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Doug Brutlag 2011

Genomics Bioinformatics & Medicinehttp://biochem158.stanford.edu/

Biochem 158/258 and HumBio 158G

Doug BrutlagProfessor Emeritus

Biochemistry and Medicine (by courtesy)[email protected]
mailto:http://creativecommons.org/licenses/by/3.0/http://biochem158.stanford.edu/mailto:[email protected]:[email protected]://biochem158.stanford.edu/mailto:http://creativecommons.org/licenses/by/3.0/

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Doug Brutlag 2011

Greg Gibson & Spencer V. Muse

A Primer of Genome Science

$62
mailto:http://creativecommons.org/licenses/by/3.0/http://www.sinauer.com/genomics/http://www.sinauer.com/genomics/mailto:http://creativecommons.org/licenses/by/3.0/

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Doug Brutlag 2011

Greg Gibson

It Takes a Genome
mailto:http://creativecommons.org/licenses/by/3.0/mailto:http://creativecommons.org/licenses/by/3.0/

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Doug Brutlag 2011

Course Syllabushttp://biochem158.stanford.edu/

Sept 27 Introduction to Genes, Diseases and Preventive Medicine

Sept 29 Diseases and Disease DatabasesOct 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 numbervariations.

Oct 25 Discovering Variations Associated with Disease

Oct 27 Discovering Causal Mutations for Disease

Nov 1 Personal Genomics

Nov 3 Stem CellsNov 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
mailto:http://creativecommons.org/licenses/by/3.0/http://biochem158.stanford.edu/http://biochem158.stanford.edu/mailto:http://creativecommons.org/licenses/by/3.0/

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Course Requirementshttp://biochem158.stanford.edu/

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

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Research Projects and Grading Policyhttp://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 HumanGenome 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
mailto:http://creativecommons.org/licenses/by/3.0/http://biochem118.stanford.edu/http://biochem118.stanford.edu/http://explorecourses.stanford.edu/CourseSearch/search?view=catalog&filter-coursestatus-Active=on&page=0&catalog=&q=Bio+109A&collapse=http://explorecourses.stanford.edu/CourseSearch/search?view=catalog&filter-coursestatus-Active=on&page=0&catalog=&q=Bio+109A&collapse=http://explorecourses.stanford.edu/CourseSearch/search?view=catalog&filter-coursestatus-Active=on&page=0&catalog=&q=humbio+157&collapse=http://explorecourses.stanford.edu/CourseSearch/search?view=catalog&filter-coursestatus-Active=on&page=0&catalog=&q=HUMBIO+159&collapse=http://stanford.edu/class/gene210/web/html/welcome.htmlhttp://www.stanford.edu/class/gene211/http://www.stanford.edu/class/cs262/cgi-bin/index.phphttp://www.stanford.edu/class/cs273a/cgi-bin/index.phphttp://biochem218.stanford.edu/http://www-helix.stanford.edu/bmi214/http://www-helix.stanford.edu/bmi214/http://www-helix.stanford.edu/bmi214/http://www-helix.stanford.edu/bmi214/http://biochem218.stanford.edu/http://www.stanford.edu/class/cs273a/cgi-bin/index.phphttp://www.stanford.edu/class/cs262/cgi-bin/index.phphttp://www.stanford.edu/class/gene211/http://stanford.edu/class/gene210/web/html/welcome.htmlhttp://explorecourses.stanford.edu/CourseSearch/search?view=catalog&filter-coursestatus-Active=on&page=0&catalog=&q=HUMBIO+159&collapse=http://explorecourses.stanford.edu/CourseSearch/search?view=catalog&filter-coursestatus-Active=on&page=0&catalog=&q=humbio+157&collapse=http://explorecourses.stanford.edu/CourseSearch/search?view=catalog&filter-coursestatus-Active=on&page=0&catalog=&q=Bio+109A&collapse=http://explorecourses.stanford.edu/CourseSearch/search?view=catalog&filter-coursestatus-Active=on&page=0&catalog=&q=Bio+109A&collapse=http://biochem118.stanford.edu/http://biochem118.stanford.edu/mailto:http://creativecommons.org/licenses/by/3.0/

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BioMedical SeminarsBiomedical Seminars Calendar

Frontiers in Biology Seminar Series

Atul Butte, StanfordExploring Systems and Personalized Medicine ThroughTranslational Bioinformatics

Sep 28 4:00 PM Clark Center Auditorium

Nick Schork, ScrippsFunctional Genomic Variants and Human Diversity

Oct 26 4:00 PM Clark Center Auditorium

Marisa Bartolomei, U of Pennsylvania

Epigenetic regulation of genomic imprintingNov 16 28 4:00 PM Clark Center Auditorium
mailto:http://creativecommons.org/licenses/by/3.0/http://med.stanford.edu/seminars/http://med.stanford.edu/seminars/eventDetails.do?semid=76271http://med.stanford.edu/seminars/eventDetails.do?semid=76271http://med.stanford.edu/seminars/eventDetails.do?semid=76267http://med.stanford.edu/seminars/eventDetails.do?semid=76270http://med.stanford.edu/seminars/eventDetails.do?semid=76270http://med.stanford.edu/seminars/eventDetails.do?semid=76267http://med.stanford.edu/seminars/eventDetails.do?semid=76271http://med.stanford.edu/seminars/eventDetails.do?semid=76271http://med.stanford.edu/seminars/mailto:http://creativecommons.org/licenses/by/3.0/

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Leveraging Genomic Information

Novel DiagnosticsMicrochips & Microarrays - DNA

Gene Expression - RNA

Proteomics - Protein

Understanding Metabolism

Understanding DiseaseInherited Diseases - OMIMInfectious Diseases

Pathogenic BacteriaViruses

Novel TherapeuticsDrug Target DiscoveryRational Drug DesignMolecular DockingGene TherapyStem Cell Therapy

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Impact of Genomics on MedicineI. 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 MedicineII. 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

Pharmacogenomics 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 MedicineIII. Ethical, Legal and Social Issues

Personal Privacy Insurability

Employability

Discrimination

Genetic selection versus eugenics Cosmetic genetics

Patentability of genes, proteins and other naturalproducts

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Impact of Genomics on MedicineIV. 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

medicine.

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Preventive Medicine

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Founder of Preventive Medicine:Louis Pasteur

When thinking about diseases, I never thinkabout how to cure them, but instead I think abouthow 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 wemay soon sequence every childs 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 thanmaintaining health (Illness care?)

Future health care prevent disease

Reduce need for expensive interventions

Need policies that incentivize patients and doctors toprevent disease.

Need social pressures to control behavior andincrease 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 2years 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 notonly if you have the disease, and if you do, when you will die

from it. Would you take the genetic test or not?

Why?

Documents

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