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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 October 13, 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.