Epidemiology 243 - Molecular Epidemiology of Cancer

Professor Zuo-Feng Zhang

Tuesday and Thursday 10:00 AM-11:50 A.M., 71-257 CHS

Spring 2008

Syllabus [Updated: 04/23/08]

Labs

4/1/08

Lecture 1: Introduction to Molecular Epidemiology (ppt)

Reading

A road map for efficient and reliable human genome epidemiology (pdf)

Epidemiology, cancer genetics and microarrays: making correct inferences, using approriate designs (pdf)

A vision for the National Cancer Program in the United States (pdf)

4/3/08

Lecture 2: Exposure Markers (ppt)

Reading

Molecular epidemiology studies of carcinogenic environmental pollutants: effects of polycyclic aromatic hydrocarbons (PAHs) in environmental pollution on exogenous and oxidative DNA damage (pdf)

4/8/08

Lecture 3: Tumor Marker (ppt)

Reading

Gene-Promoter Hypermethylation as a Biomarker in Lung Cancer (pdf)

Promoter methylation and inactivation of tumour-suppressor genes in oral squamous-cell carcinoma (pdf)

Methodological issues in the use of tumour markers in cancer epidemiology (pdf)

TP53 mutations as biomarkers for cancer epidemiology in Latin America: Current knowledge and perspectives (pdf)

CpG island methylator phenotype in cancer (pdf)

4/10/08

Lecture 4: Susceptibility Genes (ppt)

Reading

Common deletions and SNPs are in linkage disequilibrium in the human genome (pdf)

Widening the spectrum of human genetic variation (pdf)

4/15/08

Lecture 5: Molecular Biology in Epidemiology (ppt)

Reading

Molecular Biology in Epidemiology (pdf)

Comparison of methods for DNA extraction from paraffin-embedded tissues and buccal cells (pdf)

4/17/08

Lecture 6 & 7: Study Design in Molecular Epidemiology of Cancer (ppt)

Reading

Betting Odds and Genetic Associations (pdf)

4/22/08

Lecture 6 & 7: Study Design in Molecular Epidemiology of Cancer (ppt)

Reading

Assessing the Probability That a Positive Report is False: An Approach for Molecular Epidemiology Studies (pdf)

4/24/08

Lecture 8: Sample Collection, Processing and Storage (ppt)

Reading

Sample Collection, Processing and Storage (pdf)

4/29/08

Lecture 9: Selection of Candidate Genes for Population Studies (ppt)

Some Practical Considerations for Planning Candidate Gene Association Studies Based on TagSNPs (ppt)

Reading

Selection and validation of biomarkers for chemoprevention: the contribution of epidemiology (pdf)

5/1/08

Lecture 10: Cancer Chemoprevention and Surrogate End Markers

Reading

Cancer Chemoprevention with dietary phytochemicals (pdf)

The promise and peril of surrogate end points in cancer research (pdf)

5/6/08

Lecture 11: Polymorphisms of DNA Repair Genes and Lung Cancer Risk(ppt)

Reading

Cancer Pharmacogenetics: Polymorphisms, Pathways and Beyond (pdf)

5/8/08

Lecture 12: Aflatoxin B1, Hepatitis B, and IFNA17 on the Risk of Liver Cancer: An example of the application of exposure markers in cancer epidemiology (ppt)

5/13/08

Lecture 6/7: JCCC Genotyping Core: High Throughput SNP Genotyping in Cancer Studies (pdf)

5/15/08

Lecture 6/5 Part 1: DNA Methylation and Cancer (ppt)

Lecture 6/5 Part 2: Taqman Techniques in Molecular Epidemiology (ppt)

Summary of Molecular Epidemiology of Cancer

5/20/08

Lecture: Genome-Wide Association Studies (GWAS)

Reading

1: A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25

2: Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1

3: A variant associated with nicotine dependence, lung cancer and peripheral arterial disease

4: When the smoke clears …

5: The success of the genome-wide association

approach: a brief story of a long struggle

6: The road to genome-wide

association studies

7: Genome-wide association studies

for complex traits: consensus,

uncertainty and challenges

8: Common statistical issues in genome-wide association studies: a

review on power, data quality control, genotype calling and

population structure

9: Genome-wide association studies:

progress and potential for drug

discovery and development

FINAL EXAMINATION

Lab Sessions (Beginning May 22, 2008)

5/22/08

Lab 1 (doc)

5/27/08

Lab 2 (doc)

5/29/08

Lab 3 (doc)

6/3/08

Lab 4 (doc)

6/5/08

Lab 5 (doc)