Genomics Bioinformatics & Medicine


Oct 2, 2013 (4 years and 9 months ago)


Doug Brutlag 2011

Genomics Bioinformatics & Medicine

Biochem 158/258 and HumBio 158G

Doug Brutlag

Professor Emeritus

Biochemistry and Medicine (by courtesy)

Doug Brutlag 2011

Greg Gibson & Spencer V. Muse

A Primer of Genome Science


Doug Brutlag 2011

Greg Gibson

It Takes a Genome

Doug Brutlag 2011

Course Syllabus

Sept 27

Introduction to Genes, Diseases and Preventive Medicine

Sept 29

Diseases and Disease Databases

Oct 4

Sequencing the Human Genome

Oct 6

Finishing the Human Genome

Oct 11

Next Generation Sequencing Methods

Oct 13

Bioinformatics and Functional Genomics

Oct 18

Sequence Variations in the Human Genome

Oct 20

Structural Variations: Insertions, deletions, transpositions, & copy number

Oct 25

Discovering Variations Associated with Disease

Oct 27

Discovering Causal Mutations for Disease

Nov 1

Personal Genomics

Nov 3

Stem Cells

Nov 8

Stem Cell Therapies

Nov 10

Gene Expression and Cancer Diagnostics

Nov 15


Nov 17

Drug Development

Nov 29


Dec 1

Ethical Issues and Genetic Discrimination

Doug Brutlag 2011

Course Requirements

Four research assignments

Disease case presentation

Bioinformatics analysis of gene function

Description of a genome
wide association study

Final project (paper or presentation) on

The molecular basis of a disease

A novel diagnosis or treatment of a disease

A technological advance in genomics & disease

An ethical, legal or social issue in genomics or medicine

Participation in Class Discussion

Doug Brutlag 2011

Research Projects and Grading Policy


% of Grade

Date Due

Inherited Disease

Case Presentation


Oct. 11

Functional Analysis of

a Human Gene




Review of Genome
Wide Association Studies


Nov. 8

Final Project

on Genomics and Medicine


Dec. 9

Second chance on homework!

Doug Brutlag 2011

Cognate Courses

Undergraduate Courses

Biochem 118 Genomics and Medicine Sophomore Seminar

Bio 109A and 109B (HumBio 158A and B) The Human
Genome and Disease

HumBio 157 The Biology of Stem Cells

HumBio 159 Genes and Environment in Disease Causation

Graduate Level Courses

Genetics 210 Genomics and Personalized Medicine

Genetics 211 Genomics

CS 262 Computational Genomics

CS 273A A Computational Tour of the Human Genome

Biochem 218/BMI 231 Computational Molecular Biology

BMI 214/CS 274 Representations and Algorithms for
Computational Molecular Biology

Doug Brutlag 2011

BioMedical Seminars

Biomedical Seminars Calendar

Frontiers in Biology Seminar Series

Atul Butte, Stanford

Exploring Systems and Personalized Medicine Through
Translational Bioinformatics

Sep 28 4:00 PM Clark Center Auditorium

Nick Schork, Scripps

Functional Genomic Variants and Human Diversity

Oct 26 4:00 PM Clark Center Auditorium

Marisa Bartolomei, U of Pennsylvania

Epigenetic regulation of genomic imprinting

Nov 16 28 4:00 PM Clark Center Auditorium

Doug Brutlag 2011

Leveraging Genomic Information

Novel Diagnostics

Microchips & Microarrays


Gene Expression




Understanding Metabolism

Understanding Disease

Inherited Diseases


Infectious Diseases

Pathogenic Bacteria


Novel Therapeutics

Drug Target Discovery

Rational Drug Design

Molecular Docking

Gene Therapy

Stem Cell Therapy

Doug Brutlag 2011

Impact of Genomics on Medicine

I. Diagnostics

Genomics: Identifying all known human genes

Functional Genomics: Functional analysis of genes

In what tissues are they important?

When in development are the genes used?

How are they regulated?

Novel diagnostics

Linking genes to diseases and to traits

Predisposition to diseases

Expression of genes and disease

Personal Genomics

Understanding the link between genomics and

Increased vigilance and taking action to prevent disease

Improving health care

Doug Brutlag 2011

Impact of Genomics on Medicine

II. Therapeutics

Novel Drug Development

Identifying novel drug targets

Validating drug targets

Predicting toxicity and adverse reactions

Improving clinical trials and testing

Gene therapy

Replacing the gene rather than the gene product

Stem cells therapies

Replacing the entire cell type or tissue to cure a disease


Personalized medicine

Adjusting drug, amounts and delivery to suit patients

Maximize efficacy and minimize side effects

Identify genetics of adverse reactions

Identify patients who respond optimally

Doug Brutlag 2011

Impact of Genomics on Medicine

III. Ethical, Legal and Social Issues

Personal Privacy




Genetic selection versus eugenics

Cosmetic genetics

Patentability of genes, proteins and other natural

Doug Brutlag 2011

Impact of Genomics on Medicine

IV. Strategic

Genomics can discover disease associated genes

Genomics can discover disease causing genes.

Genomics provides understanding of disease

Genomics and bioinformatics provides basis for
novel drug development

Genomics provides basis for novel genetic and stem
cell therapies

Genomics provides the basis for preventive

Doug Brutlag 2011

Preventive Medicine

Doug Brutlag 2011

Founder of Preventive Medicine:

Louis Pasteur

When thinking about diseases, I never think
about how to cure them, but instead I think about
how to prevent them.

Doug Brutlag 2011

Preventive Medicine

The goal is to prevent disease from occurring.

First one must identify the cause of the disease.

Treat the cause of the disease rather than the symptoms

Example 1: Peptic Ulcers

Example 2: Pyrogens

Genomics identifies genetic causes of inherited disease.

When Paul Wise (a Stanford pediatrician) heard that we
may soon sequence every child’s genome at birth, he

… all medicine may soon become pediatrics!

Overlooked accidents, infectious disease, auto immune
disease and aging: environmental or acquired diseases

Genetic penetrance and environment

Doug Brutlag 2011

Health Care Policy

Current health care treats disease rather than
maintaining health (Illness care?)

Future health care prevent disease

Reduce need for expensive interventions

Need policies that incentivize patients and doctors to
prevent disease.

Need social pressures to control behavior and
increase vigilance.

Doug Brutlag 2011

Huntington Disease Film

Doug Brutlag 2011

The Inheritance

You are 18 years old.

Your father abandoned you and your mother when you only 2
years old.

Your father died this year and left you an inheritance.

He died from an autosomal dominant disease known as

s Chorea or Huntington

s Disease.

You have a 50% chance of inheriting this invariably fatal
neurodegenerative disease.

But there is a genetic test for this disease that can tell you not
only if you have the disease, and if you do, when you will die
from it.

Would you take the genetic test or not?