Segmental duplications and indel polymorphisms

6.1 Introduction

In this chapter the theme of structural genomic variation is continued, in particular focusing on segmental duplications. Segmental duplications (Box 6.1) are blocks of DNA ranging in size from one to several hundred kilobases which map to more than one location in the genome. They can be found in tandem or at interspersed locations, inter- or intrachromosomally and are estimated to comprise 5% of the human genome (Cheung et al. 2001, 2003a; Bailey et al. 2002). There is evidence that the majority of segmental duplications have arisen relatively recently in our evolutionary past, notably in the last 35 million years (Hattori et al. 2000; Lander et al. 2001; Bailey et al. 2002; Cheung et al. 2003a). The study of duplications has been of particular interest to evolutionary biologists as a substrate for adaptive evolution and this theme is explored over the course of this chapter. At the end of the chapter, smaller scale insertions and deletions involving one or more contiguous nucleotides, collectively described as 'indels', are discussed. Such diversity occurs more commonly than was originally thought and can have significant phenotypic consequences.

6.2 Nature and extent of segmental duplications

6.2.1 Segmental duplications are common in the human genome

The publication of the human genome sequence in 2001 highlighted the abundance of segmental duplications within the human genome (Fig. 6.1) (Lander et al. 2001, 2001). The extent of segmentally duplicated sequence varies significantly between chromosomes, estimated at between 1% and 14% among all 24 chromosomes (Fig. 6.2) (Zhang et al. 2005a). A number of databases catalogue segmental duplications across the human genome, for example as part of the Human Genome Structural

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