1. Basic Genetics and Cytogenetics

   1. Mendelian Inheritance
   2. Recombination and Genetic Linkage
   3. Linkage Groups and Synteny
   4. Crossing Over and Map Distance
   5. Map Functions
   6. The Human Chromosomes

2. Genes and Genetic Polymorphisms

   1. Nomenclature and Characterization of Genes
   2. The Degree of Polymorphism
   3. Blood Cell Antigens
   4. Blood Proteins
   5. DNA Polymorphisms and the Genome Project
   6. Variants in Chromosome Morphology
   7. Marker Coverage of the Human Genome

3. Aspects of Statistical Inference

   1. Likelihood
   2. Maximum Likelihood Estimation
   3. Statistical Properties of Maximum Likelihood Estimates
   4. Significance Tests
   5. The Likelihood Method
   6. Interval Estimation
   7. Bayes Theorem

4. Methods of Linkage Analysis

   1. A Brief Historical Review
   2. Prior and Posterior Distribution of Theta
   3. The Lod Score Method
   4. Testing for Linkage
   5. Equivalent Observations
   6. Exact Tests in Simple Family Types
   7. Multiple Comparisons
   8. The Likelihood of Family Data
   9. Nonparametric Approaches
   10. Some Special Methods

5. The Informativeness of Family Data

   1. Measures of Informativeness
   2. Expected Lod Score
   3. Expected Information
   4. Mating Type
   5. Double Intercross with Two Alleles
   6. Double Intercross with More Than Two Alleles
   7. Phase-known Double Backcross
   8. Phase-unknown Double Backcross with Two Offspring
   9. Phase-unknown Double Backcross with More Than Two Offspring
   10. The Number of Observations Required to Detect Linkage

6. Multipoint Linkage Analysis

   1. Notation and Terminology
   2. Three-point Analysis
   3. Phase-unknown Triple Backcross with Two Offspring
   4. Interference
   5. Multilocus Map Functions
   6. Ordering Loci
   7. Mapping under Complete Inteference
   8. Other Methodologic Issues

7. Penetrance

   1. Definition of Penetrance
   2. The Cost of Incomplete Penetrance
   3. Estimating Penetrance and Recombination
   4. Age-dependent Penetrance
   5. The Factors Influencing Penetrance
   6. Quantitative Phenotypes

8. Numerical and Computerized Methods

   1. Calculating Lod Scores Analytically
   2. The Elston-Stewart Algorithm
   3. Computer Programs for Linkage Analysis
   4. Special Applications of Linkage Programs
   5. Linkage Utility Programs
   6. Paternity Calculations
   7. Computer Simulation Methods

9. Variability of the Recombination Fraction

   1. Male and Female Recombination Fractions
   2. Recombination Fraction and Age
   3. Heterogeneity between Classes of Families
   4. Heterogeneity due to a Mixture of Families
   5. Hierarchical and Mixed Models of Heterogeneity
   6. Covariates in the Test for Admixture

10. Inconsistencies

    1. Ascertainment Bias
    2. Misclassification
    3. Misspecification of Penetrance
    4. Misspecification of Heterogeneity
    5. Pedigree Errors
    6. Other Model Misspecifications

11. Linkage Analysis with Disease Loci

    1. Genetic Involvement
    2. Disease Phenotype
    3. Mode of Inheritance
    4. Associations between Phenotypes and Alleles
    5. Candidate Loci
    6. Exclusion Mapping
    7. Genetic Risks
    8. Irregular Segregation
    9. Planning a Linkage Analysis