Biochemistry 158/258 - HumBio 158G

BioMedical Informatics 258

Genomics, Bioinformatics & Medicine

Autumn Quarter 2015-2016

A Human Genome Stained by Fluourescent in Situ Hybridization

Doug Brutlag

Course Description

This course covers the molecular basis of inherited disease.  We will discuss both simple Mendelian diseases and complex, multifactorial diseases in which both genetics and environmental factors are involved. We will discuss genomics, functional genomics, epigenetics, gene expression, SNPs, copy number and other structural genomic variations involved in disease.  In addition to these diagnostic approaches, we will discuss novel therapeutic methods such as stem cell therapy, gene therapy and drug developments that depend on the knowledge of genomics. We will discuss personal genomics, pharmacogenomics and clinical genomics and their role in the future of preventive medicine.

Course Requirements

Students in this course will become familiar with many web resources and will be expected to complete several short research projects during the course (see below). The research projects will include a personal introduction, a case presentation of a Mendelian inherited disease, a functional analysis of a human gene, a review of a genome wide-association study on a multifactorial disease, a description of causal mutants in disease, a stem cell therapy in a disease and a final paper on a topic of personal interest related to Genomics, Bioinformatics & Medicine.

The research projects must be submitted to by midnight on the dates in the project table below. The methods essential for each assignment and examples of how to perform each assignment is demonstrated in the lectures. Examples of previous final papers in the course appear at:

Examples of Previous Final Papers

Student Profile

This course will be of interest to anyone considering a career in genomics, bioinformatics or treatment of disease.   It will be especially valuable to premedical, medical or graduate students interested in human genomics.  It will also be of value to those interested in health care policy or biotechnology law.

This course is approved as an elective for Biology Majors, and is approved for Natural-Science GER credit for students in other majors .

It has also been approved for Ways of Thinking and Ways of Doing: Scientific Methods and Analysis.


Prerequites for the course are Biology 41 or HumBio 2A or consent of the instructor.

Students with credit in Biochem 118 may not take this course for credit.

Lecture Videos

Videos of the lectures will also be available on the course web page and on the SCPD file server.

Recommended text books

A Primer of Human Genetics 1st edition is not required for the course but it provides an excellent introduction to the material discussed including basic genetics and genomics used in medicine and research. This book would also be a good reference book for those continuing to work in this field.

A Primer of Human Genetics by Greg Gibson

A primer of human genetics


An Elementary Introduction to Genetics, Genomics and Medicine

This free, downloadable book covers the essential introductory material that every student should know before taking this course.

GHR Handbook

Genetics Home Reference Handbook

The End of Illness by David Agus

A layman's introduction to personal genomics

The End of Illness


My Beautiful Genome by Lone Frank

This entertaining and enlightening book is readable by all and is the author's story of the impact of hte knowledge of her genome.

my beutiful genome

You Tube Video of Lone Frank



Course Syllabus

Each of the lectures above has its own handout. Please click on the lecture title to see the handout. The handouts include the lecture slides, literature references and web references used in that lecture. Lecture Video Links are for download only. You must right-click (on a Macintosh Control-Click) on the video link and save the video file to your comuter. Then you may watch the lecture using which ever media viewer you may have on your computer (Quicktime, VLC, Windows Media Player etc.). You should also download the slide document for that lecture and view it in Adobe Reader so you can see the slides in high resolution. Registered students may also view the SCPD videos at

Research Projects



Date Due


Oct 1


Mendelian disease case presentation (4 page max)

Oct 8


Functional analysis of a human gene (4 page max)

Oct 22


Summary of a genome-wide association study (4 page max)

Oct 29


Describe genomic variations known to cause a specific inherited disease (4 page max)

Nov 5


Describe a disease that could be cured using stem cell therapy (4 page max)

Nov 12


Final project (10 page max)

Dec 6

Examples of Previous Final Papers

Each assignment is a short research project. Click on each project title to see how to perform the research project and an outline of what is expected. The assignments are due on midnight Pacific time at the end of the due date day (usually a Thursday at midnight except the final paper which is due on Sunday December 6th at midnight.). Please submit your assignments in electronic form (Word , text , PDF, postscript, HTML or Google document) to If you are late, you will loose 1 point for each day you are late. If you are late with the final project you will loose 5 points per day late (1/2 grade point, A to A- etc). The date of submission is determined by the time stamp on the email message you send with the homework. Please be sure to give web-links (URL pointers) to the disease, gene, GWAS paper and all references and web sites used in your bibliography or footnotes in your paper. Also please be sure to put any copied material in quotes with complete reference or URL ponter to the source of the material copied in your paper. Failure to properly reference copied source material, even from the Internet, is plagiarism (Please see Stanford Honor Code). If you do not get 100% on each of the first six assignments you will be given a description of what you did wrong and then have one week from the time of my message to you, to resubmit for full credit. The final project may only be submitted once

© Doug Brutlag 2015

*** Web Site Last Updated June 12, 2015***