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- Statistical Genetics of Complex Diseases
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1. Population genetics considerations
- Prof. Nan Laird
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2. Gene-by-environment interaction: study designs and analytical methods
- Prof. L. Adrienne Cupples
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3. Analysis of SNP haplotypes
- Prof. Lyle Palmer
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4. Statistical issues in epidemiological studies of gene-environment interaction
- Dr. Peter Kraft
- Prof. Donna Spiegelman
- Molecular Epidemiology of Pulmonary Diseases
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5. Molecular epidemiology of lung cancer
- Prof. David Christiani
- Autoimmune Diffuse Connective Tissue Diseases
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7. Environmental scleroderma: the evidence for putative triggers
- Prof. Maureen Mayes
- Drug-Induced Disease
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8. Drug-induced lupus
- Prof. Evelyn Hess
- Archived Lectures *These may not cover the latest advances in the field
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9. Biomarkers of exposure
- Prof. Thomas Smith
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10. GIS and spatial statistics
- Prof. Louise Ryan
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11. Gene-by-environment interactions in COPD
- Prof. Edwin Silverman
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14. Indians, twins and scleroderma: genetic and genomic studies
- Prof. Frank Arnett
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15. Gene by environment interaction in asthma
- Prof. Scott Weiss
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16. Molecular epidemiology of lung cancer
- Prof. David Christiani
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18. Infectious environmental factors and systemic lupus erythematosus
- Prof. Judith James
Printable Handouts
Navigable Slide Index
- Introduction
- Genes underlying complex phenotypes
- Phenotype - genotype association
- SNP association with disease allele
- LD maps and allelic association
- How does LD occur?
- LD through the generations
- Decay of LD
- Decay of LD with physical distance
- Variability in LD overwhelms the mean
- The role of LD in facilitating allelic association
- LD patterns and allelic association
- What is a haplotype?
- Haplotype vs. single-locus analyses
- Illustration of phase
- Haplotypes
- Single or multiple locus approach
- The importance of haplotypes
- Haplotype tagging for efficient genotyping
- Block definition is non-trivial
- Ambiguity phase (haplotype) information problem
- Haplotype determination options
- Dealing with ambiguous phase
- Types of statistical estimation
- Statistical estimation - EM algorithm
- Haplotype frequency estimation via EM
- Steps of haplotype frequency estimation via EM
- Graphic representation of the steps
- Framework of haplotype-based genetic studies
- APOE c19 region
- APOE SNPs: single-locus frequency comparisons
- APOE region: 4-locus estimated frequencies
- LRT results for APOE and control regions
- Statistical challenge - sparse data
- Empirical null distribution estimation
- Haplotype estimation and permutation testing
- Empirical null distributions from permutation tests
- LRT results for APOE and control regions
- Example for distribution of LRT values
- Statistical challenge - multiple tests
- Correction for multiple tests
- Haplotype-phenotype association
- Available software
- Some software packages
Topics Covered
- Phenotype-genotype association
- Linkage disequilibrium maps and allelic association
- What is linkage disequilibrium?
- The role of linkage disequilibrium in facilitating allelic association
- What is a haplotype?
- The importance of haplotypes
- Haplotype tagging
- The missing phase information problem
- Haplotype determination options
- Statistical estimation of haplotypes
- General framework for case-control studies using haplotypes
- Haplotype estimation and permutation testing
- Statistical challenges
- Software packages
Talk Citation
Palmer, L. (2007, October 1). Analysis of SNP haplotypes [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved November 2, 2024, from https://doi.org/10.69645/RAUD4480.Export Citation (RIS)
Publication History
Financial Disclosures
- Prof. Lyle Palmer has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.