Pharmacogenomics: The convergence of pharmacology and genetics dealing with genetically determined responses to drugs.

 

Biomedical Informatics 204

 

Pharmacogenomics

Caroline Thorn Russ Altman

Offered Aut, Win, Spr, Sum

1 unit

Instructor: Russ Altman

Guest Lecturer: Caroline Thorn

The Pharmacogenomics course introduces students to informatics applications in the area, with a special focus on the PharmGKB database, a publicly available internet research tool developed by Stanford University to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. Class sessions will be a mixture of lectures, demonstrations and exercises. All sessions are offered over the Internet via streaming media. The class is structured for self-paced study with an assessment at the end of the class.

Class Topics

  • Introduction to Pharmacogenomics, the Genome and Genetics
  • Human Polymorphisms, frequencies, significance and populations
  • Basic Pharmacology
  • Informatics in PGx
  • Classical Examples
  • Genotype to phenotype approaches and phenotype to genotype approaches
  • Non-classical Pharmacogenomics
  • How drugs are discovered and validated
  • Methods for genomic variation discovery & genotyping
  • Pharmacogenomics related terminologies & ontologies
  • Adverse drug reactions and drug interactions
  • Methods for molecular/cellular/clinical phenotypes & data exchange
  • Cancer pharmacogenomics
  • Pathways of drug metabolism and action & data exchange

Demonstrations and Exercises

Introduction to PharmGKB, an online resource for pharmacogenomics

Supplemental Material

  • How MDs prescribe
  • Literature as data
  • Cardiovascular Pharmacogenomics
  • HIV Pharmacogenomics

Prerequisites

Prerequisites include four semesters or quarters of basic biology with preference for cell biology, biochemistry, molecular biology, genetics and genomics. Classes that use textbooks such as “Molecular Biology of the Cell” by Alberts, et. al. are suitable prerequisite classes. Some students have been able to participate in the class with prior readings from suitable texts. Essential topics required by the class are covered in the first six chapters of "Molecular Biology of the Cell". If you have a Sunet ID, you can also view courselets on the essential topics covered in the first six chapters.

Terry Brown. Genomes 2. 2002. A concise reference on molecular biology, with specific focus on genome-era measurement tools. This text is free at ncbi. There is also a third edition but this is not freely available.

Class Registration and Access

Anyone with a SUNet ID may register for the class via Coursework. You will find videos and lecture notes under the "Course Materials" section.

Use Axess to sign up for the course for a grade.

Contact bcheng@ stanford.edu if you have further questions.

Sample the video

Download the first 10 minutes of the introductory Pharmacogenomics lecture (38.1 MB mp4 file - You will need Real Player, QuickTime, iTunes or other compatible video player to view). This mp4 file has been reduced in resolution and size for faster downloads.

DVD's of Class Lectures

The pharmacogenomics class was originally developed for the Stanford-South Africa Biomedical Informatics program. As part of that program, the lectures have been recorded and made available on DVD's. For more information on how to obtain the DVD's: Pharmacogenomics Lectures on DVD