Chapter 4 – Dependent markers

The chapter introduces the concept of dependency between markers and alleles. With the constant increase in the number of genetic markers analyzed, linkage is unavoidable. Efficient computational models to handle linked markers exist, and we explain the Lander–Green algorithm as well as present an extension to account for association between alleles. The chapter also introduces the so-called λ model for haplotype frequency estimation. We briefly explore the model and its effect on the results, leaving some theoretical points to Chapter 6. The software programs FamLink for linked autosomal markers and FamLinkX for X-chromosomal marker data are introduced and used in the exercises. In addition, we explore some theoretical derivations for illustrative purposes.