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This chapter describes the basic principles behind the most widely used human genetic strategies to identify inherited disease susceptibility factors. There are many extensions and modifications to the basis linkage and linkage disequilibrium (LD) mapping approaches. The chapter describes the intuitions and basic strategies behind a few of the more widely used extensions. There are also a number of issues that plague linkage and LD mapping strategies for identifying genetic variants that influence disease susceptibility. The chapter discusses a few of these issues and notes that all of them are well-recognized by the genetics community and that concerted efforts to deal with them in various ways have been made. Advances in DNA sequencing technologies have facilitated studies of rare variants, as these technologies can be used to exhaustively identify all forms of variation, common and rare, in a genomic region for a group of individuals.
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