species and pathogen.
We anticipate a great time for all at our workshop celebration party to be held in the evening with dinner and social time at a local venue in downtown Fort Collins CO
Day 7 – Saturday June 10, 2023
Putting it all together: Participant NGS Workflow Evaluation and Summary
Participants will gather for a morning session to conclude at 12 PM. Topics will include presentation and discussion of NGS workflow schemes that each team of participants will develop during the workshop.
We encourage participants to enjoy the local flavor of the Fort Collins area and natural beauty of Colorado by extending their stay either before the workshop begins or at the conclusion of the workshop. Please contact CSU conference staff for recommendations and tips for advanced planning.
Workshop Concludes Saturday June 10, 2023 at 12 PM
Questions? Email us at [email protected].