Biomed Sci 270 Genomics and Next-Generation Sequencing Applications in Microbiology

Module: 3
Sponsoring Program: BMS
Administrator: Ned Molyneaux

Course Number: Biomed Sci 270
Course Name: Genomics and Next-Generation Sequencing Applications in Microbiology
Units: 3
Grading Option: S/U
Course Director: Charles Chiu

Additional Course Director(s):
Room Number: RH-202
Campus: Mission Bay
Schedule: 5/11-5/22; MTWThF; 1:00-3:00
Prerequisites: none
Maximum Class Size:

Course Description: This mini-course focuses on the use of genomic approaches, in particular next-generation sequencing (NGS), to analyze data for clinical and translational applications in microbiology.  Students are not required to know or perform any programming, but they will be trained within a Unix/Linux environment on running shell scripts, manipulating files and directories, converting data into various formats for NGS analysis, and combining individual tools into a functional analysis pipeline.  By the end of the course, students should have familiarity with the core concepts of genomics in clinical microbiology and be comfortable in downloading and running basic bioinformatics tools available as open-source or commercially for NGS data analysis.  Specific applications that will be covered in this course include (1) infectious disease diagnosis by unbiased NGS with clinical case studies, (2) NGS for pathogen discovery in outbreaks, (3) whole-genome sequencing and analysis of bacteria, (4) 16S microbiome analyses, and (5) transcriptome profiling using RNASeq.  Tools that will be employed include BLAST, Geneious, Tophat/Cufflinks, AbySS/Velvet de novo assembly, the SURPI pipeline for pathogen identification (Naccache and Chiu, submitted), and Ingenuity Pathways Analysis.  Class time will consist of core lectures, small group project sessions, simple quizzes, and relevant research papers to be read outside of class.  A Windows or MacOS laptop will be required, and necessary software and network access will be provided on the first day of class.