Bioinformatics of Genomic Medicine

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Course Objectives

Genomic medicine is the practice of utilizing multi-omic (genomic, transcriptomic, epigenomic) data to improve the diagnosis and treatment of patients. The CBW has developed a 2-day course that will explore various aspects of genomic medicine, covering and teaching popular tools and methods in the field. The course will start with topics that are important to the analysis of genetic disorders, including phenotyping and the annotation of genetic variants. Next, we will cover multi-omic approaches that can be used to identify homogenous clusters of patients, build patient trajectories to identify likely outcomes, and improve these outcomes through better selection of therapies. This workshop will not cover cancer.

Participants will gain practical experience and skills to be able to:

  • Identify disease variants:
    • Conduct basic exome analysis to identify disease-causing mutations
    • Perform deep phenotyping of patients using the Human Phenotype Ontology (HPO)
    • Conduct detailed variant annotation and prioritization
  • Perform patient classification:
    • Understand and select appropriate epigenomic datasets for patient classification
    • Conduct data fusion to identify homogenous patient subgroups
    • Identify potential therapies based on molecular profiles

Target Audience

Graduates, postgraduates, PIs, and clinician-researchers working or about to embark on an analysis of omics (genomes, transcriptomes, epigenomes) for analysis of patient samples. Attendees may be familiar with some aspect of genome data analysis (e.g. exome analysis or gene expression analysis) or have no direct experience.

Prerequisites: Basic familiarity with Linux environment and S, R, or Matlab. Must be able to complete and understand the following simple Linux and R tutorials (up to and including “Descriptive Statistics”) before attending:

You will also require your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 2GB RAM, 10GB free disk space, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements).If you do not have access to your own computer, you may loan one from the CBW. Please contact course_info@bioinformatics.ca for more information.

Pre-work and pre-readings can be found at https://bioinformaticsdotca.github.io/genmed_2018.

Course Material