Linkage mapping

Linkage mapping refers to the specification of a particular chromosomal segment or segments within the genome that carry a causal DNA variant or mutation leading to a biological phenotype of interest. The appropriate chromosomal segment is determined through the use of anonymous polymorphic DNA markers as tags in different individuals who share the phenotype. Statistical analysis of data is usually critical in the determination. For whole-genome linkage analysis, the most commonly used polymorphic markers are short tandem repeats, known as microsatellites or STRs. The experimental use of these markers has many subtleties and pitfalls, which are reviewed. Successful linkage mapping for a phenotypic trait is followed by the process of positional cloning, whereby the true underlying genetic variant is discovered. The final step from anonymous chromosomal segment to sequence variant detection can be relatively straightforward or highly demanding, depending on the complexity of the phenotype, the severity of the mutation in affecting gene function, and the extent to which carriers of the mutation are predisposed to the phenotype.

Keywords: linkage mapping; Mendelian monogenic disease; microsatellite; STR; genotyping; genome scan; population isolates; homozygosity mapping