Intro to Precision Medicine
Analysis of high throughput genome and transcriptome data is major component of many research projects ranging from large-scale precision medicine efforts to focused investigations in model systems. This analysis involves the identification of specific genome or transcriptome features that predispose individuals to disease, predict response to therapies, influence diagnosis/prognosis, or provide mechanistic insights into disease models. During this course (IBDR01), students will perform an example end-to-end bioinformatics analysis of genome (WGS and Exome) and transcriptome (RNA-seq) data.
Basic principles of this course
- Key genomics and bioinformatics concepts are introduced by lectures and reinforced by hands-on exercises.
- Use of real (not simulated) genomics data.
- Try to be self-contained. As much as possible everything needed to understand and run the analyses described here should be explained within this site.
- One goal of the hands-on tutorials is that they be a helpful guide for students to analyze their own data. Student are encouraged to bring their own data and discuss with the instructors.
- The analysis should not rely on being run on a particular pre-configured server. Students will learn to install bioinformatics tools themselves and anything that is pre-configured should be clearly documented. We will perform all analysis within a Linux instance on a cloud service (AWS EC2). Most analyses should work with minimal modification on another Linux distribution, a different cloud platform, and in some cases on a Mac OS system.
- Each bioinformatics command is accompanied by explanation of its intent, inputs, parameters, etc.
- While this course uses a hypothetical cancer precision medicine case for demonstration purposes, the concepts covered here should be generally applicable to other human diseases as well as other organisms and experimental systems. Similarly, while we focus on Whole Genome, Exome and RNA-seq data, many of the concepts covered here will be informative for analyses involving other assay types (particularly those that involve sequencing on the Illumina platform).
- Introduction to the intructors, course overview, precision medicine.
- Cloud computing, UNIX/Linux OS, bioinformatics tool installation, course website review.
- Navigation of the course website and other online learning resources.
- Start a cloud compute instance and log into it.
- Become familiar with basic Linux terminal commands (the “command line”).
- Install bioinformatics tools that will be used for genomics analysis.