Transcript Genomics Bioinformatics & Medicine

Genomics Bioinformatics & Medicine
http://biochem158.stanford.edu/
Biochem 158/258 and HumBio 158G
Doug Brutlag
Professor Emeritus
Biochemistry and Medicine (by courtesy)
[email protected]
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Greg Gibson & Spencer V. Muse
A Primer of Genome Science
$62
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Greg Gibson
It Takes a Genome
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Course Syllabus
http://biochem158.stanford.edu/
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
variations.
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
Epigenetics
Nov 17
Drug Development
Nov 29
Pharmacogenomics
Dec 1
Ethical Issues and Genetic Discrimination
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Course Requirementshttp://biochem158.stanford.edu/
• Four research assignments
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Disease case presentation
Bioinformatics analysis of gene function
Description of a genome-wide association study
Final project (paper or presentation) on
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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
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Research Projects and Grading Policy
http://biochem158.stanford.edu/
Assignment
% of Grade
Date Due
Inherited Disease Case Presentation
20%
Oct. 11
Functional Analysis of a Human Gene
20%
Oct. 25
Review of Genome-Wide Association Studies
20%
Nov. 8
Final Project on Genomics and Medicine
40%
Dec. 9
Second chance on homework!
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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
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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
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Leveraging Genomic Information
Novel Diagnostics
Microchips & Microarrays - DNA
Gene Expression - RNA
Proteomics - Protein
Novel Therapeutics
Drug Target Discovery
Rational Drug Design
Molecular Docking
Gene Therapy
Stem Cell Therapy
Understanding Metabolism
Understanding Disease
Inherited Diseases - OMIM
Infectious Diseases
Pathogenic Bacteria
Viruses
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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
environment
– Increased vigilance and taking action to prevent disease
– Improving health care
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Impact of Genomics on Medicine
II. Therapeutics
• Novel Drug Development
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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
• Pharmacogenomics
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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
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Impact of Genomics on Medicine
III. Ethical, Legal and Social Issues
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Personal Privacy
Insurability
Employability
Discrimination
Genetic selection versus eugenics
Cosmetic genetics
Patentability of genes, proteins and other natural
products
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Impact of Genomics on Medicine
IV. Strategic
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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
medicine.
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Preventive Medicine
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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.
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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
stated:
– “… all medicine may soon become pediatrics!”
• Overlooked accidents, infectious disease, auto immune
disease and aging: environmental or acquired diseases
• Genetic penetrance and environment
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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.
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Huntington Disease Film
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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
Huntington’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?
• Why?
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