Statistical Genetics and Genomics

4.

Linkage Analysis and Gene Mapping

4.1.

Principles of Linkage Analysis

4.1.1.

Recombination and Crossing Over

4.1.1.1.

Meiotic Recombination

4.1.1.2.

Crossover Formation

4.1.1.3.

Interference and Coincidence

4.1.2.

Genetic Distance Measurement

4.1.2.1.

Map Units and Centimorgans

4.1.2.2.

4.1.2.3.

Haldane Map Function

4.1.2.4.

Kosambi Map Function

4.1.3.

Linkage in Different Organisms

4.1.3.1.

Autosomal Linkage

4.1.3.2.

Sex-Linked Inheritance

4.1.3.3.

Mitochondrial Linkage

4.2.

LOD Score Analysis

4.2.1.

Likelihood Functions

4.2.1.1.

Construction of Likelihood

4.2.1.2.

Recombination Fraction Estimation

4.2.2.

LOD Score Calculation

4.2.2.1.

Two-Point Analysis

4.2.2.2.

Multipoint Analysis

4.2.2.3.

Interpretation of LOD Scores

4.2.3.

Significance Thresholds

4.2.3.1.

Evidence for Linkage

4.2.3.2.

Evidence Against Linkage

4.2.3.3.

Inconclusive Evidence

4.3.

Parametric Linkage Analysis

4.3.1.

Model-Based Approaches

4.3.1.1.

Penetrance Models

4.3.1.2.

Phenocopy Rates

4.3.1.3.

Gene Frequencies

4.3.2.

Disease Gene Mapping

4.3.2.1.

Mendelian Disease Mapping

4.3.2.2.

Genetic Heterogeneity

4.3.2.3.

Locus Heterogeneity

4.4.

Non-Parametric Linkage Analysis

4.4.1.

Model-Free Methods

4.4.1.1.

Affected Sib-Pair Analysis

4.4.1.2.

Identity-by-Descent Sharing

4.4.1.3.

Haseman-Elston Regression

4.4.2.

Allele-Sharing Methods

4.4.2.1.

4.4.2.2.

4.4.2.3.

Transmission Disequilibrium Test

4.5.

Linkage Analysis Software and Tools

4.5.1.

LINKAGE Package

4.5.2.

4.5.3.

4.5.4.

Data Preparation and Quality Control

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