NCSU Summer Institute of Statistical Genetics, Raleigh 2004: Genome Science Session 3: Genomic Variation.

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Presentation transcript:

NCSU Summer Institute of Statistical Genetics, Raleigh 2004: Genome Science Session 3: Genomic Variation

Human Regulatory SNPs

Polymorphism and LD

Human LD Nature 411, (2001)

9.7 kb Human LPL African Finnish Minnesota

LD in Human ApoE

International HapMap Project

Tests of Neutrality Neutral evolution (most genes)Neutral evolution (Ras genes) Recent selective sweep (Ksr)Balanced polymorphism (Adh)

Interval Mapping

Pedigree Mapping

Linkage Disequilibrium Mapping Heritability / relative risk Number of genes and distribution of effects Penetrance and Expressivity Distribution of linkage disequilibrium (LD) Genetic heterogeneity Population stratification Hidden environmental structure Genotype-by-environment interaction Incomplete genotyping

Population stratification Population 1 Population 2 f(A) = 0.8 f(A) = 0.2 f(a) = 0.2 f(a) = 0.8 diabetics = 20%diabetics = 10% P(A)diabetic = (.8x20 +.2x10) = 18% P(a)diabetic = (.2x20 +.8x10) = 12% Stratification may be environmental, cultural or genetic

Case-control and family designs Observed Expected Allele M Allele m Allele M Allele m Affected Unaffected  2 = 14.0 P <0.01 Transmitted Allele Mm Observed7846 Expected6262  2 = 8.2 P <

Hierarchical Association Mapping

Genetic Association Database

SNPs Online Seattle SNPs The SNP Consortium

VDAs: Variant Detector Arrays

Gel-based SBE

Allele-specific primer extension

Pyrosequencing

Homogeneous Assays

The Invader Assay