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Genomics Bioinformatics & Medicine http://biochem158.stanford.edu/ Biochem 158/258 and HumBio 158G Doug Brutlag Professor Emeritus Biochemistry and Medicine (by courtesy) [email protected] Doug Brutlag 2011 Greg Gibson & Spencer V. Muse A Primer of Genome Science $62 Doug Brutlag 2011 Greg Gibson It Takes a Genome Doug Brutlag 2011 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 Doug Brutlag 2011 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 Doug Brutlag 2011 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! 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 - 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 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 environment – 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 • 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 Doug Brutlag 2011 Impact of Genomics on Medicine III. Ethical, Legal and Social Issues • • • • • • • Personal Privacy Insurability Employability Discrimination Genetic selection versus eugenics Cosmetic genetics Patentability of genes, proteins and other natural products 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 medicine. 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 stated: – “… 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 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? Doug Brutlag 2011