Syllabus and Course Schedule (tentative)

Note: All Lab sessions (Lab0-Lab4) will be held in Near and Far computer lab in Hunt Library.
Date Lectures    Topics    Readings    Assignments
   Introduction
Week 1: Tue 8/26 Course overview
[slides]
  • Brief history: from Human Genome Sequencing Project to 1000 Genome Project
  • Personal genomes and personalized medicine
Week 1: Thur 8/28 Lab 0: Molecular biology in a nutshell, UCSC genome browser
[slides]
[lab material]
  • DNA, RNA, protein, central dogma, SNPs
  • UCSC genome browser and Craig Venter's genome
   Understanding your own genome
Week 2: Tue 9/2 Human genome sequencing project
[slides]
  • International consortium for Human Genome Sequencing Project
  • What did we learn from the first draft of human genome sequence?
Week 2: Thur 9/4 Lab I: Matlab (See blackboard for lab material)
  • Basics on how to use Matlab
  • Loading and visualizing genome data in Matlab
Week 3: Tue 9/9 Sanger sequencing
(Dr. Thickman)
[slides]
  • Shot-gun sequencing, Sanger sequencing
  • Sequencing technology for Human Genome Sequencing Project
Week 3: Thur 9/11 Mendelian/monogenic disease
(Dr. Thickman)
[slides]
  • Diseases caused by mutations in a single gene
  • Cystic fibrosis, huntington disease
  • Family-based studies for disease-gene discovery
Report due for Lab I
   Your genome and others' genome
Week 4: Tue 9/16 Genotyping and genetic variation
(Dr. Thickman)
[slides]
  • SNP microarray technology for genotyping
Week 4: Thur 9/18 Stretches of DNA and genome regions
[slides]
  • Alleles, genotypes, phenotypes
  • Haplotypes, correlated genome regions
Week 5: Tue 9/23 Lab II: international HapMap project (see blackboard for lab material)
  • Genomes of a large number of individuals
  • Understanding SNP data
Week 5: Thur 9/25 Genomes and ancestry I
[slides]
  • Population structure: Genomes of Africans, Caucasians, and Asians
  • How populations diverge and migrate from Africa to Europe and Asia
  • Book chapter on Hardy-Weinberg Equilibrium
Week 6: Tue 9/30 Genomes and ancestry II
  • Admixture: population melting pot
  • Different disease-mutations in different ethinic groups
  • Ethical issues involved in studying population structure
Report due for Lab II
Week 6: Thur 10/2 Genomes and complex diseases
[slides]
  • Genome-wide association studies
  • Chi-squared test, regression analysis
  • Tag SNPs
Week 7: Tue 10/7 Lab III: discovering disease-causing genes
  • Genome-wide association analysis with chi-squared test, regression analysis via Matlab toolbox
   Genomes and biology
Week 7: Thur 10/9 From genomes to biological system
[slides]
  • Measuring gene expressions with gene expression microarray technology
  • What can we learn from gene expressions?
  • Hierarchical clustering
  • Expression quantitative trait locus (eQTL) mapping
Week 8: Tue 10/14 Microarray lab tour
  • Visit to UPitt microarray lab
Report due for Lab III
Week 8: Thur 10/16 Genomes and complex diseases in the future
[slides]
  • Missing heritability
  • Gene-gene interactions, rare genetic variants
Week 9: Tue 10/21 Lab IV: How genomes control gene expressions
  • eQTL mapping in HapMap data via Matlab toolbox
Week 9: Thur 10/23 Personalized medicine and ethical issues
[slides]
  • Genetic tests, genetic counseling
   Personal genomes and big data
Week 10: Tue 10/28 Next generation sequencing technology, lab tour
(Dr. Thickman)
[slides]
  • Biotechnology behind next generation sequencing technology
  • Ion Torrent genome sequencer
Report due for Lab IV
Week 10: Thur 10/30 Going beyond SNPs: Other types of genetic variation
[slides]
  • 1000 Genome Sequencing Project
  • Insertions, deletions, copy number variations in genomes
Week 11: Tue 11/4 Midterm review
[slides]
Week 11: Thur 11/6 Midterm
   Genomes and medicine
Week 12: Tue 11/11 Case studies: Asthma (Dr. Wei Wu)
[slides]
  • Research to improve asthma therapies
Week 12: Thur 11/13 Case studies: Cancer I
[slides]
  • Cancer genes and cancer mutations
  • Tumor genomes vs. normal genomes
  • [Molecular Biology of the Cell Chapter 20] Cancer (copies available in blackboard)
Term-paper proposal due
Week 13: Tue 11/18 Case studies: Cancer II
[slides]
  • Cancer subtypes
  • Personalized medicine and cancer
Week 13: Thur 11/20 Personal genomes, policy making
[slides]
  • Social/ethical/legal issues in personal genomes and personalized medicine
   Other fun topics
Week 14: Tue 11/25 Genomes of microbiomes (Dr. Thickman)
[slides]
  • Microbiome sequencing project
  • Gut microbiomes and human health
Week 14: Thur 11/27
  • No class, Thanksgiving
Week 15: Tue 12/2
  • Student presentation
Week 15: Thur 12/4
  • Student presentation